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Iron in PDB 4wna: Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon

Enzymatic activity of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon

All present enzymatic activity of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon:
1.18.6.1;

Protein crystallography data

The structure of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon, PDB code: 4wna was solved by C.N.Morrison, J.A.Hoy, L.Zhang, O.Einsle, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.72 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.123, 129.780, 107.543, 90.00, 108.94, 90.00
R / Rfree (%) 16.7 / 21.9

Other elements in 4wna:

The structure of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Xenon (Xe) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon (pdb code 4wna). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon, PDB code: 4wna:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in 4wna

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Iron binding site 1 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:18.9
occ:1.00
FE1 A:ICS502 0.0 18.9 1.0
SG A:CYS275 2.2 23.7 1.0
S2A A:ICS502 2.2 18.1 1.0
S4A A:ICS502 2.3 19.9 1.0
S1A A:ICS502 2.3 19.8 1.0
FE4 A:ICS502 2.6 18.0 1.0
FE3 A:ICS502 2.7 17.6 1.0
FE2 A:ICS502 2.7 18.7 1.0
CB A:CYS275 3.2 19.5 1.0
CX A:ICS502 3.5 16.2 1.0
OG A:SER278 4.0 15.4 1.0
CB A:LEU358 4.1 23.6 1.0
CB A:SER278 4.4 17.9 1.0
CE2 A:TYR229 4.4 17.2 1.0
CA A:CYS275 4.5 20.6 1.0
CD2 A:LEU358 4.7 20.6 1.0
S3A A:ICS502 4.8 19.6 1.0
S2B A:ICS502 4.8 20.0 1.0
S5A A:ICS502 4.8 15.9 1.0
CD2 A:TYR229 4.9 17.2 1.0
N A:SER278 4.9 20.1 1.0

Iron binding site 2 out of 36 in 4wna

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Iron binding site 2 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:18.7
occ:1.00
FE2 A:ICS502 0.0 18.7 1.0
CX A:ICS502 2.0 16.2 1.0
S2B A:ICS502 2.2 20.0 1.0
S1A A:ICS502 2.3 19.8 1.0
S2A A:ICS502 2.3 18.1 1.0
FE6 A:ICS502 2.6 17.2 1.0
FE4 A:ICS502 2.6 18.0 1.0
FE3 A:ICS502 2.7 17.6 1.0
FE1 A:ICS502 2.7 18.9 1.0
FE5 A:ICS502 3.7 18.0 1.0
FE7 A:ICS502 3.7 17.1 1.0
S4A A:ICS502 3.9 19.9 1.0
CZ A:PHE381 4.0 20.8 1.0
NE2 A:HIS195 4.1 22.8 1.0
CE1 A:HIS195 4.2 24.1 1.0
S1B A:ICS502 4.2 21.7 1.0
S3B A:ICS502 4.2 18.8 1.0
S3A A:ICS502 4.5 19.6 1.0
CG1 A:VAL70 4.5 21.0 1.0
S5A A:ICS502 4.5 15.9 1.0
CE1 A:PHE381 4.5 21.4 1.0
SG A:CYS275 4.6 23.7 1.0

Iron binding site 3 out of 36 in 4wna

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Iron binding site 3 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:17.6
occ:1.00
FE3 A:ICS502 0.0 17.6 1.0
CX A:ICS502 2.0 16.2 1.0
S5A A:ICS502 2.2 15.9 1.0
S4A A:ICS502 2.2 19.9 1.0
S2A A:ICS502 2.3 18.1 1.0
FE7 A:ICS502 2.6 17.1 1.0
FE4 A:ICS502 2.6 18.0 1.0
FE2 A:ICS502 2.7 18.7 1.0
FE1 A:ICS502 2.7 18.9 1.0
FE5 A:ICS502 3.7 18.0 1.0
FE6 A:ICS502 3.7 17.2 1.0
S1A A:ICS502 3.8 19.8 1.0
NH2 A:ARG96 4.0 21.8 1.0
CD2 A:TYR229 4.1 17.2 1.0
O A:HOH690 4.1 15.7 1.0
S3B A:ICS502 4.3 18.8 1.0
S4B A:ICS502 4.3 18.4 1.0
CE2 A:TYR229 4.4 17.2 1.0
S2B A:ICS502 4.5 20.0 1.0
S3A A:ICS502 4.5 19.6 1.0
SG A:CYS275 4.8 23.7 1.0
CG A:TYR229 5.0 17.5 1.0

