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Fluorine in PDB 3ss8: Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+

Protein crystallography data

The structure of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+, PDB code: 3ss8 was solved by M.R.Ash, M.J.Maher, J.M.Guss, M.Jormakka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.346, 75.401, 156.494, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.2

Other elements in 3ss8:

The structure of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ (pdb code 3ss8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+, PDB code: 3ss8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 1 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:23.7
occ:1.00
 F1 A:ALF303 0.0 23.7 1.0
AL A:ALF303 1.8 24.6 1.0
O2B A:GDP300 2.5 16.6 1.0
F3 A:ALF303 2.5 23.7 1.0
F4 A:ALF303 2.5 25.6 1.0
O A:HOH273 2.6 12.0 1.0
NZ A:LYS14 2.7 16.6 1.0
N A:GLY56 3.1 25.9 1.0
CA A:GLY56 3.2 26.1 1.0
CE A:LYS14 3.3 17.4 1.0
O1B A:GDP300 3.3 19.8 1.0
PB A:GDP300 3.4 18.5 1.0
CA A:PRO10 3.4 20.5 1.0
F2 A:ALF303 3.6 24.0 1.0
N A:ASN11 3.6 20.8 1.0
O A:HOH279 3.8 28.1 1.0
MG A:MG302 3.9 17.2 1.0
O A:HOH271 4.0 26.2 1.0
O3B A:GDP300 4.0 18.6 1.0
C A:PRO10 4.0 20.5 1.0
CB A:PRO10 4.1 20.5 1.0
O A:ASN9 4.1 20.3 1.0
C A:PRO55 4.2 25.6 1.0
N A:PRO10 4.4 20.5 1.0
C A:GLY56 4.6 26.3 1.0
C A:ASN9 4.6 20.4 1.0
CA A:PRO55 4.7 25.3 1.0
O3A A:GDP300 4.7 19.5 1.0
K A:K301 4.8 20.8 1.0
CD A:LYS14 4.8 16.9 1.0
O A:LEU54 4.8 24.8 1.0
CA A:ASN11 4.8 21.0 1.0
CG A:PRO10 4.9 20.7 1.0

Fluorine binding site 2 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 2 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:24.0
occ:1.00
 F2 A:ALF303 0.0 24.0 1.0
AL A:ALF303 1.8 24.6 1.0
F4 A:ALF303 2.5 25.6 1.0
F3 A:ALF303 2.5 23.7 1.0
O A:HOH273 2.6 12.0 1.0
N A:VAL34 2.6 20.6 1.0
K A:K301 2.6 20.8 1.0
O2B A:GDP300 2.7 16.6 1.0
N A:THR35 3.2 20.9 1.0
CA A:VAL34 3.3 20.7 1.0
CB A:VAL34 3.3 20.9 1.0
O A:HOH272 3.4 7.2 1.0
N A:GLY33 3.4 21.0 1.0
F1 A:ALF303 3.6 23.7 1.0
C A:GLY33 3.6 20.9 1.0
C A:VAL34 3.7 20.8 1.0
CA A:GLY33 3.8 20.8 1.0
MG A:MG302 3.8 17.2 1.0
CG2 A:VAL34 3.9 20.6 1.0
O A:TRP31 4.1 21.2 1.0
OG1 A:THR35 4.1 20.0 1.0
PB A:GDP300 4.2 18.5 1.0
O2A A:GDP300 4.3 19.4 1.0
CA A:THR35 4.3 21.0 1.0
O3B A:GDP300 4.3 18.6 1.0
C A:PRO32 4.4 21.2 1.0
CB A:THR35 4.4 21.1 1.0
CG1 A:VAL34 4.6 20.5 1.0
O A:THR35 4.6 21.3 1.0
O A:GLY33 4.7 20.9 1.0
CA A:PRO32 4.8 21.3 1.0
O3A A:GDP300 4.8 19.5 1.0
O A:VAL34 4.9 21.3 1.0
C A:THR35 4.9 21.3 1.0
O A:HOH279 5.0 28.1 1.0

Fluorine binding site 3 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 3 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:23.7
occ:1.00
 F3 A:ALF303 0.0 23.7 1.0
AL A:ALF303 1.8 24.6 1.0
F1 A:ALF303 2.5 23.7 1.0
F2 A:ALF303 2.5 24.0 1.0
O A:HOH273 2.6 12.0 1.0
O2B A:GDP300 2.7 16.6 1.0
N A:GLY33 2.8 21.0 1.0
N A:ASN11 3.1 20.8 1.0
CB A:PRO10 3.3 20.5 1.0
CA A:PRO10 3.3 20.5 1.0
K A:K301 3.4 20.8 1.0
CA A:PRO32 3.5 21.3 1.0
O A:HOH279 3.5 28.1 1.0
F4 A:ALF303 3.6 25.6 1.0
C A:PRO10 3.6 20.5 1.0
C A:PRO32 3.6 21.2 1.0
CA A:GLY33 3.8 20.8 1.0
CA A:ASN11 4.0 21.0 1.0
O A:TRP31 4.1 21.2 1.0
N A:VAL34 4.2 20.6 1.0
PB A:GDP300 4.3 18.5 1.0
CB A:PRO32 4.3 21.4 1.0
CG A:PRO10 4.5 20.7 1.0
C A:GLY33 4.5 20.9 1.0
CB A:ASN11 4.6 21.1 1.0
N A:PRO32 4.6 21.3 1.0
N A:GLY56 4.7 25.9 1.0
O1B A:GDP300 4.7 19.8 1.0
O A:PRO10 4.7 20.6 1.0
N A:PRO10 4.8 20.5 1.0
CA A:GLY56 4.8 26.1 1.0
C A:TRP31 4.8 21.2 1.0
O A:PRO32 4.8 21.4 1.0
NZ A:LYS14 4.9 16.6 1.0
OD1 A:ASN11 4.9 22.3 1.0

