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Fluorine in PDB 2gj9: Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+

Protein crystallography data

The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+, PDB code: 2gj9 was solved by A.Scrima, A.Wittinghofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.240, 70.100, 90.210, 90.00, 95.76, 90.00
R / Rfree (%) 25 / 29.9

Other elements in 2gj9:

The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ also contains other interesting chemical elements:

Rubidium (Rb) 4 atoms
Magnesium (Mg) 4 atoms
Aluminium (Al) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ (pdb code 2gj9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+, PDB code: 2gj9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 2gj9

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Fluorine binding site 1 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:13.2
occ:1.00
F1 A:ALF401 0.0 13.2 1.0
AL A:ALF401 1.8 15.1 1.0
O A:HOH9 2.5 7.8 1.0
F4 A:ALF401 2.6 11.7 1.0
F3 A:ALF401 2.6 13.2 1.0
NZ A:LYS229 2.7 9.2 1.0
N A:GLY273 2.7 13.5 1.0
O2B A:GDP400 2.8 9.0 1.0
CA A:GLY273 3.1 14.2 1.0
CA A:PRO225 3.3 12.6 1.0
O1B A:GDP400 3.4 11.2 1.0
F2 A:ALF401 3.5 13.4 1.0
PB A:GDP400 3.5 9.8 1.0
CE A:LYS229 3.6 8.2 1.0
N A:ASN226 3.8 12.3 1.0
C A:ALA272 3.9 12.9 1.0
O A:HOH8 3.9 10.5 1.0
O3B A:GDP400 4.0 10.8 1.0
O A:HOH12 4.1 8.0 1.0
C A:PRO225 4.1 13.2 1.0
CB A:PRO225 4.1 13.5 1.0
N A:PRO225 4.1 12.6 1.0
MG A:MG402 4.2 13.7 1.0
O A:ARG224 4.2 11.5 1.0
O A:THR271 4.4 14.6 1.0
CA A:ALA272 4.4 12.1 1.0
C A:GLY273 4.4 15.3 1.0
C A:ARG224 4.5 11.3 1.0
CG A:PRO225 4.7 11.6 1.0
O A:GLY273 4.8 14.0 1.0
O A:ALA272 4.9 11.5 1.0
CD A:LYS229 4.9 12.0 1.0
O3A A:GDP400 5.0 10.2 1.0
N A:GLY249 5.0 12.8 1.0

Fluorine binding site 2 out of 16 in 2gj9

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Fluorine binding site 2 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:13.4
occ:1.00
F2 A:ALF401 0.0 13.4 1.0
AL A:ALF401 1.8 15.1 1.0
F4 A:ALF401 2.3 11.7 1.0
F3 A:ALF401 2.5 13.2 1.0
N A:THR250 2.6 12.9 1.0
O A:HOH9 2.6 7.8 1.0
O2B A:GDP400 2.8 9.0 1.0
RB A:RB403 2.8 18.5 1.0
CB A:THR250 3.1 12.0 1.0
CA A:THR250 3.3 12.8 1.0
N A:GLY249 3.3 12.8 1.0
N A:THR251 3.4 13.0 1.0
F1 A:ALF401 3.5 13.2 1.0
O A:HOH11 3.5 7.7 1.0
OG1 A:THR250 3.6 14.6 1.0
C A:GLY249 3.6 14.4 1.0
O A:ILE247 3.7 10.4 1.0
MG A:MG402 3.8 13.7 1.0
CA A:GLY249 3.8 13.4 1.0
C A:THR250 3.8 12.9 1.0
PB A:GDP400 4.0 9.8 1.0
C A:ALA248 4.1 12.7 1.0
OG1 A:THR251 4.2 13.0 1.0
O3B A:GDP400 4.3 10.8 1.0
CA A:ALA248 4.4 11.4 1.0
CG2 A:THR250 4.4 11.2 1.0
CA A:THR251 4.5 13.4 1.0
CB A:THR251 4.5 14.7 1.0
O2A A:GDP400 4.5 9.6 1.0
OD1 A:ASN226 4.6 12.9 1.0
O A:THR251 4.6 15.4 1.0
C A:ILE247 4.7 11.1 1.0
N A:ASN226 4.7 12.3 1.0
O A:GLY249 4.8 12.9 1.0
O3A A:GDP400 4.8 10.2 1.0
O A:HOH8 4.9 10.5 1.0