Iron binding site 4 out of 36 in 4wna

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Iron binding site 4 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:18.0
occ:1.00
FE4 A:ICS502 0.0 18.0 1.0
CX A:ICS502 2.0 16.2 1.0
S3A A:ICS502 2.2 19.6 1.0
S1A A:ICS502 2.3 19.8 1.0
S4A A:ICS502 2.3 19.9 1.0
FE5 A:ICS502 2.6 18.0 1.0
FE2 A:ICS502 2.6 18.7 1.0
FE3 A:ICS502 2.6 17.6 1.0
FE1 A:ICS502 2.6 18.9 1.0
FE7 A:ICS502 3.7 17.1 1.0
FE6 A:ICS502 3.7 17.2 1.0
S2A A:ICS502 3.8 18.1 1.0
CB A:LEU358 4.0 23.6 1.0
N A:LEU358 4.0 23.8 1.0
N A:GLY357 4.1 18.0 1.0
S1B A:ICS502 4.3 21.7 1.0
S4B A:ICS502 4.3 18.4 1.0
S5A A:ICS502 4.5 15.9 1.0
S2B A:ICS502 4.5 20.0 1.0
SG A:CYS275 4.5 23.7 1.0
CA A:LEU358 4.6 19.3 1.0
C A:GLY357 4.6 24.1 1.0
CG A:ARG359 4.7 16.1 1.0
N A:ARG359 4.7 17.4 1.0
CA A:GLY357 4.7 21.9 1.0
CD A:ARG359 4.8 16.3 1.0
CA A:GLY356 4.9 16.5 1.0
CZ A:PHE381 5.0 20.8 1.0
NE A:ARG359 5.0 16.5 1.0

Iron binding site 5 out of 36 in 4wna

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Iron binding site 5 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:18.0
occ:1.00
FE5 A:ICS502 0.0 18.0 1.0
CX A:ICS502 2.0 16.2 1.0
S1B A:ICS502 2.2 21.7 1.0
S4B A:ICS502 2.2 18.4 1.0
S3A A:ICS502 2.3 19.6 1.0
FE7 A:ICS502 2.6 17.1 1.0
FE4 A:ICS502 2.6 18.0 1.0
FE6 A:ICS502 2.6 17.2 1.0
MO1 A:ICS502 2.7 17.1 1.0
FE2 A:ICS502 3.7 18.7 1.0
FE3 A:ICS502 3.7 17.6 1.0
ND1 A:HIS442 3.8 15.9 1.0
S3B A:ICS502 3.9 18.8 1.0
N A:GLY356 4.2 18.5 1.0
CA A:GLY356 4.2 16.5 1.0
CE1 A:HIS442 4.2 17.0 1.0
CG2 A:ILE355 4.2 14.4 1.0
S1A A:ICS502 4.3 19.8 1.0
S4A A:ICS502 4.4 19.9 1.0
S2B A:ICS502 4.4 20.0 1.0
S5A A:ICS502 4.4 15.9 1.0
O7 A:HCA501 4.5 18.4 1.0
CD A:ARG359 4.6 16.3 1.0
O5 A:HCA501 4.7 20.1 1.0
CG A:HIS442 4.7 15.3 1.0
N A:GLY357 4.8 18.0 1.0
CZ A:PHE381 5.0 20.8 1.0

