Iron in PDB 5bvg: Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii

Enzymatic activity of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii

All present enzymatic activity of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii:
1.18.6.1;

Protein crystallography data

The structure of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii, PDB code: 5bvg was solved by T.Spatzal, K.A.Perez, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.38 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.582, 130.825, 107.128, 90.00, 108.85, 90.00
R / Rfree (%) 15.2 / 17.9

Other elements in 5bvg:

The structure of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii (pdb code 5bvg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii, PDB code: 5bvg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 5bvg

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Iron binding site 1 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:9.9
occ:1.00
FE1 A:ICG502 0.0 9.9 1.0
S2A A:ICG502 2.2 9.5 1.0
SG A:CYS275 2.2 9.2 1.0
S4A A:ICG502 2.3 10.3 1.0
S1A A:ICG502 2.3 9.8 1.0
FE4 A:ICG502 2.6 9.8 1.0
FE3 A:ICG502 2.7 9.2 1.0
FE2 A:ICG502 2.7 9.3 1.0
CB A:CYS275 3.3 10.1 1.0
CX A:ICG502 3.5 9.1 1.0
OG A:SER278 4.1 9.9 1.0
CB A:LEU358 4.2 10.4 1.0
CB A:SER278 4.4 9.7 1.0
CE2 A:TYR229 4.5 8.2 1.0
CA A:CYS275 4.5 10.6 1.0
CD2 A:LEU358 4.7 10.4 1.0
S3A A:ICG502 4.8 9.2 1.0
S5A A:ICG502 4.8 8.9 1.0
N A:SER278 4.9 10.0 1.0
CD2 A:TYR229 5.0 9.2 1.0
SE2B A:ICG502 5.0 11.6 1.0
N A:LEU358 5.0 10.3 1.0
FE7 A:ICG502 5.0 8.9 1.0

Iron binding site 2 out of 32 in 5bvg

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Iron binding site 2 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:9.3
occ:1.00
FE2 A:ICG502 0.0 9.3 1.0
CX A:ICG502 2.0 9.1 1.0
S2A A:ICG502 2.2 9.5 1.0
S1A A:ICG502 2.2 9.8 1.0
SE2B A:ICG502 2.4 11.6 1.0
FE6 A:ICG502 2.6 9.2 1.0
FE4 A:ICG502 2.7 9.8 1.0
FE3 A:ICG502 2.7 9.2 1.0
FE1 A:ICG502 2.7 9.9 1.0
FE7 A:ICG502 3.7 8.9 1.0
FE5 A:ICG502 3.7 9.4 1.0
S4A A:ICG502 3.9 10.3 1.0
CZ A:PHE381 4.0 9.9 1.0
NE2 A:HIS195 4.1 11.7 1.0
S1B A:ICG502 4.2 9.6 1.0
S3B A:ICG502 4.2 9.4 1.0
CE1 A:HIS195 4.3 12.1 1.0
CG1 A:VAL70 4.5 10.1 1.0
S3A A:ICG502 4.5 9.2 1.0
CE1 A:PHE381 4.5 10.3 1.0
S5A A:ICG502 4.5 8.9 1.0
SG A:CYS275 4.6 9.2 1.0

Iron binding site 3 out of 32 in 5bvg

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Iron binding site 3 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:9.2
occ:1.00
FE3 A:ICG502 0.0 9.2 1.0
CX A:ICG502 2.0 9.1 1.0
S5A A:ICG502 2.2 8.9 1.0
S2A A:ICG502 2.2 9.5 1.0
S4A A:ICG502 2.3 10.3 1.0
FE7 A:ICG502 2.6 8.9 1.0
FE4 A:ICG502 2.7 9.8 1.0
FE1 A:ICG502 2.7 9.9 1.0
FE2 A:ICG502 2.7 9.3 1.0
FE6 A:ICG502 3.7 9.2 1.0
FE5 A:ICG502 3.7 9.4 1.0
S1A A:ICG502 3.8 9.8 1.0
O A:HOH849 4.0 11.0 1.0
NH2 A:ARG96 4.1 9.8 1.0
CD2 A:TYR229 4.1 9.2 1.0
S3B A:ICG502 4.2 9.4 1.0
S4B A:ICG502 4.2 9.0 1.0
CE2 A:TYR229 4.4 8.2 1.0
S3A A:ICG502 4.5 9.2 1.0
SE2B A:ICG502 4.6 11.6 1.0
SG A:CYS275 4.8 9.2 1.0