Fluorine binding site 3 out of 16 in 2gj9

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Fluorine binding site 3 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:13.2
occ:1.00
F3 A:ALF401 0.0 13.2 1.0
AL A:ALF401 1.8 15.1 1.0
MG A:MG402 2.0 13.7 1.0
O A:HOH9 2.5 7.8 1.0
F2 A:ALF401 2.5 13.4 1.0
F1 A:ALF401 2.6 13.2 1.0
OG1 A:THR251 2.7 13.0 1.0
O2B A:GDP400 2.8 9.0 1.0
CB A:THR251 2.9 14.7 1.0
O A:HOH12 2.9 8.0 1.0
O3B A:GDP400 3.0 10.8 1.0
PB A:GDP400 3.3 9.8 1.0
N A:THR251 3.4 13.0 1.0
O A:HOH11 3.4 7.7 1.0
F4 A:ALF401 3.5 11.7 1.0
CA A:THR251 3.7 13.4 1.0
OG A:SER230 3.9 14.5 1.0
O A:THR251 4.0 15.4 1.0
O1B A:GDP400 4.1 11.2 1.0
CG2 A:THR251 4.1 10.8 1.0
O A:THR271 4.1 14.6 1.0
N A:GLY273 4.3 13.5 1.0
C A:THR251 4.3 15.8 1.0
NZ A:LYS229 4.3 9.2 1.0
N A:THR250 4.4 12.9 1.0
C A:THR250 4.5 12.9 1.0
RB A:RB403 4.5 18.5 1.0
CA A:ALA272 4.6 12.1 1.0
CB A:THR250 4.6 12.0 1.0
O3A A:GDP400 4.7 10.2 1.0
CA A:THR250 4.7 12.8 1.0
CE A:LYS229 4.8 8.2 1.0
O2A A:GDP400 4.9 9.6 1.0
C A:ALA272 5.0 12.9 1.0

Fluorine binding site 4 out of 16 in 2gj9

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Fluorine binding site 4 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:11.7
occ:1.00
F4 A:ALF401 0.0 11.7 1.0
AL A:ALF401 1.7 15.1 1.0
F2 A:ALF401 2.3 13.4 1.0
F1 A:ALF401 2.6 13.2 1.0
O2B A:GDP400 2.6 9.0 1.0
O A:HOH9 2.8 7.8 1.0
N A:ASN226 2.9 12.3 1.0
N A:GLY249 3.0 12.8 1.0
CA A:PRO225 3.1 12.6 1.0
CB A:PRO225 3.2 13.5 1.0
C A:PRO225 3.4 13.2 1.0
F3 A:ALF401 3.5 13.2 1.0
CA A:ALA248 3.6 11.4 1.0
RB A:RB403 3.7 18.5 1.0
C A:ALA248 3.7 12.7 1.0
OD1 A:ASN226 4.0 12.9 1.0
CA A:GLY249 4.0 13.4 1.0
CA A:ASN226 4.0 13.1 1.0
O A:HOH8 4.0 10.5 1.0
PB A:GDP400 4.0 9.8 1.0
CB A:ALA248 4.1 9.2 1.0
N A:THR250 4.2 12.9 1.0
O A:ILE247 4.3 10.4 1.0
CG A:PRO225 4.4 11.6 1.0
O1B A:GDP400 4.4 11.2 1.0
CG A:ASN226 4.5 13.8 1.0
N A:PRO225 4.5 12.6 1.0
CB A:ASN226 4.6 13.4 1.0
C A:GLY249 4.6 14.4 1.0
O A:PRO225 4.7 9.8 1.0
N A:GLY273 4.7 13.5 1.0
N A:ALA248 4.7 10.4 1.0
NZ A:LYS229 4.8 9.2 1.0
O3A A:GDP400 4.8 10.2 1.0
CA A:GLY273 4.9 14.2 1.0
O3B A:GDP400 4.9 10.8 1.0
O A:ALA248 4.9 13.9 1.0
C A:ILE247 5.0 11.1 1.0

