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Fluorine in PDB 2gja: Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+

Protein crystallography data

The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+, PDB code: 2gja 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) 19.37 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.280, 90.650, 138.470, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.8

Other elements in 2gja:

The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+ also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+ (pdb code 2gja). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+, PDB code: 2gja:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 1 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:12.9
occ:1.00
 F1 A:ALF401 0.0 12.9 1.0
AL A:ALF401 1.8 11.2 1.0
F4 A:ALF401 2.5 13.5 1.0
F3 A:ALF401 2.5 15.8 1.0
NZ A:LYS229 2.6 11.7 1.0
O2B A:GDP400 2.6 7.8 1.0
O A:HOH2 2.6 9.2 1.0
N A:GLY273 2.8 11.5 1.0
CA A:GLY273 3.0 10.9 1.0
CE A:LYS229 3.4 9.6 1.0
PB A:GDP400 3.4 10.4 1.0
O1B A:GDP400 3.5 11.4 1.0
CA A:PRO225 3.5 9.3 1.0
F2 A:ALF401 3.5 12.7 1.0
O3B A:GDP400 3.9 8.6 1.0
O A:HOH100 3.9 13.2 1.0
C A:ALA272 3.9 11.5 1.0
N A:ASN226 3.9 11.6 1.0
O A:HOH1 4.1 15.2 1.0
MG A:MG402 4.1 11.5 1.0
O A:ARG224 4.2 9.7 1.0
C A:PRO225 4.2 10.3 1.0
CB A:PRO225 4.3 10.1 1.0
O A:THR271 4.3 13.4 1.0
N A:PRO225 4.3 9.8 1.0
C A:GLY273 4.4 11.4 1.0
CA A:ALA272 4.5 11.4 1.0
C A:ARG224 4.6 10.2 1.0
CG A:PRO225 4.7 10.2 1.0
O A:ALA272 4.9 10.4 1.0
CD A:LYS229 4.9 7.8 1.0
O A:GLY273 4.9 10.9 1.0
O3A A:GDP400 4.9 7.8 1.0
N A:GLY249 5.0 11.3 1.0
CB A:THR251 5.0 11.6 1.0

Fluorine binding site 2 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 2 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:12.7
occ:1.00
 F2 A:ALF401 0.0 12.7 1.0
AL A:ALF401 1.8 11.2 1.0
F3 A:ALF401 2.5 15.8 1.0
F4 A:ALF401 2.5 13.5 1.0
N A:NH4403 2.5 11.4 1.0
O2B A:GDP400 2.6 7.8 1.0
N A:THR250 2.7 11.7 1.0
O A:HOH2 2.8 9.2 1.0
CB A:THR250 3.1 11.8 1.0
N A:THR251 3.3 11.3 1.0
CA A:THR250 3.4 11.6 1.0
N A:GLY249 3.4 11.3 1.0
O A:HOH101 3.4 11.4 1.0
F1 A:ALF401 3.5 12.9 1.0
O A:ILE247 3.5 14.0 1.0
OG1 A:THR250 3.7 13.7 1.0
C A:GLY249 3.8 12.1 1.0
MG A:MG402 3.8 11.5 1.0
C A:THR250 3.9 12.3 1.0
PB A:GDP400 3.9 10.4 1.0
CA A:GLY249 3.9 12.0 1.0
O3B A:GDP400 4.1 8.6 1.0
C A:ALA248 4.2 13.3 1.0
OG1 A:THR251 4.4 10.5 1.0
O2A A:GDP400 4.4 10.0 1.0
CG2 A:THR250 4.4 9.7 1.0
CA A:ALA248 4.4 13.6 1.0
CA A:THR251 4.5 11.8 1.0
CB A:THR251 4.6 11.6 1.0
C A:ILE247 4.6 14.6 1.0
O3A A:GDP400 4.6 7.8 1.0
OD1 A:ASN226 4.7 14.6 1.0
N A:ASN226 4.8 11.6 1.0
O A:THR251 4.9 12.5 1.0
O A:GLY249 4.9 13.3 1.0
N A:ALA248 5.0 13.7 1.0

