Atomistry » Iron » PDB 4mv0-4nfg » 4nd8
Atomistry »
  Iron »
    PDB 4mv0-4nfg »
      4nd8 »

Iron in PDB 4nd8: Av Nitrogenase Mofe Protein High pH Form

Enzymatic activity of Av Nitrogenase Mofe Protein High pH Form

All present enzymatic activity of Av Nitrogenase Mofe Protein High pH Form:
1.18.6.1;

Protein crystallography data

The structure of Av Nitrogenase Mofe Protein High pH Form, PDB code: 4nd8 was solved by K.-Y.Yang, C.A.Haynes, T.Spatzal, D.C.Rees, J.B.Howard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.74 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.527, 127.915, 107.082, 90.00, 108.90, 90.00
R / Rfree (%) 15.6 / 20.4

Other elements in 4nd8:

The structure of Av Nitrogenase Mofe Protein High pH Form also contains other interesting chemical elements:

Molybdenum (Mo) 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 Av Nitrogenase Mofe Protein High pH Form (pdb code 4nd8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Av Nitrogenase Mofe Protein High pH Form, PDB code: 4nd8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 1 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:24.6
occ:1.00
FE1 A:ICS502 0.0 24.6 1.0
S4A A:ICS502 2.3 18.5 1.0
S2A A:ICS502 2.3 23.8 1.0
S1A A:ICS502 2.3 23.6 1.0
SG A:CYS275 2.4 26.0 1.0
FE4 A:ICS502 2.6 20.5 1.0
FE2 A:ICS502 2.7 22.8 1.0
FE3 A:ICS502 2.7 23.6 1.0
CB A:CYS275 3.4 23.3 1.0
CX A:ICS502 3.4 18.6 1.0
OG A:SER278 4.0 22.6 1.0
CB A:LEU358 4.0 23.3 1.0
CB A:SER278 4.3 23.0 1.0
CA A:CYS275 4.6 27.9 1.0
CE2 A:TYR229 4.6 22.2 1.0
CD2 A:LEU358 4.7 20.8 1.0
S3A A:ICS502 4.8 23.3 1.0
N A:LEU358 4.8 22.8 1.0
S2B A:ICS502 4.8 22.3 1.0
S5A A:ICS502 4.8 22.8 1.0
N A:SER278 4.9 22.6 1.0
FE6 A:ICS502 5.0 24.9 1.0
FE5 A:ICS502 5.0 21.0 1.0
CG A:LEU358 5.0 24.3 1.0

Iron binding site 2 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 2 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:22.8
occ:1.00
FE2 A:ICS502 0.0 22.8 1.0
CX A:ICS502 2.0 18.6 1.0
S2A A:ICS502 2.2 23.8 1.0
S2B A:ICS502 2.2 22.3 1.0
S1A A:ICS502 2.3 23.6 1.0
FE6 A:ICS502 2.5 24.9 1.0
FE1 A:ICS502 2.7 24.6 1.0
FE4 A:ICS502 2.7 20.5 1.0
FE3 A:ICS502 2.7 23.6 1.0
FE5 A:ICS502 3.7 21.0 1.0
FE7 A:ICS502 3.7 21.4 1.0
S4A A:ICS502 3.9 18.5 1.0
CZ A:PHE381 4.1 26.4 1.0
S3B A:ICS502 4.2 23.5 1.0
S1B A:ICS502 4.2 19.1 1.0
NE2 A:HIS195 4.2 26.2 1.0
CE1 A:HIS195 4.3 22.9 1.0
S3A A:ICS502 4.5 23.3 1.0
S5A A:ICS502 4.5 22.8 1.0
CG1 A:VAL70 4.6 26.5 1.0
CE1 A:PHE381 4.6 25.7 1.0
SG A:CYS275 4.7 26.0 1.0
CG2 A:VAL70 4.8 24.9 1.0
CB A:SER278 4.9 23.0 1.0
N A:GLY357 5.0 22.9 1.0