Fluorine binding site 5 out of 16 in 2gj9

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Fluorine binding site 5 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:12.6
occ:1.00
F1 B:ALF501 0.0 12.6 1.0
AL B:ALF501 1.7 15.2 1.0
MG B:MG502 2.1 14.4 1.0
F4 B:ALF501 2.3 13.9 1.0
O B:HOH14 2.4 12.7 1.0
F3 B:ALF501 2.6 16.1 1.0
O2B B:GDP500 2.8 18.2 1.0
OG1 B:THR251 2.8 16.0 1.0
O3B B:GDP500 2.9 19.4 1.0
CB B:THR251 3.0 14.9 1.0
N B:THR251 3.2 15.8 1.0
PB B:GDP500 3.3 16.7 1.0
F2 B:ALF501 3.5 16.6 1.0
CA B:THR251 3.6 15.6 1.0
OG B:SER230 4.1 18.5 1.0
O B:THR251 4.1 13.8 1.0
O1B B:GDP500 4.2 15.0 1.0
O B:THR271 4.3 19.0 1.0
N B:THR250 4.3 17.0 1.0
C B:THR250 4.4 16.6 1.0
C B:THR251 4.4 14.9 1.0
N B:GLY273 4.4 14.5 1.0
RB B:RB503 4.4 25.8 1.0
CG2 B:THR251 4.4 16.0 1.0
NZ B:LYS229 4.5 12.0 1.0
CB B:THR250 4.6 15.2 1.0
O3A B:GDP500 4.6 20.7 1.0
CE B:LYS229 4.6 10.9 1.0
CA B:THR250 4.7 15.2 1.0
CA B:ALA272 4.8 14.2 1.0
O2A B:GDP500 5.0 14.2 1.0

Fluorine binding site 6 out of 16 in 2gj9

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Fluorine binding site 6 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:16.6
occ:1.00
F2 B:ALF501 0.0 16.6 1.0
AL B:ALF501 1.7 15.2 1.0
F3 B:ALF501 2.4 16.1 1.0
O2B B:GDP500 2.5 18.2 1.0
F4 B:ALF501 2.6 13.9 1.0
O B:HOH14 2.6 12.7 1.0
N B:ASN226 3.0 18.9 1.0
CA B:PRO225 3.1 18.1 1.0
N B:GLY249 3.1 14.4 1.0
CB B:PRO225 3.2 17.4 1.0
F1 B:ALF501 3.5 12.6 1.0
C B:PRO225 3.5 19.3 1.0
RB B:RB503 3.7 25.8 1.0
CA B:ALA248 3.7 16.9 1.0
PB B:GDP500 3.9 16.7 1.0
C B:ALA248 3.9 15.9 1.0
O B:HOH13 4.0 13.3 1.0
CA B:GLY249 4.0 16.4 1.0
OD1 B:ASN226 4.0 22.8 1.0
CA B:ASN226 4.1 20.1 1.0
N B:THR250 4.2 17.0 1.0
CG B:PRO225 4.3 17.7 1.0
CB B:ALA248 4.4 17.4 1.0
N B:PRO225 4.4 17.8 1.0
NZ B:LYS229 4.5 12.0 1.0
O1B B:GDP500 4.5 15.0 1.0
O B:ILE247 4.5 19.8 1.0
N B:GLY273 4.5 14.5 1.0
CG B:ASN226 4.5 19.7 1.0
CA B:GLY273 4.5 13.8 1.0
O B:PRO225 4.7 19.9 1.0
C B:GLY249 4.7 16.8 1.0
CB B:ASN226 4.7 20.6 1.0
N B:ALA248 4.8 18.1 1.0
O3B B:GDP500 4.8 19.4 1.0
O3A B:GDP500 4.9 20.7 1.0
O B:ARG224 5.0 16.7 1.0