Iron binding site 4 out of 32 in 5bvg

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Iron binding site 4 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:9.8
occ:1.00
FE4 A:ICG502 0.0 9.8 1.0
CX A:ICG502 2.0 9.1 1.0
S3A A:ICG502 2.2 9.2 1.0
S4A A:ICG502 2.3 10.3 1.0
S1A A:ICG502 2.3 9.8 1.0
FE5 A:ICG502 2.6 9.4 1.0
FE1 A:ICG502 2.6 9.9 1.0
FE3 A:ICG502 2.7 9.2 1.0
FE2 A:ICG502 2.7 9.3 1.0
FE7 A:ICG502 3.7 8.9 1.0
FE6 A:ICG502 3.7 9.2 1.0
S2A A:ICG502 3.8 9.5 1.0
N A:LEU358 4.0 10.3 1.0
N A:GLY357 4.1 10.2 1.0
CB A:LEU358 4.1 10.4 1.0
S4B A:ICG502 4.3 9.0 1.0
S1B A:ICG502 4.3 9.6 1.0
S5A A:ICG502 4.5 8.9 1.0
SG A:CYS275 4.6 9.2 1.0
CA A:LEU358 4.6 10.0 1.0
C A:GLY357 4.6 10.8 1.0
N A:ARG359 4.6 10.2 1.0
SE2B A:ICG502 4.7 11.6 1.0
CA A:GLY357 4.7 10.6 1.0
CG A:ARG359 4.8 9.8 1.0
CA A:GLY356 4.9 10.3 1.0
CD A:ARG359 4.9 9.8 1.0
CZ A:PHE381 5.0 9.9 1.0

Iron binding site 5 out of 32 in 5bvg

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Iron binding site 5 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:9.4
occ:1.00
FE5 A:ICG502 0.0 9.4 1.0
CX A:ICG502 2.0 9.1 1.0
S4B A:ICG502 2.2 9.0 1.0
S1B A:ICG502 2.2 9.6 1.0
S3A A:ICG502 2.3 9.2 1.0
FE4 A:ICG502 2.6 9.8 1.0
FE6 A:ICG502 2.6 9.2 1.0
FE7 A:ICG502 2.6 8.9 1.0
MO1 A:ICG502 2.7 8.9 1.0
FE2 A:ICG502 3.7 9.3 1.0
FE3 A:ICG502 3.7 9.2 1.0
ND1 A:HIS442 3.8 10.2 1.0
S3B A:ICG502 3.9 9.4 1.0
N A:GLY356 4.1 10.4 1.0
CG2 A:ILE355 4.2 10.0 1.0
CA A:GLY356 4.2 10.3 1.0
CE1 A:HIS442 4.3 9.9 1.0
S1A A:ICG502 4.3 9.8 1.0
S4A A:ICG502 4.3 10.3 1.0
S5A A:ICG502 4.5 8.9 1.0
SE2B A:ICG502 4.6 11.6 1.0
O7 A:HCA501 4.6 9.6 1.0
CD A:ARG359 4.7 9.8 1.0
CG A:HIS442 4.8 10.1 1.0
N A:GLY357 4.8 10.2 1.0
O6 A:HCA501 4.8 9.1 1.0