Fluorine binding site 3 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 3 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:15.8
occ:1.00
 F3 A:ALF401 0.0 15.8 1.0
AL A:ALF401 1.8 11.2 1.0
MG A:MG402 1.9 11.5 1.0
F2 A:ALF401 2.5 12.7 1.0
F1 A:ALF401 2.5 12.9 1.0
O2B A:GDP400 2.6 7.8 1.0
O A:HOH2 2.7 9.2 1.0
O A:HOH100 2.7 13.2 1.0
OG1 A:THR251 2.7 10.5 1.0
O3B A:GDP400 2.8 8.6 1.0
CB A:THR251 2.9 11.6 1.0
O A:HOH101 3.1 11.4 1.0
PB A:GDP400 3.2 10.4 1.0
N A:THR251 3.3 11.3 1.0
F4 A:ALF401 3.5 13.5 1.0
CA A:THR251 3.7 11.8 1.0
OG A:SER230 4.0 8.7 1.0
O1B A:GDP400 4.1 11.4 1.0
O A:THR251 4.2 12.5 1.0
CG2 A:THR251 4.3 12.7 1.0
O A:THR271 4.3 13.4 1.0
N A:GLY273 4.4 11.5 1.0
NZ A:LYS229 4.4 11.7 1.0
N A:NH4403 4.4 11.4 1.0
C A:THR251 4.4 12.0 1.0
C A:THR250 4.5 12.3 1.0
N A:THR250 4.5 11.7 1.0
O3A A:GDP400 4.5 7.8 1.0
CB A:THR250 4.6 11.8 1.0
O2A A:GDP400 4.8 10.0 1.0
CA A:THR250 4.8 11.6 1.0
CE A:LYS229 4.8 9.6 1.0
CA A:ALA272 4.9 11.4 1.0

Fluorine binding site 4 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 4 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:13.5
occ:1.00
 F4 A:ALF401 0.0 13.5 1.0
AL A:ALF401 1.8 11.2 1.0
F2 A:ALF401 2.5 12.7 1.0
F1 A:ALF401 2.5 12.9 1.0
O2B A:GDP400 2.7 7.8 1.0
O A:HOH2 2.7 9.2 1.0
N A:GLY249 2.9 11.3 1.0
CB A:PRO225 3.1 10.1 1.0
N A:ASN226 3.1 11.6 1.0
CA A:PRO225 3.1 9.3 1.0
C A:PRO225 3.5 10.3 1.0
F3 A:ALF401 3.5 15.8 1.0
CA A:ALA248 3.5 13.6 1.0
C A:ALA248 3.7 13.3 1.0
N A:NH4403 3.8 11.4 1.0
CA A:GLY249 3.9 12.0 1.0
O A:HOH1 3.9 15.2 1.0
CG A:PRO225 4.0 10.2 1.0
PB A:GDP400 4.1 10.4 1.0
CA A:ASN226 4.2 11.9 1.0
N A:THR250 4.2 11.7 1.0
CB A:ALA248 4.2 13.7 1.0
OD1 A:ASN226 4.4 14.6 1.0
O A:ILE247 4.4 14.0 1.0
N A:PRO225 4.4 9.8 1.0
CA A:GLY273 4.5 10.9 1.0
N A:GLY273 4.5 11.5 1.0
C A:GLY249 4.6 12.1 1.0
NZ A:LYS229 4.6 11.7 1.0
O1B A:GDP400 4.6 11.4 1.0
CG A:ASN226 4.6 14.7 1.0
N A:ALA248 4.7 13.7 1.0
O A:PRO225 4.7 9.8 1.0
CB A:ASN226 4.9 13.2 1.0
O A:ALA248 4.9 12.3 1.0
O3B A:GDP400 4.9 8.6 1.0
C A:ILE247 5.0 14.6 1.0
O3A A:GDP400 5.0 7.8 1.0