Fluorine binding site 7 out of 16 in 2gj9

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Fluorine binding site 7 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:16.1
occ:1.00
F3 B:ALF501 0.0 16.1 1.0
AL B:ALF501 1.8 15.2 1.0
F2 B:ALF501 2.4 16.6 1.0
O B:HOH14 2.4 12.7 1.0
NZ B:LYS229 2.6 12.0 1.0
F1 B:ALF501 2.6 12.6 1.0
O2B B:GDP500 2.7 18.2 1.0
N B:GLY273 2.8 14.5 1.0
CA B:GLY273 3.0 13.8 1.0
CE B:LYS229 3.3 10.9 1.0
CA B:PRO225 3.5 18.1 1.0
PB B:GDP500 3.5 16.7 1.0
O1B B:GDP500 3.5 15.0 1.0
F4 B:ALF501 3.6 13.9 1.0
N B:ASN226 3.8 18.9 1.0
O3B B:GDP500 3.9 19.4 1.0
C B:ALA272 3.9 13.5 1.0
O B:HOH13 3.9 13.3 1.0
O B:ARG224 4.1 16.7 1.0
C B:PRO225 4.1 19.3 1.0
CB B:PRO225 4.3 17.4 1.0
MG B:MG502 4.3 14.4 1.0
N B:PRO225 4.3 17.8 1.0
O B:THR271 4.3 19.0 1.0
C B:GLY273 4.4 13.7 1.0
CA B:ALA272 4.5 14.2 1.0
C B:ARG224 4.6 17.3 1.0
CD B:LYS229 4.7 15.4 1.0
O B:ALA272 4.9 11.5 1.0
O B:GLY273 4.9 13.0 1.0
CG B:PRO225 4.9 17.7 1.0
O3A B:GDP500 5.0 20.7 1.0

Fluorine binding site 8 out of 16 in 2gj9

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Fluorine binding site 8 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:13.9
occ:1.00
F4 B:ALF501 0.0 13.9 1.0
AL B:ALF501 1.8 15.2 1.0
F1 B:ALF501 2.3 12.6 1.0
RB B:RB503 2.6 25.8 1.0
F2 B:ALF501 2.6 16.6 1.0
O2B B:GDP500 2.6 18.2 1.0
N B:THR250 2.7 17.0 1.0
O B:HOH14 2.7 12.7 1.0
CB B:THR250 3.0 15.2 1.0
N B:THR251 3.2 15.8 1.0
CA B:THR250 3.2 15.2 1.0
OG1 B:THR250 3.5 15.9 1.0
F3 B:ALF501 3.6 16.1 1.0
N B:GLY249 3.7 14.4 1.0
C B:THR250 3.7 16.6 1.0
MG B:MG502 3.7 14.4 1.0
O B:ILE247 3.8 19.8 1.0
C B:GLY249 3.8 16.8 1.0
PB B:GDP500 3.8 16.7 1.0
CA B:GLY249 4.1 16.4 1.0
O3B B:GDP500 4.1 19.4 1.0
OG1 B:THR251 4.2 16.0 1.0
CG2 B:THR250 4.3 11.5 1.0
CA B:THR251 4.4 15.6 1.0
C B:ALA248 4.5 15.9 1.0
CB B:THR251 4.5 14.9 1.0
O2A B:GDP500 4.6 14.2 1.0
O3A B:GDP500 4.6 20.7 1.0
OD1 B:ASN226 4.7 22.8 1.0
O B:THR251 4.7 13.8 1.0
CA B:ALA248 4.7 16.9 1.0
O B:GLY249 4.9 17.3 1.0
C B:ILE247 4.9 20.1 1.0
N B:ASN226 4.9 18.9 1.0
O B:THR250 4.9 16.0 1.0