Iron binding site 6 out of 32 in 5bvg

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Iron binding site 6 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:9.2
occ:1.00
FE6 A:ICG502 0.0 9.2 1.0
CX A:ICG502 2.0 9.1 1.0
S1B A:ICG502 2.2 9.6 1.0
S3B A:ICG502 2.2 9.4 1.0
SE2B A:ICG502 2.3 11.6 1.0
FE2 A:ICG502 2.6 9.3 1.0
FE7 A:ICG502 2.6 8.9 1.0
FE5 A:ICG502 2.6 9.4 1.0
MO1 A:ICG502 2.7 8.9 1.0
FE3 A:ICG502 3.7 9.2 1.0
FE4 A:ICG502 3.7 9.8 1.0
O7 A:HCA501 3.8 9.6 1.0
S4B A:ICG502 3.8 9.0 1.0
CZ A:PHE381 4.2 9.9 1.0
S2A A:ICG502 4.2 9.5 1.0
S1A A:ICG502 4.3 9.8 1.0
CG2 A:VAL70 4.4 10.7 1.0
S5A A:ICG502 4.5 8.9 1.0
O6 A:HCA501 4.5 9.1 1.0
S3A A:ICG502 4.5 9.2 1.0
O2 A:HCA501 4.6 10.9 1.0
CE2 A:PHE381 4.6 10.1 1.0
ND1 A:HIS442 4.8 10.2 1.0
C3 A:HCA501 4.8 9.4 1.0
C2 A:HCA501 5.0 9.5 1.0

Iron binding site 7 out of 32 in 5bvg

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Iron binding site 7 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:8.9
occ:1.00
FE7 A:ICG502 0.0 8.9 1.0
CX A:ICG502 2.0 9.1 1.0
S5A A:ICG502 2.2 8.9 1.0
S4B A:ICG502 2.2 9.0 1.0
S3B A:ICG502 2.2 9.4 1.0
FE3 A:ICG502 2.6 9.2 1.0
FE6 A:ICG502 2.6 9.2 1.0
FE5 A:ICG502 2.6 9.4 1.0
MO1 A:ICG502 2.7 8.9 1.0
FE2 A:ICG502 3.7 9.3 1.0
FE4 A:ICG502 3.7 9.8 1.0
O A:HOH709 3.7 7.7 1.0
O6 A:HCA501 3.8 9.1 1.0
S1B A:ICG502 3.8 9.6 1.0
NE A:ARG96 4.1 9.4 1.0
NH2 A:ARG96 4.2 9.8 1.0
S2A A:ICG502 4.3 9.5 1.0
S4A A:ICG502 4.3 10.3 1.0
S3A A:ICG502 4.5 9.2 1.0
SE2B A:ICG502 4.5 11.6 1.0
O7 A:HCA501 4.6 9.6 1.0
CZ A:ARG96 4.7 9.3 1.0
C7 A:HCA501 4.7 9.6 1.0
ND1 A:HIS442 4.7 10.2 1.0
CZ A:ARG359 4.9 10.0 1.0
NH1 A:ARG359 4.9 9.3 1.0
FE1 A:ICG502 5.0 9.9 1.0

Iron binding site 8 out of 32 in 5bvg

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Iron binding site 8 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe505

b:11.7
occ:1.00
FE1 A:CLF505 0.0 11.7 1.0
S3A A:CLF505 2.3 10.8 1.0
S2A A:CLF505 2.3 11.4 1.0
SG B:CYS95 2.4 10.7 1.0
S1 A:CLF505 2.4 11.3 1.0
FE2 A:CLF505 2.5 11.5 1.0
FE4 A:CLF505 2.6 11.2 1.0
FE3 A:CLF505 2.7 11.0 1.0
FE8 A:CLF505 2.9 11.5 1.0
N B:CYS95 3.3 10.0 1.0
CB B:CYS95 3.5 10.9 1.0
CA B:CYS95 3.6 10.6 1.0
S4A A:CLF505 3.8 11.2 1.0
FE5 A:CLF505 3.8 12.8 1.0
S4B A:CLF505 3.9 11.3 1.0
C B:GLY94 4.0 10.2 1.0
O B:HOH717 4.4 14.7 1.0
CA B:GLY94 4.5 10.6 1.0
SG A:CYS154 4.5 12.4 1.0
CB B:SER92 4.5 13.3 0.7
SG A:CYS88 4.6 10.8 1.0
CB B:SER92 4.6 13.3 0.3
FE6 A:CLF505 4.6 14.3 1.0
O B:GLY94 4.7 9.8 1.0
SG A:CYS62 4.8 10.5 1.0
OG B:SER92 4.8 13.8 0.3
O B:SER92 4.8 12.8 0.3
N B:GLY94 4.9 11.1 1.0