Iron binding site 3 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 3 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:23.6
occ:1.00
FE3 A:ICS502 0.0 23.6 1.0
CX A:ICS502 2.0 18.6 1.0
S5A A:ICS502 2.2 22.8 1.0
S2A A:ICS502 2.3 23.8 1.0
S4A A:ICS502 2.3 18.5 1.0
FE7 A:ICS502 2.6 21.4 1.0
FE4 A:ICS502 2.7 20.5 1.0
FE2 A:ICS502 2.7 22.8 1.0
FE1 A:ICS502 2.7 24.6 1.0
FE6 A:ICS502 3.7 24.9 1.0
FE5 A:ICS502 3.7 21.0 1.0
S1A A:ICS502 3.9 23.6 1.0
O A:HOH648 4.0 16.6 1.0
NH2 A:ARG96 4.1 21.6 1.0
S3B A:ICS502 4.2 23.5 1.0
CD2 A:TYR229 4.2 21.6 1.0
S4B A:ICS502 4.2 22.8 1.0
S2B A:ICS502 4.5 22.3 1.0
CE2 A:TYR229 4.5 22.2 1.0
S3A A:ICS502 4.5 23.3 1.0
SG A:CYS275 4.9 26.0 1.0

Iron binding site 4 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 4 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:20.5
occ:1.00
FE4 A:ICS502 0.0 20.5 1.0
CX A:ICS502 2.0 18.6 1.0
S3A A:ICS502 2.2 23.3 1.0
S1A A:ICS502 2.3 23.6 1.0
S4A A:ICS502 2.3 18.5 1.0
FE5 A:ICS502 2.6 21.0 1.0
FE1 A:ICS502 2.6 24.6 1.0
FE3 A:ICS502 2.7 23.6 1.0
FE2 A:ICS502 2.7 22.8 1.0
FE7 A:ICS502 3.7 21.4 1.0
FE6 A:ICS502 3.7 24.9 1.0
S2A A:ICS502 3.8 23.8 1.0
N A:LEU358 3.8 22.8 1.0
CB A:LEU358 4.0 23.3 1.0
N A:GLY357 4.0 22.9 1.0
S4B A:ICS502 4.2 22.8 1.0
S1B A:ICS502 4.3 19.1 1.0
CA A:LEU358 4.5 25.1 1.0
S5A A:ICS502 4.5 22.8 1.0
N A:ARG359 4.5 22.8 1.0
C A:GLY357 4.5 27.6 1.0
S2B A:ICS502 4.6 22.3 1.0
CA A:GLY357 4.6 25.4 1.0
CG A:ARG359 4.7 19.6 1.0
SG A:CYS275 4.7 26.0 1.0
CA A:GLY356 4.9 20.5 1.0
C A:GLY356 4.9 23.0 1.0
CD A:ARG359 5.0 21.3 1.0

Iron binding site 5 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 5 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:21.0
occ:1.00
FE5 A:ICS502 0.0 21.0 1.0
CX A:ICS502 2.0 18.6 1.0
S4B A:ICS502 2.2 22.8 1.0
S1B A:ICS502 2.3 19.1 1.0
S3A A:ICS502 2.3 23.3 1.0
FE4 A:ICS502 2.6 20.5 1.0
FE6 A:ICS502 2.6 24.9 1.0
FE7 A:ICS502 2.6 21.4 1.0
MO1 A:ICS502 2.7 25.0 1.0
FE2 A:ICS502 3.7 22.8 1.0
FE3 A:ICS502 3.7 23.6 1.0
ND1 A:HIS442 3.8 21.1 1.0
S3B A:ICS502 3.9 23.5 1.0
CG2 A:ILE355 4.1 22.9 1.0
CA A:GLY356 4.1 20.5 1.0
N A:GLY356 4.1 23.6 1.0
S1A A:ICS502 4.2 23.6 1.0
CE1 A:HIS442 4.3 29.6 1.0
S4A A:ICS502 4.4 18.5 1.0
S2B A:ICS502 4.5 22.3 1.0
S5A A:ICS502 4.5 22.8 1.0
N A:GLY357 4.6 22.9 1.0
O7 A:HCA501 4.7 23.9 1.0
CD A:ARG359 4.8 21.3 1.0
CG A:HIS442 4.8 23.7 1.0
O5 A:HCA501 4.9 19.2 1.0
C A:GLY356 4.9 23.0 1.0
FE1 A:ICS502 5.0 24.6 1.0

