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Fluorine in PDB 7bvu: Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-

Protein crystallography data

The structure of Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-, PDB code: 7bvu was solved by S.Batra, B.Prakash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.619, 72.402, 157.957, 90, 90, 90
R / Rfree (%) 19.1 / 22.9

Other elements in 7bvu:

The structure of Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- (pdb code 7bvu). 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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-, PDB code: 7bvu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 1 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:35.3
occ:1.00
 F1 A:ALF303 0.0 35.3 1.0
AL A:ALF303 1.8 28.8 1.0
N A:VAL34 2.5 33.9 1.0
F4 A:ALF303 2.5 31.9 1.0
F3 A:ALF303 2.5 32.3 1.0
K A:K305 2.8 38.2 1.0
O A:HOH420 2.9 29.6 1.0
O1B A:GDP302 3.0 25.9 1.0
N A:GLY33 3.1 34.6 1.0
N A:THR35 3.2 29.6 1.0
CA A:VAL34 3.2 31.4 1.0
CB A:VAL34 3.2 34.9 1.0
C A:GLY33 3.4 28.7 1.0
F2 A:ALF303 3.6 30.4 1.0
CA A:GLY33 3.6 30.6 1.0
C A:VAL34 3.7 32.6 1.0
O A:HOH438 3.7 25.2 1.0
CG2 A:VAL34 3.7 28.7 1.0
MG A:MG304 3.8 24.4 1.0
C A:PRO32 4.1 32.4 1.0
O A:TRP31 4.1 36.3 1.0
PB A:GDP302 4.3 27.8 1.0
CA A:THR35 4.4 28.4 1.0
CA A:PRO32 4.4 36.3 1.0
O3B A:GDP302 4.4 24.1 1.0
O A:GLY33 4.5 35.5 1.0
OG1 A:THR35 4.5 29.9 1.0
O A:THR35 4.5 30.2 1.0
O A:HOH470 4.5 28.9 1.0
CB A:THR35 4.5 26.8 1.0
O1A A:GDP302 4.5 22.9 1.0
CG1 A:VAL34 4.5 27.0 1.0
N A:ASN11 4.9 30.1 1.0
O A:VAL34 4.9 32.5 1.0
C A:THR35 4.9 30.3 1.0

Fluorine binding site 2 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 2 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:30.4
occ:1.00
 F2 A:ALF303 0.0 30.4 1.0
AL A:ALF303 1.8 28.8 1.0
NZ A:LYS14 2.5 26.8 1.0
F4 A:ALF303 2.5 31.9 1.0
F3 A:ALF303 2.5 32.3 1.0
O1B A:GDP302 2.8 25.9 1.0
N A:GLY56 3.0 27.0 1.0
CA A:GLY56 3.2 26.1 1.0
O A:HOH420 3.2 29.6 1.0
O2B A:GDP302 3.3 29.7 1.0
CA A:PRO10 3.4 31.8 1.0
CE A:LYS14 3.4 31.0 1.0
N A:ASN11 3.5 30.1 1.0
PB A:GDP302 3.5 27.8 1.0
O A:HOH470 3.5 28.9 1.0
F1 A:ALF303 3.6 35.3 1.0
C A:PRO10 3.9 30.9 1.0
O3B A:GDP302 4.0 24.1 1.0
C A:PRO55 4.1 28.7 1.0
O A:ASN9 4.1 24.5 1.0
CB A:PRO10 4.2 27.9 1.0
O A:HOH416 4.2 28.1 1.0
MG A:MG304 4.2 24.4 1.0
N A:PRO10 4.2 30.3 1.0
C A:ASN9 4.5 26.7 1.0
CA A:PRO55 4.6 28.3 1.0
C A:GLY56 4.6 25.2 1.0
CA A:ASN11 4.7 32.8 1.0
O A:LEU54 4.7 29.3 1.0
CD A:LYS14 4.8 26.1 1.0
CG A:PRO10 4.8 27.2 1.0
O A:PRO55 4.9 28.4 1.0
O3A A:GDP302 5.0 30.8 1.0