Iron binding site 9 out of 32 in 5bvg

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Iron binding site 9 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe505

b:11.5
occ:1.00
FE2 A:CLF505 0.0 11.5 1.0
S2A A:CLF505 2.3 11.4 1.0
S4A A:CLF505 2.3 11.2 1.0
SG A:CYS154 2.3 12.4 1.0
S1 A:CLF505 2.4 11.3 1.0
FE1 A:CLF505 2.5 11.7 1.0
FE4 A:CLF505 2.6 11.2 1.0
FE3 A:CLF505 2.8 11.0 1.0
CB A:CYS154 3.4 12.6 1.0
S3A A:CLF505 3.8 10.8 1.0
O B:HOH717 3.9 14.7 1.0
N A:CYS154 3.9 11.5 1.0
CA A:GLY185 4.0 12.5 1.0
N A:GLY185 4.1 12.7 1.0
CA A:CYS154 4.2 12.1 1.0
SG B:CYS95 4.2 10.7 1.0
OG B:SER92 4.4 13.8 0.3
FE8 A:CLF505 4.4 11.5 1.0
CB B:SER92 4.5 13.3 0.7
CB B:SER92 4.5 13.3 0.3
OG B:SER92 4.5 15.3 0.7
FE5 A:CLF505 4.6 12.8 1.0
SG A:CYS88 4.6 10.8 1.0
C A:GLY185 4.7 13.0 1.0
FE6 A:CLF505 4.8 14.3 1.0
SG A:CYS62 4.9 10.5 1.0
SG B:CYS153 5.0 13.0 1.0

Iron binding site 10 out of 32 in 5bvg

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Iron binding site 10 out of 32 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe505

b:11.0
occ:1.00
FE3 A:CLF505 0.0 11.0 1.0
S3A A:CLF505 2.2 10.8 1.0
S2A A:CLF505 2.3 11.4 1.0
SG A:CYS62 2.3 10.5 1.0
S4A A:CLF505 2.3 11.2 1.0
FE4 A:CLF505 2.7 11.2 1.0
FE1 A:CLF505 2.7 11.7 1.0
FE2 A:CLF505 2.8 11.5 1.0
CB A:CYS62 3.4 11.2 1.0
CA A:GLY185 4.0 12.5 1.0
CB A:TYR64 4.1 10.2 1.0
S1 A:CLF505 4.2 11.3 1.0
CA B:GLY94 4.3 10.6 1.0
C B:GLY94 4.5 10.2 1.0
N A:GLY185 4.5 12.7 1.0
N B:CYS95 4.6 10.0 1.0
CD1 A:TYR64 4.6 9.9 1.0
CG A:TYR64 4.7 10.3 1.0
CA A:CYS62 4.8 11.1 1.0
SG A:CYS154 4.8 12.4 1.0
O B:HOH914 4.8 12.3 1.0
SG A:CYS88 4.8 10.8 1.0
N A:TYR64 4.9 9.7 1.0
CE2 B:TYR98 4.9 9.9 1.0

Reference:

T.Spatzal, K.A.Perez, J.B.Howard, D.C.Rees. Catalysis-Dependent Selenium Incorporation and Migration in the Nitrogenase Active Site Iron-Molybdenum Cofactor. Elife V. 4 11620 2015.
ISSN: ESSN 2050-084X
PubMed: 26673079
DOI: 10.7554/ELIFE.11620
Page generated: Sun Dec 13 15:57:24 2020

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