Iron binding site 6 out of 36 in 4wna

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Iron binding site 6 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:17.2
occ:1.00
FE6 A:ICS502 0.0 17.2 1.0
CX A:ICS502 2.0 16.2 1.0
S2B A:ICS502 2.2 20.0 1.0
S1B A:ICS502 2.2 21.7 1.0
S3B A:ICS502 2.3 18.8 1.0
FE2 A:ICS502 2.6 18.7 1.0
FE7 A:ICS502 2.6 17.1 1.0
FE5 A:ICS502 2.6 18.0 1.0
MO1 A:ICS502 2.6 17.1 1.0
O7 A:HCA501 3.6 18.4 1.0
FE3 A:ICS502 3.7 17.6 1.0
FE4 A:ICS502 3.7 18.0 1.0
S4B A:ICS502 3.8 18.4 1.0
CZ A:PHE381 4.1 20.8 1.0
S1A A:ICS502 4.3 19.8 1.0
S2A A:ICS502 4.3 18.1 1.0
CG2 A:VAL70 4.4 19.6 1.0
O5 A:HCA501 4.4 20.1 1.0
S5A A:ICS502 4.5 15.9 1.0
O1 A:HCA501 4.5 26.6 1.0
S3A A:ICS502 4.5 19.6 1.0
CE2 A:PHE381 4.5 22.9 1.0
ND1 A:HIS442 4.7 15.9 1.0
C3 A:HCA501 4.7 20.8 1.0
C7 A:HCA501 4.9 19.1 1.0
C2 A:HCA501 4.9 23.7 1.0

Iron binding site 7 out of 36 in 4wna

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Iron binding site 7 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:17.1
occ:1.00
FE7 A:ICS502 0.0 17.1 1.0
CX A:ICS502 2.0 16.2 1.0
S5A A:ICS502 2.2 15.9 1.0
S3B A:ICS502 2.2 18.8 1.0
S4B A:ICS502 2.3 18.4 1.0
FE5 A:ICS502 2.6 18.0 1.0
FE6 A:ICS502 2.6 17.2 1.0
FE3 A:ICS502 2.6 17.6 1.0
MO1 A:ICS502 2.6 17.1 1.0
O5 A:HCA501 3.7 20.1 1.0
FE2 A:ICS502 3.7 18.7 1.0
FE4 A:ICS502 3.7 18.0 1.0
S1B A:ICS502 3.8 21.7 1.0
O A:HOH675 3.9 19.0 1.0
NE A:ARG96 4.0 22.9 1.0
NH2 A:ARG96 4.2 21.8 1.0
S4A A:ICS502 4.3 19.9 1.0
S2A A:ICS502 4.3 18.1 1.0
S2B A:ICS502 4.4 20.0 1.0
S3A A:ICS502 4.5 19.6 1.0
O7 A:HCA501 4.5 18.4 1.0
C7 A:HCA501 4.6 19.1 1.0
CZ A:ARG96 4.6 23.3 1.0
ND1 A:HIS442 4.7 15.9 1.0
CZ A:ARG359 4.9 19.5 1.0
NH1 A:ARG359 4.9 15.5 1.0
CD A:ARG96 5.0 20.8 1.0

Iron binding site 8 out of 36 in 4wna

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Iron binding site 8 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:21.1
occ:1.00
FE1 A:CLF503 0.0 21.1 1.0
S2A A:CLF503 2.3 17.8 1.0
S3A A:CLF503 2.3 18.1 1.0
SG B:CYS95 2.4 17.3 1.0
S1 A:CLF503 2.5 21.0 1.0
FE2 A:CLF503 2.5 20.5 1.0
FE4 A:CLF503 2.5 18.1 1.0
FE3 A:CLF503 2.7 19.2 1.0
FE8 A:CLF503 3.0 20.2 1.0
N B:CYS95 3.2 18.1 1.0
CA B:CYS95 3.5 18.7 1.0
CB B:CYS95 3.5 19.6 1.0
S4A A:CLF503 3.7 18.9 1.0
C B:GLY94 3.9 19.4 1.0
S4B A:CLF503 4.0 20.3 1.0
CA B:GLY94 4.3 20.1 1.0
OG B:SER92 4.3 34.9 1.0
O B:HOH842 4.4 20.1 1.0
FE5 A:CLF503 4.5 20.2 0.4
SG A:CYS88 4.5 18.0 1.0
SG A:CYS154 4.6 16.4 1.0
SG A:CYS62 4.7 18.5 1.0
O B:GLY94 4.7 17.4 1.0
N B:GLY94 4.7 17.9 1.0
O B:SER92 4.9 19.8 1.0
FE5 A:CLF503 4.9 29.8 0.6
CB B:SER92 5.0 23.0 1.0

