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Iron in PDB 3min: Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State

Enzymatic activity of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State

All present enzymatic activity of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State, PDB code: 3min was solved by J.W.Peters, M.H.B.Stowell, S.M.Soltis, M.W.Day, J.Kim, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 108.000, 131.300, 81.000, 90.00, 110.70, 90.00
R / Rfree (%) 20.6 / 26.4

Other elements in 3min:

The structure of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State (pdb code 3min). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State, PDB code: 3min:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 30 in 3min

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Iron binding site 1 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe496

b:18.8
occ:1.00
 FE1 A:CFM496 0.0 18.8 1.0
S2A A:CFM496 2.2 18.2 1.0
S4A A:CFM496 2.3 17.9 1.0
S1A A:CFM496 2.3 18.8 1.0
SG A:CYS275 2.3 20.6 1.0
FE3 A:CFM496 2.5 19.3 1.0
FE4 A:CFM496 2.6 17.3 1.0
FE2 A:CFM496 2.6 17.7 1.0
CB A:CYS275 3.4 19.1 1.0
OG A:SER278 3.8 21.4 1.0
CB A:LEU358 4.1 18.3 1.0
CB A:SER278 4.4 20.0 1.0
CE2 A:TYR229 4.4 19.4 1.0
S5 A:CFM496 4.6 15.1 1.0
CD2 A:LEU358 4.6 15.2 1.0
CA A:CYS275 4.6 21.9 1.0
S2B A:CFM496 4.7 18.4 1.0
S3A A:CFM496 4.8 17.1 1.0
CD2 A:TYR229 4.8 17.0 1.0
FE6 A:CFM496 4.9 19.8 1.0
N A:LEU358 4.9 15.2 1.0
FE7 A:CFM496 4.9 16.2 1.0
FE5 A:CFM496 4.9 17.7 1.0
N A:SER278 4.9 18.9 1.0

Iron binding site 2 out of 30 in 3min

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Iron binding site 2 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe496

b:17.7
occ:1.00
 FE2 A:CFM496 0.0 17.7 1.0
S1A A:CFM496 2.1 18.8 1.0
S2B A:CFM496 2.2 18.4 1.0
S2A A:CFM496 2.3 18.2 1.0
FE6 A:CFM496 2.5 19.8 1.0
FE3 A:CFM496 2.6 19.3 1.0
FE4 A:CFM496 2.6 17.3 1.0
FE1 A:CFM496 2.6 18.8 1.0
FE5 A:CFM496 3.6 17.7 1.0
FE7 A:CFM496 3.6 16.2 1.0
S4A A:CFM496 3.8 17.9 1.0
CZ A:PHE381 4.0 15.2 1.0
S1B A:CFM496 4.1 16.8 1.0
S3B A:CFM496 4.1 18.1 1.0
S5 A:CFM496 4.3 15.1 1.0
NE2 A:HIS195 4.3 27.7 1.0
S3A A:CFM496 4.3 17.1 1.0
CE1 A:PHE381 4.4 13.2 1.0
CE1 A:HIS195 4.5 26.6 1.0
SG A:CYS275 4.6 20.6 1.0
MO1 A:CFM496 4.9 19.1 1.0
N A:GLY357 4.9 17.7 1.0

Iron binding site 3 out of 30 in 3min

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Iron binding site 3 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe496

b:19.3
occ:1.00
 FE3 A:CFM496 0.0 19.3 1.0
S5 A:CFM496 2.1 15.1 1.0
S4A A:CFM496 2.2 17.9 1.0
S2A A:CFM496 2.2 18.2 1.0
FE1 A:CFM496 2.5 18.8 1.0
FE7 A:CFM496 2.6 16.2 1.0
FE4 A:CFM496 2.6 17.3 1.0
FE2 A:CFM496 2.6 17.7 1.0
FE6 A:CFM496 3.6 19.8 1.0
FE5 A:CFM496 3.6 17.7 1.0
S1A A:CFM496 3.7 18.8 1.0
NH1 A:ARG96 4.0 20.4 1.0
S4B A:CFM496 4.1 18.8 1.0
O A:HOH506 4.1 22.3 1.0
CD2 A:TYR229 4.2 17.0 1.0
S3B A:CFM496 4.2 18.1 1.0
S2B A:CFM496 4.4 18.4 1.0
S3A A:CFM496 4.4 17.1 1.0
CE2 A:TYR229 4.5 19.4 1.0
SG A:CYS275 4.8 20.6 1.0
NH1 A:ARG359 4.9 22.6 1.0
MO1 A:CFM496 5.0 19.1 1.0