Fluorine binding site 4 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 4 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:25.6
occ:1.00
 F4 A:ALF303 0.0 25.6 1.0
MG A:MG302 1.8 17.2 1.0
AL A:ALF303 1.8 24.6 1.0
O2B A:GDP300 2.5 16.6 1.0
F2 A:ALF303 2.5 24.0 1.0
F1 A:ALF303 2.5 23.7 1.0
O A:HOH273 2.7 12.0 1.0
OG1 A:THR35 2.7 20.0 1.0
O A:HOH271 2.7 26.2 1.0
O3B A:GDP300 2.9 18.6 1.0
O A:HOH272 3.0 7.2 1.0
CB A:THR35 3.0 21.1 1.0
PB A:GDP300 3.2 18.5 1.0
N A:THR35 3.5 20.9 1.0
F3 A:ALF303 3.6 23.7 1.0
OG1 A:THR15 3.8 19.2 1.0
CA A:THR35 3.8 21.0 1.0
O1B A:GDP300 4.0 19.8 1.0
O A:THR35 4.2 21.3 1.0
K A:K301 4.2 20.8 1.0
CG2 A:THR35 4.3 20.3 1.0
NZ A:LYS14 4.4 16.6 1.0
N A:GLY56 4.4 25.9 1.0
CE A:LYS14 4.4 17.4 1.0
C A:THR35 4.5 21.3 1.0
O3A A:GDP300 4.6 19.5 1.0
O A:LEU54 4.6 24.8 1.0
O2A A:GDP300 4.7 19.4 1.0
C A:VAL34 4.7 20.8 1.0
N A:VAL34 4.7 20.6 1.0
CA A:PRO55 4.8 25.3 1.0

Fluorine binding site 5 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 5 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:21.7
occ:1.00
 F1 B:ALF303 0.0 21.7 1.0
MG B:MG302 1.8 19.8 1.0
AL B:ALF303 1.8 19.9 1.0
F3 B:ALF303 2.5 19.7 1.0
F4 B:ALF303 2.5 20.2 1.0
O2B B:GDP300 2.6 14.6 1.0
O B:HOH273 2.6 21.2 1.0
O B:HOH271 2.7 11.7 1.0
OG1 B:THR35 2.7 21.7 1.0
O B:HOH272 2.9 13.7 1.0
O3B B:GDP300 3.0 17.2 1.0
CB B:THR35 3.0 21.9 1.0
PB B:GDP300 3.4 15.5 1.0
N B:THR35 3.5 22.1 1.0
F2 B:ALF303 3.6 19.6 1.0
CA B:THR35 3.8 21.8 1.0
OG1 B:THR15 3.9 19.1 1.0
O1B B:GDP300 4.2 17.1 1.0
O B:THR35 4.2 21.9 1.0
CG2 B:THR35 4.3 21.1 1.0
NZ B:LYS14 4.3 17.3 1.0
K B:K301 4.3 23.4 1.0
CE B:LYS14 4.4 17.4 1.0
N B:GLY56 4.5 22.7 1.0
C B:THR35 4.5 21.8 1.0
O B:LEU54 4.5 22.2 1.0
N B:VAL34 4.7 22.3 1.0
C B:VAL34 4.7 22.2 1.0
O3A B:GDP300 4.7 16.7 1.0
O2A B:GDP300 4.7 15.0 1.0
CA B:PRO55 4.7 22.5 1.0
CA B:VAL34 5.0 22.1 1.0

Fluorine binding site 6 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 6 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:19.6
occ:1.00
 F2 B:ALF303 0.0 19.6 1.0
AL B:ALF303 1.8 19.9 1.0
F4 B:ALF303 2.5 20.2 1.0
F3 B:ALF303 2.5 19.7 1.0
O2B B:GDP300 2.7 14.6 1.0
O B:HOH273 2.8 21.2 1.0
N B:GLY33 2.9 23.1 1.0
N B:ASN11 3.0 20.5 1.0
K B:K301 3.4 23.4 1.0
CB B:PRO10 3.4 20.1 1.0
CA B:PRO32 3.4 23.2 1.0
CA B:PRO10 3.4 19.9 1.0
F1 B:ALF303 3.6 21.7 1.0
C B:PRO32 3.6 23.3 1.0
C B:PRO10 3.7 20.2 1.0
CA B:GLY33 3.9 22.7 1.0
CA B:ASN11 4.0 20.9 1.0
O B:TRP31 4.1 23.0 1.0
N B:VAL34 4.2 22.3 1.0
CB B:PRO32 4.2 23.2 1.0
PB B:GDP300 4.2 15.5 1.0
O B:HOH296 4.3 33.1 1.0
CB B:ASN11 4.5 21.1 1.0
N B:PRO32 4.5 23.3 1.0
C B:GLY33 4.6 22.6 1.0
CG B:PRO10 4.6 20.0 1.0
O1B B:GDP300 4.7 17.1 1.0
C B:TRP31 4.7 23.0 1.0
O B:PRO32 4.8 23.5 1.0
N B:PRO10 4.8 19.9 1.0
O B:PRO10 4.9 19.9 1.0
NZ B:LYS14 4.9 17.3 1.0
OD1 B:ASN11 4.9 23.7 1.0
N B:GLY56 4.9 22.7 1.0

Fluorine binding site 7 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 7 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:19.7
occ:1.00
 F3 B:ALF303 0.0 19.7 1.0
AL B:ALF303 1.8 19.9 1.0
F1 B:ALF303 2.5 21.7 1.0
F2 B:ALF303 2.5 19.6 1.0
O2B B:GDP300 2.6 14.6 1.0
O B:HOH273 2.6 21.2 1.0
NZ B:LYS14 2.7 17.3 1.0
N B:GLY56 3.0 22.7 1.0
CA B:GLY56 3.3 23.0 1.0
CE B:LYS14 3.4 17.4 1.0
CA B:PRO10 3.4 19.9 1.0
O1B B:GDP300 3.5 17.1 1.0
PB B:GDP300 3.5 15.5 1.0
F4 B:ALF303 3.6 20.2 1.0
N B:ASN11 3.7 20.5 1.0
MG B:MG302 3.9 19.8 1.0
O B:HOH271 4.1 11.7 1.0
C B:PRO55 4.1 22.6 1.0
O3B B:GDP300 4.1 17.2 1.0
C B:PRO10 4.1 20.2 1.0
CB B:PRO10 4.1 20.1 1.0
O B:HOH296 4.2 33.1 1.0
O B:ASN9 4.3 19.7 1.0
N B:PRO10 4.4 19.9 1.0
CA B:PRO55 4.5 22.5 1.0
C B:GLY56 4.6 23.4 1.0
O B:LEU54 4.7 22.2 1.0
C B:ASN9 4.7 19.8 1.0
CG B:PRO10 4.8 20.0 1.0
CD B:LYS14 4.9 17.9 1.0
K B:K301 4.9 23.4 1.0
CA B:ASN11 4.9 20.9 1.0
O3A B:GDP300 4.9 16.7 1.0

Fluorine binding site 8 out of 8 in 3ss8

Go back to Fluorine Binding Sites List in 3ss8
Fluorine binding site 8 out of 8 in the Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Nfeob From S. Thermophilus Bound to Gdp.ALF4- and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:20.2
occ:1.00
 F4 B:ALF303 0.0 20.2 1.0
AL B:ALF303 1.8 19.9 1.0
F2 B:ALF303 2.5 19.6 1.0
F1 B:ALF303 2.5 21.7 1.0
K B:K301 2.5 23.4 1.0
O2B B:GDP300 2.7 14.6 1.0
N B:VAL34 2.7 22.3 1.0
O B:HOH273 2.8 21.2 1.0
O B:HOH272 3.1 13.7 1.0
CB B:VAL34 3.3 22.2 1.0
N B:THR35 3.3 22.1 1.0
CA B:VAL34 3.4 22.1 1.0
F3 B:ALF303 3.6 19.7 1.0
N B:GLY33 3.6 23.1 1.0
C B:GLY33 3.8 22.6 1.0
MG B:MG302 3.8 19.8 1.0
C B:VAL34 3.8 22.2 1.0
CG2 B:VAL34 3.9 21.4 1.0
O B:TRP31 4.0 23.0 1.0
CA B:GLY33 4.0 22.7 1.0
O2A B:GDP300 4.1 15.0 1.0
PB B:GDP300 4.1 15.5 1.0
OG1 B:THR35 4.2 21.7 1.0
O3B B:GDP300 4.3 17.2 1.0
CA B:THR35 4.4 21.8 1.0
C B:PRO32 4.5 23.3 1.0
CB B:THR35 4.5 21.9 1.0
CG1 B:VAL34 4.6 21.8 1.0
O3A B:GDP300 4.7 16.7 1.0
CA B:PRO32 4.8 23.2 1.0
O B:THR35 4.8 21.9 1.0
O B:GLY33 4.9 22.7 1.0
N B:ASN11 4.9 20.5 1.0

Reference:

M.R.Ash, M.J.Maher, J.M.Guss, M.Jormakka. The Initiation of Gtp Hydrolysis By the G-Domain of Feob: Insights From A Transition-State Complex Structure Plos One V. 6 23355 2011.
ISSN: ESSN 1932-6203
PubMed: 21858085
DOI: 10.1371/JOURNAL.PONE.0023355
Page generated: Wed Jul 31 22:36:48 2024

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