Iron binding site 6 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 6 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:24.9
occ:1.00
FE6 A:ICS502 0.0 24.9 1.0
CX A:ICS502 2.1 18.6 1.0
S2B A:ICS502 2.2 22.3 1.0
S3B A:ICS502 2.2 23.5 1.0
S1B A:ICS502 2.2 19.1 1.0
FE2 A:ICS502 2.5 22.8 1.0
FE5 A:ICS502 2.6 21.0 1.0
FE7 A:ICS502 2.6 21.4 1.0
MO1 A:ICS502 2.7 25.0 1.0
FE3 A:ICS502 3.7 23.6 1.0
FE4 A:ICS502 3.7 20.5 1.0
O7 A:HCA501 3.8 23.9 1.0
S4B A:ICS502 3.8 22.8 1.0
S2A A:ICS502 4.2 23.8 1.0
S1A A:ICS502 4.2 23.6 1.0
CZ A:PHE381 4.2 26.4 1.0
CG2 A:VAL70 4.3 24.9 1.0
S5A A:ICS502 4.5 22.8 1.0
S3A A:ICS502 4.5 23.3 1.0
CE2 A:PHE381 4.6 23.6 1.0
O5 A:HCA501 4.7 19.2 1.0
ND1 A:HIS442 4.9 21.1 1.0
O A:HOH807 4.9 28.0 1.0
C3 A:HCA501 4.9 25.9 1.0
FE1 A:ICS502 5.0 24.6 1.0

Iron binding site 7 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 7 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:21.4
occ:1.00
FE7 A:ICS502 0.0 21.4 1.0
CX A:ICS502 2.0 18.6 1.0
S4B A:ICS502 2.2 22.8 1.0
S5A A:ICS502 2.2 22.8 1.0
S3B A:ICS502 2.2 23.5 1.0
FE3 A:ICS502 2.6 23.6 1.0
FE6 A:ICS502 2.6 24.9 1.0
FE5 A:ICS502 2.6 21.0 1.0
MO1 A:ICS502 2.7 25.0 1.0
O A:HOH693 3.2 23.1 1.0
FE2 A:ICS502 3.7 22.8 1.0
FE4 A:ICS502 3.7 20.5 1.0
O5 A:HCA501 3.8 19.2 1.0
S1B A:ICS502 3.8 19.1 1.0
NE A:ARG96 4.3 21.9 1.0
S2A A:ICS502 4.3 23.8 1.0
NH2 A:ARG96 4.3 21.6 1.0
S4A A:ICS502 4.4 18.5 1.0
S2B A:ICS502 4.5 22.3 1.0
S3A A:ICS502 4.5 23.3 1.0
O7 A:HCA501 4.6 23.9 1.0
ND1 A:HIS442 4.8 21.1 1.0
C7 A:HCA501 4.8 27.9 1.0
CZ A:ARG96 4.8 22.6 1.0
CZ A:ARG359 4.8 21.3 1.0
NH1 A:ARG359 4.8 22.6 1.0