Fluorine binding site 5 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 5 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:15.4
occ:1.00
 F1 B:ALF501 0.0 15.4 1.0
AL B:ALF501 1.8 13.4 1.0
NZ B:LYS229 2.5 10.7 1.0
F3 B:ALF501 2.5 14.9 1.0
F4 B:ALF501 2.6 16.4 1.0
O2B B:GDP500 2.6 6.6 1.0
O B:HOH99 2.6 9.9 1.0
N B:GLY273 2.7 12.4 1.0
CA B:GLY273 3.0 12.0 1.0
CE B:LYS229 3.3 12.0 1.0
PB B:GDP500 3.4 10.1 1.0
CA B:PRO225 3.5 11.4 1.0
O1B B:GDP500 3.5 11.8 1.0
F2 B:ALF501 3.6 14.8 1.0
N B:ASN226 3.9 11.1 1.0
C B:ALA272 3.9 12.1 1.0
O B:HOH114 4.0 11.3 1.0
O B:HOH4 4.0 14.3 1.0
O3B B:GDP500 4.0 9.6 1.0
MG B:MG502 4.1 11.8 1.0
O B:ARG224 4.2 11.6 1.0
C B:PRO225 4.2 12.1 1.0
CB B:PRO225 4.2 12.2 1.0
N B:PRO225 4.3 11.8 1.0
O B:THR271 4.3 14.2 1.0
C B:GLY273 4.4 12.6 1.0
CA B:ALA272 4.5 12.4 1.0
C B:ARG224 4.6 11.3 1.0
CG B:PRO225 4.7 12.1 1.0
CD B:LYS229 4.8 11.2 1.0
O B:GLY273 4.8 10.9 1.0
O B:ALA272 4.9 11.7 1.0
O3A B:GDP500 4.9 10.6 1.0
N B:GLY249 5.0 13.1 1.0

Fluorine binding site 6 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 6 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:14.8
occ:1.00
 F2 B:ALF501 0.0 14.8 1.0
AL B:ALF501 1.8 13.4 1.0
F4 B:ALF501 2.5 16.4 1.0
F3 B:ALF501 2.5 14.9 1.0
O2B B:GDP500 2.6 6.6 1.0
N B:NH4503 2.6 8.7 1.0
N B:THR250 2.7 11.8 1.0
O B:HOH99 2.7 9.9 1.0
CB B:THR250 3.1 11.9 1.0
CA B:THR250 3.3 12.2 1.0
N B:THR251 3.4 10.6 1.0
N B:GLY249 3.4 13.1 1.0
O B:ILE247 3.5 15.9 1.0
O B:HOH113 3.5 11.4 1.0
OG1 B:THR250 3.5 13.5 1.0
F1 B:ALF501 3.6 15.4 1.0
C B:GLY249 3.7 13.0 1.0
MG B:MG502 3.8 11.8 1.0
C B:THR250 3.9 11.9 1.0
PB B:GDP500 3.9 10.1 1.0
CA B:GLY249 3.9 13.4 1.0
C B:ALA248 4.1 15.2 1.0
O3B B:GDP500 4.2 9.6 1.0
OG1 B:THR251 4.3 11.3 1.0
O2A B:GDP500 4.3 10.0 1.0
CA B:ALA248 4.3 15.0 1.0
CG2 B:THR250 4.4 10.5 1.0
CA B:THR251 4.6 11.4 1.0
C B:ILE247 4.6 17.0 1.0
O3A B:GDP500 4.6 10.6 1.0
CB B:THR251 4.6 10.6 1.0
OD1 B:ASN226 4.7 14.8 1.0
O B:THR251 4.7 11.9 1.0
N B:ASN226 4.8 11.1 1.0
O B:GLY249 4.8 13.9 1.0
N B:ALA248 5.0 15.5 1.0