Fluorine binding site 3 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 3 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:32.3
occ:1.00
 F3 A:ALF303 0.0 32.3 1.0
AL A:ALF303 1.8 28.8 1.0
F1 A:ALF303 2.5 35.3 1.0
F2 A:ALF303 2.5 30.4 1.0
N A:GLY33 2.8 34.6 1.0
N A:ASN11 2.9 30.1 1.0
O1B A:GDP302 3.0 25.9 1.0
O A:HOH420 3.0 29.6 1.0
O A:HOH470 3.1 28.9 1.0
CA A:PRO32 3.3 36.3 1.0
CA A:PRO10 3.3 31.8 1.0
CB A:PRO10 3.3 27.9 1.0
C A:PRO32 3.5 32.4 1.0
C A:PRO10 3.5 30.9 1.0
F4 A:ALF303 3.6 31.9 1.0
K A:K305 3.7 38.2 1.0
CB A:PRO32 3.8 33.1 1.0
CA A:GLY33 3.8 30.6 1.0
CA A:ASN11 3.9 32.8 1.0
N A:VAL34 4.2 33.9 1.0
CB A:ASN11 4.4 33.1 1.0
PB A:GDP302 4.4 27.8 1.0
CG A:PRO10 4.5 27.2 1.0
O A:TRP31 4.5 36.3 1.0
C A:GLY33 4.5 28.7 1.0
N A:PRO32 4.5 40.1 1.0
O A:HOH480 4.6 31.8 1.0
N A:PRO10 4.7 30.3 1.0
O A:PRO10 4.7 32.5 1.0
OD1 A:ASN11 4.7 35.5 1.0
O2B A:GDP302 4.7 29.7 1.0
O A:PRO32 4.7 36.5 1.0
N A:GLY56 4.7 27.0 1.0
NZ A:LYS14 4.8 26.8 1.0
CA A:GLY56 4.8 26.1 1.0
CG A:ASN11 5.0 35.4 1.0
C A:TRP31 5.0 38.2 1.0

Fluorine binding site 4 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 4 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:31.9
occ:1.00
 F4 A:ALF303 0.0 31.9 1.0
AL A:ALF303 1.8 28.8 1.0
MG A:MG304 2.0 24.4 1.0
F2 A:ALF303 2.5 30.4 1.0
F1 A:ALF303 2.5 35.3 1.0
O1B A:GDP302 2.8 25.9 1.0
O A:HOH416 2.9 28.1 1.0
O3B A:GDP302 3.0 24.1 1.0
O A:HOH420 3.1 29.6 1.0
CB A:THR35 3.1 26.8 1.0
OG1 A:THR35 3.1 29.9 1.0
PB A:GDP302 3.4 27.8 1.0
O A:HOH438 3.5 25.2 1.0
N A:THR35 3.5 29.6 1.0
F3 A:ALF303 3.6 32.3 1.0
CA A:THR35 3.8 28.4 1.0
O2B A:GDP302 4.0 29.7 1.0
OG1 A:THR15 4.0 28.4 1.0
O A:THR35 4.1 30.2 1.0
NZ A:LYS14 4.2 26.8 1.0
N A:GLY56 4.3 27.0 1.0
CG2 A:THR35 4.4 24.7 1.0
CE A:LYS14 4.4 31.0 1.0
O A:LEU54 4.4 29.3 1.0
K A:K305 4.4 38.2 1.0
C A:THR35 4.5 30.3 1.0
N A:VAL34 4.6 33.9 1.0
CA A:PRO55 4.6 28.3 1.0
C A:VAL34 4.6 32.6 1.0
O A:HOH470 4.8 28.9 1.0
O3A A:GDP302 4.8 30.8 1.0
CB A:VAL34 4.8 34.9 1.0
C A:PRO55 4.8 28.7 1.0
O1A A:GDP302 4.9 22.9 1.0
CA A:VAL34 4.9 31.4 1.0