Iron binding site 4 out of 30 in 3min

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Iron binding site 4 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe496

b:17.3
occ:1.00
 FE4 A:CFM496 0.0 17.3 1.0
S1A A:CFM496 2.2 18.8 1.0
S4A A:CFM496 2.2 17.9 1.0
S3A A:CFM496 2.2 17.1 1.0
FE3 A:CFM496 2.6 19.3 1.0
FE1 A:CFM496 2.6 18.8 1.0
FE2 A:CFM496 2.6 17.7 1.0
FE5 A:CFM496 2.6 17.7 1.0
FE6 A:CFM496 3.6 19.8 1.0
FE7 A:CFM496 3.7 16.2 1.0
S2A A:CFM496 3.8 18.2 1.0
N A:LEU358 3.8 15.2 1.0
CB A:LEU358 4.0 18.3 1.0
N A:GLY357 4.0 17.7 1.0
S4B A:CFM496 4.2 18.8 1.0
CG A:ARG359 4.2 22.8 1.0
S1B A:CFM496 4.3 16.8 1.0
S5 A:CFM496 4.3 15.1 1.0
S2B A:CFM496 4.5 18.4 1.0
C A:GLY357 4.5 15.4 1.0
CA A:LEU358 4.5 15.2 1.0
SG A:CYS275 4.6 20.6 1.0
N A:ARG359 4.6 22.6 1.0
CA A:GLY357 4.6 14.3 1.0
CD A:ARG359 4.8 21.8 1.0
CZ A:PHE381 4.9 15.2 1.0
C A:GLY356 5.0 17.8 1.0
CA A:GLY356 5.0 14.6 1.0

Iron binding site 5 out of 30 in 3min

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Iron binding site 5 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe496

b:17.7
occ:1.00
 FE5 A:CFM496 0.0 17.7 1.0
S3A A:CFM496 2.1 17.1 1.0
S4B A:CFM496 2.2 18.8 1.0
S1B A:CFM496 2.2 16.8 1.0
FE6 A:CFM496 2.5 19.8 1.0
FE7 A:CFM496 2.6 16.2 1.0
FE4 A:CFM496 2.6 17.3 1.0
MO1 A:CFM496 2.7 19.1 1.0
FE2 A:CFM496 3.6 17.7 1.0
FE3 A:CFM496 3.6 19.3 1.0
ND1 A:HIS442 3.7 17.8 1.0
S3B A:CFM496 3.8 18.1 1.0
S1A A:CFM496 4.1 18.8 1.0
CE1 A:HIS442 4.2 14.6 1.0
N A:GLY356 4.2 14.8 1.0
S4A A:CFM496 4.2 17.9 1.0
CA A:GLY356 4.3 14.6 1.0
CG2 A:ILE355 4.3 12.6 1.0
S5 A:CFM496 4.3 15.1 1.0
S2B A:CFM496 4.4 18.4 1.0
O7 A:HCA494 4.4 17.0 1.0
O5 A:HCA494 4.5 16.8 1.0
CG A:HIS442 4.5 14.9 1.0
CG A:ARG359 4.5 22.8 1.0
N A:GLY357 4.7 17.7 1.0
NE A:ARG359 4.8 22.5 1.0
FE1 A:CFM496 4.9 18.8 1.0
CZ A:PHE381 4.9 15.2 1.0