Iron binding site 9 out of 36 in 4wna

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Iron binding site 9 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:20.5
occ:1.00
FE2 A:CLF503 0.0 20.5 1.0
S2A A:CLF503 2.3 17.8 1.0
S4A A:CLF503 2.3 18.9 1.0
SG A:CYS154 2.3 16.4 1.0
S1 A:CLF503 2.4 21.0 1.0
FE1 A:CLF503 2.5 21.1 1.0
FE4 A:CLF503 2.6 18.1 1.0
FE3 A:CLF503 2.8 19.2 1.0
CB A:CYS154 3.4 18.9 1.0
O B:HOH842 3.7 20.1 1.0
N A:CYS154 3.8 20.3 1.0
S3A A:CLF503 3.8 18.1 1.0
OG B:SER92 3.9 34.9 1.0
CA A:GLY185 4.0 21.0 1.0
N A:GLY185 4.1 19.4 1.0
CA A:CYS154 4.1 20.5 1.0
SG B:CYS95 4.2 17.3 1.0
FE8 A:CLF503 4.4 20.2 1.0
SG A:CYS88 4.6 18.0 1.0
C A:GLY185 4.7 21.8 1.0
CB B:SER92 4.7 23.0 1.0
SG A:CYS62 4.8 18.5 1.0
N A:PHE186 4.9 24.2 1.0
C A:GLU153 5.0 20.9 1.0

Iron binding site 10 out of 36 in 4wna

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Iron binding site 10 out of 36 in the Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of the Nitrogenase Mofe Protein From Azotobacter Vinelandii Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:19.2
occ:1.00
FE3 A:CLF503 0.0 19.2 1.0
S3A A:CLF503 2.2 18.1 1.0
SG A:CYS62 2.2 18.5 1.0
S4A A:CLF503 2.3 18.9 1.0
S2A A:CLF503 2.3 17.8 1.0
FE4 A:CLF503 2.7 18.1 1.0
FE1 A:CLF503 2.7 21.1 1.0
FE2 A:CLF503 2.8 20.5 1.0
CB A:CYS62 3.3 21.1 1.0
CA A:GLY185 4.0 21.0 1.0
CB A:TYR64 4.1 18.3 1.0
CA B:GLY94 4.1 20.1 1.0
S1 A:CLF503 4.2 21.0 1.0
C B:GLY94 4.4 19.4 1.0
N A:GLY185 4.5 19.4 1.0
N B:CYS95 4.6 18.1 1.0
CD1 A:TYR64 4.6 14.4 1.0
CG A:TYR64 4.7 14.8 1.0
CA A:CYS62 4.7 19.2 1.0
SG A:CYS88 4.7 18.0 1.0
CE2 B:TYR98 4.8 18.2 1.0
N A:TYR64 4.8 16.8 1.0
SG A:CYS154 4.9 16.4 1.0
O B:HOH814 4.9 21.3 1.0
N B:GLY94 4.9 17.9 1.0

Reference:

C.N.Morrison, J.A.Hoy, L.Zhang, O.Einsle, D.C.Rees. Substrate Pathways in the Nitrogenase Mofe Protein By Experimental Identification of Small Molecule Binding Sites. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25710326
DOI: 10.1021/BI501313K
Page generated: Sun Dec 13 15:51:06 2020

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