Fluorine binding site 9 out of 16 in 2gj9

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Fluorine binding site 9 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:15.6
occ:1.00
F1 C:ALF601 0.0 15.6 1.0
AL C:ALF601 1.8 15.0 1.0
F4 C:ALF601 2.4 12.3 1.0
O C:HOH2 2.5 14.8 1.0
F3 C:ALF601 2.5 15.8 1.0
O2B C:GDP600 2.7 13.1 1.0
NZ C:LYS229 2.7 6.8 1.0
N C:GLY273 2.8 14.9 1.0
CA C:GLY273 3.0 15.3 1.0
CA C:PRO225 3.2 15.9 1.0
O1B C:GDP600 3.5 12.7 1.0
F2 C:ALF601 3.6 20.4 1.0
PB C:GDP600 3.6 11.4 1.0
CE C:LYS229 3.6 10.0 1.0
N C:ASN226 3.6 15.4 1.0
O C:HOH1 3.8 11.9 1.0
C C:PRO225 3.9 14.8 1.0
C C:ALA272 4.0 15.8 1.0
CB C:PRO225 4.0 14.4 1.0
O C:ARG224 4.0 14.9 1.0
O3B C:GDP600 4.0 15.7 1.0
N C:PRO225 4.0 16.4 1.0
O C:HOH5 4.1 15.5 1.0
MG C:MG602 4.2 15.6 1.0
C C:ARG224 4.4 16.2 1.0
C C:GLY273 4.4 15.8 1.0
O C:THR271 4.5 15.2 1.0
CA C:ALA272 4.6 15.2 1.0
CG C:PRO225 4.6 15.5 1.0
N C:GLY249 4.8 14.6 1.0
O C:GLY273 4.9 15.5 1.0
CD C:PRO225 4.9 14.9 1.0
O C:ALA272 4.9 15.5 1.0
CA C:ASN226 5.0 14.5 1.0

Fluorine binding site 10 out of 16 in 2gj9

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Fluorine binding site 10 out of 16 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:20.4
occ:1.00
F2 C:ALF601 0.0 20.4 1.0
AL C:ALF601 1.8 15.0 1.0
F4 C:ALF601 2.5 12.3 1.0
F3 C:ALF601 2.6 15.8 1.0
O2B C:GDP600 2.7 13.1 1.0
N C:THR250 2.7 15.9 1.0
RB C:RB603 2.7 19.7 1.0
O C:HOH2 2.7 14.8 1.0
CB C:THR250 3.0 16.2 1.0
O C:HOH4 3.1 9.9 1.0
N C:THR251 3.2 15.0 1.0
CA C:THR250 3.3 16.4 1.0
MG C:MG602 3.5 15.6 1.0
N C:GLY249 3.5 14.6 1.0
F1 C:ALF601 3.6 15.6 1.0
OG1 C:THR250 3.7 16.5 1.0
O C:ILE247 3.7 14.8 1.0
C C:THR250 3.7 14.7 1.0
C C:GLY249 3.7 15.9 1.0
CA C:GLY249 3.9 14.8 1.0
PB C:GDP600 4.0 11.4 1.0
OG1 C:THR251 4.1 19.3 1.0
O3B C:GDP600 4.1 15.7 1.0
CG2 C:THR250 4.2 17.2 1.0
O2A C:GDP600 4.3 8.9 1.0
CA C:THR251 4.3 15.5 1.0
C C:ALA248 4.4 17.2 1.0
CB C:THR251 4.4 14.9 1.0
O C:THR251 4.5 15.5 1.0
CA C:ALA248 4.7 16.4 1.0
OD1 C:ASN226 4.7 15.1 1.0
O3A C:GDP600 4.8 11.2 1.0
C C:ILE247 4.8 16.7 1.0
O C:GLY249 4.8 17.6 1.0
N C:ASN226 4.9 15.4 1.0
O C:THR250 4.9 15.7 1.0
C C:THR251 4.9 14.4 1.0

Reference:

A.Scrima, A.Wittinghofer. Dimerisation-Dependent Gtpase Reaction of Mnme: How Potassium Acts As Gtpase-Activating Element. Embo J. V. 25 2940 2006.
ISSN: ISSN 0261-4189
PubMed: 16763562
DOI: 10.1038/SJ.EMBOJ.7601171
Page generated: Wed Oct 28 14:45:04 2020

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