Iron binding site 6 out of 30 in 3min

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Iron binding site 6 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe496

b:19.8
occ:1.00
 FE6 A:CFM496 0.0 19.8 1.0
S3B A:CFM496 2.2 18.1 1.0
S1B A:CFM496 2.2 16.8 1.0
S2B A:CFM496 2.2 18.4 1.0
FE7 A:CFM496 2.4 16.2 1.0
FE2 A:CFM496 2.5 17.7 1.0
FE5 A:CFM496 2.5 17.7 1.0
MO1 A:CFM496 2.6 19.1 1.0
FE3 A:CFM496 3.6 19.3 1.0
O7 A:HCA494 3.6 17.0 1.0
S4B A:CFM496 3.6 18.8 1.0
FE4 A:CFM496 3.6 17.3 1.0
CZ A:PHE381 4.1 15.2 1.0
S1A A:CFM496 4.1 18.8 1.0
S2A A:CFM496 4.2 18.2 1.0
O5 A:HCA494 4.3 16.8 1.0
S5 A:CFM496 4.3 15.1 1.0
S3A A:CFM496 4.3 17.1 1.0
ND1 A:HIS442 4.5 17.8 1.0
CE2 A:PHE381 4.6 13.2 1.0
CG1 A:VAL70 4.6 17.6 1.0
C3 A:HCA494 4.7 20.2 1.0
NH1 A:ARG96 4.8 20.4 1.0
FE1 A:CFM496 4.9 18.8 1.0
O1 A:HCA494 4.9 24.7 1.0
CE1 A:HIS442 4.9 14.6 1.0
C2 A:HCA494 4.9 21.8 1.0
C7 A:HCA494 5.0 19.7 1.0

Iron binding site 7 out of 30 in 3min

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Iron binding site 7 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe496

b:16.2
occ:1.00
 FE7 A:CFM496 0.0 16.2 1.0
S4B A:CFM496 2.1 18.8 1.0
S5 A:CFM496 2.2 15.1 1.0
S3B A:CFM496 2.2 18.1 1.0
FE6 A:CFM496 2.4 19.8 1.0
FE3 A:CFM496 2.6 19.3 1.0
FE5 A:CFM496 2.6 17.7 1.0
MO1 A:CFM496 2.6 19.1 1.0
O5 A:HCA494 3.5 16.8 1.0
FE2 A:CFM496 3.6 17.7 1.0
S1B A:CFM496 3.6 16.8 1.0
FE4 A:CFM496 3.7 17.3 1.0
NH1 A:ARG96 3.7 20.4 1.0
O A:HOH530 4.0 14.7 1.0
S2A A:CFM496 4.2 18.2 1.0
S4A A:CFM496 4.3 17.9 1.0
O7 A:HCA494 4.3 17.0 1.0
S2B A:CFM496 4.3 18.4 1.0
CD A:ARG96 4.4 23.5 1.0
S3A A:CFM496 4.4 17.1 1.0
ND1 A:HIS442 4.5 17.8 1.0
C7 A:HCA494 4.6 19.7 1.0
CZ A:ARG96 4.8 22.9 1.0
NH2 A:ARG359 4.8 22.0 1.0
CZ A:ARG359 4.8 25.4 1.0
FE1 A:CFM496 4.9 18.8 1.0

Iron binding site 8 out of 30 in 3min

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Iron binding site 8 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe525

b:23.5
occ:1.00
 FE1 B:CLF525 0.0 23.5 1.0
S2A B:CLF525 2.2 22.5 1.0
SG B:CYS95 2.2 21.6 1.0
S1 B:CLF525 2.3 23.6 1.0
S3A B:CLF525 2.3 23.1 1.0
FE2 B:CLF525 2.4 21.7 1.0
FE4 B:CLF525 2.6 20.1 1.0
FE3 B:CLF525 2.7 18.7 1.0
FE8 B:CLF525 3.1 22.1 1.0
N B:CYS95 3.4 21.1 1.0
CB B:CYS95 3.6 22.7 1.0
S4A B:CLF525 3.7 21.4 1.0
CA B:CYS95 3.7 21.2 1.0
FE5 B:CLF525 3.8 25.4 1.0
S4B B:CLF525 4.0 22.7 1.0
C B:GLY94 4.0 19.1 1.0
O B:HOH531 4.3 20.3 1.0
SG A:CYS88 4.4 20.5 1.0
CA B:GLY94 4.4 18.1 1.0
SG A:CYS154 4.5 21.5 1.0
SG A:CYS62 4.6 21.5 1.0
O B:SER92 4.7 22.1 1.0
CB B:SER92 4.7 26.4 1.0
O B:GLY94 4.8 17.1 1.0
N B:GLY94 4.8 19.1 1.0
FE6 B:CLF525 4.8 25.3 1.0