Fluorine binding site 5 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 5 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:28.8
occ:1.00
 F1 B:ALF303 0.0 28.8 1.0
AL B:ALF303 1.8 27.0 1.0
F3 B:ALF303 2.5 27.1 1.0
F4 B:ALF303 2.5 30.1 1.0
NZ B:LYS14 2.6 24.1 1.0
O3B B:GDP302 2.9 21.7 1.0
N B:GLY56 3.0 25.9 1.0
O B:HOH439 3.1 29.9 1.0
CA B:GLY56 3.1 25.2 1.0
CA B:PRO10 3.3 25.8 1.0
CE B:LYS14 3.5 22.4 1.0
O B:HOH473 3.5 28.2 1.0
O1B B:GDP302 3.5 28.6 1.0
F2 B:ALF303 3.6 30.2 1.0
N B:ASN11 3.6 25.6 1.0
PB B:GDP302 3.6 25.2 1.0
C B:PRO10 4.0 26.7 1.0
C B:PRO55 4.1 24.1 1.0
O2B B:GDP302 4.1 23.7 1.0
O B:ASN9 4.1 26.7 1.0
CB B:PRO10 4.1 24.5 1.0
N B:PRO10 4.2 27.7 1.0
O B:HOH426 4.2 24.4 1.0
MG B:MG304 4.2 25.2 1.0
C B:GLY56 4.5 25.6 1.0
C B:ASN9 4.5 25.6 1.0
CA B:PRO55 4.6 25.6 1.0
CG B:PRO10 4.7 25.8 1.0
CA B:ASN11 4.8 28.3 1.0
O B:LEU54 4.8 25.4 1.0
CD B:LYS14 4.9 22.7 1.0
O B:PRO55 4.9 22.1 1.0
N B:GLY33 5.0 30.2 1.0

Fluorine binding site 6 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 6 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:30.2
occ:1.00
 F2 B:ALF303 0.0 30.2 1.0
AL B:ALF303 1.8 27.0 1.0
F3 B:ALF303 2.5 27.1 1.0
F4 B:ALF303 2.5 30.1 1.0
N B:VAL34 2.6 27.1 1.0
K B:K305 2.8 33.0 1.0
O3B B:GDP302 3.0 21.7 1.0
O B:HOH439 3.0 29.9 1.0
N B:THR35 3.1 26.4 1.0
CB B:VAL34 3.2 27.8 1.0
CA B:VAL34 3.3 25.3 1.0
O B:HOH424 3.4 24.2 1.0
N B:GLY33 3.4 30.2 1.0
F1 B:ALF303 3.6 28.8 1.0
C B:GLY33 3.6 28.6 1.0
C B:VAL34 3.7 29.0 1.0
MG B:MG304 3.7 25.2 1.0
CG2 B:VAL34 3.8 25.3 1.0
CA B:GLY33 3.9 26.8 1.0
PB B:GDP302 4.2 25.2 1.0
O B:TRP31 4.2 30.6 1.0
O2B B:GDP302 4.3 23.7 1.0
O2A B:GDP302 4.3 25.4 1.0
CA B:THR35 4.3 26.9 1.0
C B:PRO32 4.3 33.8 1.0
CB B:THR35 4.4 26.4 1.0
OG1 B:THR35 4.4 30.8 1.0
CG1 B:VAL34 4.5 25.4 1.0
O B:THR35 4.5 28.2 1.0
CA B:PRO32 4.6 33.8 1.0
O B:GLY33 4.6 33.7 1.0
O B:HOH473 4.9 28.2 1.0
O B:VAL34 4.9 28.5 1.0
C B:THR35 4.9 27.8 1.0
N B:ASN11 5.0 25.6 1.0