Fluorine binding site 7 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 7 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:14.9
occ:1.00
 F3 B:ALF501 0.0 14.9 1.0
AL B:ALF501 1.8 13.4 1.0
MG B:MG502 1.9 11.8 1.0
F2 B:ALF501 2.5 14.8 1.0
F1 B:ALF501 2.5 15.4 1.0
O2B B:GDP500 2.6 6.6 1.0
O B:HOH99 2.6 9.9 1.0
O B:HOH114 2.8 11.3 1.0
OG1 B:THR251 2.8 11.3 1.0
O3B B:GDP500 2.9 9.6 1.0
CB B:THR251 3.0 10.6 1.0
PB B:GDP500 3.2 10.1 1.0
O B:HOH113 3.2 11.4 1.0
N B:THR251 3.3 10.6 1.0
F4 B:ALF501 3.5 16.4 1.0
CA B:THR251 3.7 11.4 1.0
OG B:SER230 4.0 11.2 1.0
O B:THR251 4.1 11.9 1.0
O1B B:GDP500 4.1 11.8 1.0
O B:THR271 4.2 14.2 1.0
NZ B:LYS229 4.2 10.7 1.0
N B:GLY273 4.3 12.4 1.0
CG2 B:THR251 4.3 13.4 1.0
C B:THR251 4.4 11.6 1.0
N B:THR250 4.5 11.8 1.0
N B:NH4503 4.5 8.7 1.0
C B:THR250 4.5 11.9 1.0
O3A B:GDP500 4.6 10.6 1.0
CE B:LYS229 4.6 12.0 1.0
CB B:THR250 4.6 11.9 1.0
CA B:THR250 4.8 12.2 1.0
CA B:ALA272 4.8 12.4 1.0
O2A B:GDP500 4.8 10.0 1.0

Fluorine binding site 8 out of 8 in 2gja

Go back to Fluorine Binding Sites List in 2gja
Fluorine binding site 8 out of 8 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


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 NH4+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:16.4
occ:1.00
 F4 B:ALF501 0.0 16.4 1.0
AL B:ALF501 1.8 13.4 1.0
F2 B:ALF501 2.5 14.8 1.0
F1 B:ALF501 2.6 15.4 1.0
O2B B:GDP500 2.6 6.6 1.0
O B:HOH99 2.7 9.9 1.0
N B:GLY249 2.9 13.1 1.0
CB B:PRO225 3.1 12.2 1.0
CA B:PRO225 3.1 11.4 1.0
N B:ASN226 3.1 11.1 1.0
CA B:ALA248 3.5 15.0 1.0
C B:PRO225 3.5 12.1 1.0
F3 B:ALF501 3.5 14.9 1.0
C B:ALA248 3.7 15.2 1.0
N B:NH4503 3.9 8.7 1.0
CA B:GLY249 3.9 13.4 1.0
O B:HOH4 3.9 14.3 1.0
CG B:PRO225 4.1 12.1 1.0
PB B:GDP500 4.1 10.1 1.0
CB B:ALA248 4.1 15.2 1.0
N B:THR250 4.2 11.8 1.0
CA B:ASN226 4.2 12.4 1.0
O B:ILE247 4.3 15.9 1.0
OD1 B:ASN226 4.4 14.8 1.0
N B:PRO225 4.4 11.8 1.0
CG B:ASN226 4.6 16.1 1.0
N B:GLY273 4.6 12.4 1.0
CA B:GLY273 4.6 12.0 1.0
C B:GLY249 4.6 13.0 1.0
N B:ALA248 4.6 15.5 1.0
NZ B:LYS229 4.6 10.7 1.0
O1B B:GDP500 4.7 11.8 1.0
O B:PRO225 4.7 11.6 1.0
CB B:ASN226 4.8 13.1 1.0
O B:ALA248 4.9 15.1 1.0
C B:ILE247 4.9 17.0 1.0
O3A B:GDP500 5.0 10.6 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: Sun Dec 13 11:36:34 2020

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