Iron binding site 9 out of 30 in 3min

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Iron binding site 9 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe525

b:21.7
occ:1.00
 FE2 B:CLF525 0.0 21.7 1.0
S4A B:CLF525 2.2 21.4 1.0
S2A B:CLF525 2.2 22.5 1.0
S1 B:CLF525 2.3 23.6 1.0
FE1 B:CLF525 2.4 23.5 1.0
SG A:CYS154 2.4 21.5 1.0
FE4 B:CLF525 2.5 20.1 1.0
FE3 B:CLF525 2.7 18.7 1.0
CB A:CYS154 3.6 25.8 1.0
O B:HOH531 3.7 20.3 1.0
S3A B:CLF525 3.8 23.1 1.0
CA A:GLY185 3.9 25.2 1.0
N A:CYS154 3.9 27.7 1.0
SG B:CYS95 4.0 21.6 1.0
N A:GLY185 4.0 22.7 1.0
CA A:CYS154 4.2 27.9 1.0
FE8 B:CLF525 4.5 22.1 1.0
SG A:CYS88 4.5 20.5 1.0
OG B:SER92 4.5 33.2 1.0
CB B:SER92 4.5 26.4 1.0
FE5 B:CLF525 4.6 25.4 1.0
C A:GLY185 4.7 26.2 1.0
SG A:CYS62 4.7 21.5 1.0
C A:GLU153 5.0 26.9 1.0

Iron binding site 10 out of 30 in 3min

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Iron binding site 10 out of 30 in the Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Nitrogenase Mofe Protein From Azotobacter Vinelandii, Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe525

b:18.7
occ:1.00
 FE3 B:CLF525 0.0 18.7 1.0
SG A:CYS62 2.2 21.5 1.0
S2A B:CLF525 2.2 22.5 1.0
S4A B:CLF525 2.3 21.4 1.0
S3A B:CLF525 2.3 23.1 1.0
FE4 B:CLF525 2.5 20.1 1.0
FE1 B:CLF525 2.7 23.5 1.0
FE2 B:CLF525 2.7 21.7 1.0
CB A:CYS62 3.4 23.5 1.0
CB A:TYR64 3.8 24.3 1.0
CA A:GLY185 3.8 25.2 1.0
S1 B:CLF525 4.0 23.6 1.0
N A:GLY185 4.4 22.7 1.0
CA B:GLY94 4.4 18.1 1.0
CG A:TYR64 4.4 26.2 1.0
CD2 A:TYR64 4.4 24.3 1.0
SG A:CYS88 4.6 20.5 1.0
C B:GLY94 4.6 19.1 1.0
N B:CYS95 4.7 21.1 1.0
CA A:CYS62 4.8 23.2 1.0
N A:TYR64 4.8 23.9 1.0
SG B:CYS95 4.8 21.6 1.0
CE2 B:TYR98 4.9 23.4 1.0
SG A:CYS154 4.9 21.5 1.0
O B:HOH532 4.9 15.9 1.0
CA A:TYR64 4.9 24.0 1.0
C A:GLY185 5.0 26.2 1.0

Reference:

J.W.Peters, M.H.Stowell, S.M.Soltis, M.G.Finnegan, M.K.Johnson, D.C.Rees. Redox-Dependent Structural Changes in the Nitrogenase P-Cluster. Biochemistry V. 36 1181 1997.
ISSN: ISSN 0006-2960
PubMed: 9063865
DOI: 10.1021/BI9626665
Page generated: Sun Aug 4 14:48:31 2024

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