Fluorine binding site 7 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 7 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:27.1
occ:1.00
 F3 B:ALF303 0.0 27.1 1.0
AL B:ALF303 1.8 27.0 1.0
MG B:MG304 2.0 25.2 1.0
F1 B:ALF303 2.5 28.8 1.0
F2 B:ALF303 2.5 30.2 1.0
O B:HOH426 2.8 24.4 1.0
O3B B:GDP302 2.9 21.7 1.0
O2B B:GDP302 2.9 23.7 1.0
CB B:THR35 3.1 26.4 1.0
O B:HOH439 3.2 29.9 1.0
OG1 B:THR35 3.3 30.8 1.0
PB B:GDP302 3.4 25.2 1.0
O B:HOH424 3.4 24.2 1.0
F4 B:ALF303 3.6 30.1 1.0
N B:THR35 3.6 26.4 1.0
CA B:THR35 3.9 26.9 1.0
OG1 B:THR15 4.0 22.1 1.0
O1B B:GDP302 4.0 28.6 1.0
NZ B:LYS14 4.1 24.1 1.0
O B:THR35 4.2 28.2 1.0
N B:GLY56 4.2 25.9 1.0
CE B:LYS14 4.2 22.4 1.0
O B:LEU54 4.3 25.4 1.0
CG2 B:THR35 4.3 24.0 1.0
C B:THR35 4.5 27.8 1.0
K B:K305 4.6 33.0 1.0
CA B:PRO55 4.6 25.6 1.0
N B:VAL34 4.7 27.1 1.0
C B:VAL34 4.8 29.0 1.0
C B:PRO55 4.8 24.1 1.0
O3A B:GDP302 4.8 30.8 1.0
O2A B:GDP302 4.9 25.4 1.0
O B:HOH473 5.0 28.2 1.0

Fluorine binding site 8 out of 8 in 7bvu

Go back to Fluorine Binding Sites List in 7bvu
Fluorine binding site 8 out of 8 in the Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4-


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 S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:30.1
occ:1.00
 F4 B:ALF303 0.0 30.1 1.0
AL B:ALF303 1.8 27.0 1.0
F1 B:ALF303 2.5 28.8 1.0
F2 B:ALF303 2.5 30.2 1.0
N B:GLY33 2.7 30.2 1.0
O B:HOH439 2.9 29.9 1.0
O3B B:GDP302 3.0 21.7 1.0
N B:ASN11 3.1 25.6 1.0
CA B:PRO32 3.3 33.8 1.0
O B:HOH473 3.3 28.2 1.0
CA B:PRO10 3.4 25.8 1.0
CB B:PRO10 3.5 24.5 1.0
C B:PRO32 3.5 33.8 1.0
K B:K305 3.5 33.0 1.0
F3 B:ALF303 3.6 27.1 1.0
C B:PRO10 3.7 26.7 1.0
CA B:GLY33 3.7 26.8 1.0
CB B:PRO32 3.9 33.2 1.0
CA B:ASN11 4.0 28.3 1.0
N B:VAL34 4.1 27.1 1.0
O B:TRP31 4.4 30.6 1.0
PB B:GDP302 4.4 25.2 1.0
C B:GLY33 4.4 28.6 1.0
N B:PRO32 4.6 32.9 1.0
CB B:ASN11 4.6 28.8 1.0
CG B:PRO10 4.6 25.8 1.0
OD1 B:ASN11 4.7 29.8 1.0
O B:PRO32 4.7 34.1 1.0
O B:HOH491 4.8 28.5 1.0
N B:PRO10 4.8 27.7 1.0
N B:GLY56 4.8 25.9 1.0
O1B B:GDP302 4.9 28.6 1.0
O B:PRO10 4.9 28.0 1.0
CA B:GLY56 4.9 25.2 1.0
NZ B:LYS14 4.9 24.1 1.0
C B:TRP31 4.9 32.1 1.0

Reference:

S.Batra, B.Prakash. Crystal Structure of S. Thermophilus Nfeob E66A.E67A Bound to Gdp.ALF4- To Be Published.
Page generated: Tue Jul 15 18:51:13 2025

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