Iron binding site 8 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 8 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:19.8
occ:0.96
FE1 A:1CL503 0.0 19.8 1.0
S3A A:1CL503 2.1 19.5 0.9
S2A A:1CL503 2.2 21.2 0.9
S1 A:1CL503 2.2 29.0 1.0
FE2 A:1CL503 2.5 18.3 0.9
FE4 A:1CL503 2.5 18.4 0.9
SG A:CYS154 2.5 24.5 1.0
FE3 A:1CL503 2.6 21.8 1.0
CB A:CYS154 3.5 19.4 1.0
S4A A:1CL503 3.6 20.9 0.9
O B:HOH916 3.7 22.8 1.0
N A:CYS154 3.9 25.7 1.0
CA A:GLY185 4.1 23.8 1.0
OG B:SER92 4.1 27.6 1.0
N A:GLY185 4.1 23.6 1.0
CA A:CYS154 4.2 23.1 1.0
SG B:CYS95 4.2 21.1 1.0
FE8 A:1CL503 4.3 22.8 1.0
SG A:CYS88 4.7 23.8 1.0
C A:GLY185 4.8 27.0 1.0
SG A:CYS62 4.9 25.7 1.0
C A:GLU153 5.0 24.0 1.0

Iron binding site 9 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 9 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:18.3
occ:0.88
FE2 A:1CL503 0.0 18.3 0.9
S2A A:1CL503 2.2 21.2 0.9
S4A A:1CL503 2.2 20.9 0.9
S1 A:1CL503 2.2 29.0 1.0
SG B:CYS95 2.4 21.1 1.0
FE1 A:1CL503 2.5 19.8 1.0
FE4 A:1CL503 2.5 18.4 0.9
FE3 A:1CL503 2.5 21.8 1.0
FE8 A:1CL503 3.0 22.8 1.0
N B:CYS95 3.2 20.6 1.0
CA B:CYS95 3.5 23.0 1.0
CB B:CYS95 3.5 25.0 1.0
S3A A:1CL503 3.6 19.5 0.9
C B:GLY94 3.9 21.9 1.0
S4B A:1CL503 4.0 22.7 1.0
O B:HOH916 4.3 22.8 1.0
CA B:GLY94 4.4 21.6 1.0
OG B:SER92 4.4 27.6 1.0
SG A:CYS88 4.6 23.8 1.0
O B:GLY94 4.7 23.2 1.0
SG A:CYS154 4.7 24.5 1.0
SG A:CYS62 4.7 25.7 1.0
N B:GLY94 4.8 20.9 1.0
FE5 A:1CL503 4.8 24.1 1.0
O B:SER92 4.9 22.4 1.0
S3B A:1CL503 5.0 20.8 1.0

Iron binding site 10 out of 32 in 4nd8

Go back to Iron Binding Sites List in 4nd8
Iron binding site 10 out of 32 in the Av Nitrogenase Mofe Protein High pH Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Av Nitrogenase Mofe Protein High pH Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:21.8
occ:0.96
FE3 A:1CL503 0.0 21.8 1.0
S4A A:1CL503 2.1 20.9 0.9
S2A A:1CL503 2.1 21.2 0.9
S3A A:1CL503 2.1 19.5 0.9
SG A:CYS62 2.5 25.7 1.0
FE4 A:1CL503 2.5 18.4 0.9
FE2 A:1CL503 2.5 18.3 0.9
FE1 A:1CL503 2.6 19.8 1.0
CB A:CYS62 3.6 23.6 1.0
S1 A:1CL503 3.8 29.0 1.0
CA A:GLY185 4.0 23.8 1.0
CB A:TYR64 4.1 21.2 1.0
CA B:GLY94 4.3 21.6 1.0
N A:GLY185 4.4 23.6 1.0
C B:GLY94 4.4 21.9 1.0
N B:CYS95 4.5 20.6 1.0
CG A:TYR64 4.7 22.0 1.0
CD1 A:TYR64 4.8 18.8 1.0
SG A:CYS154 4.8 24.5 1.0
SG A:CYS88 4.8 23.8 1.0
SG B:CYS95 4.9 21.1 1.0
CA A:CYS62 5.0 23.1 1.0

Reference:

K.Y.Yang, C.A.Haynes, T.Spatzal, D.C.Rees, J.B.Howard. Turnover-Dependent Inactivation of the Nitrogenase Mofe-Protein at High pH. Biochemistry V. 53 333 2014.
ISSN: ISSN 0006-2960
PubMed: 24392967
DOI: 10.1021/BI4014769
Page generated: Sun Dec 13 15:42:43 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy