Atomistry » Iron » PDB 3m38-3mma » 3ml1
Atomistry »
  Iron »
    PDB 3m38-3mma »
      3ml1 »

Iron in PDB 3ml1: Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator

Enzymatic activity of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator

All present enzymatic activity of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator:
1.7.99.4; 1.9.6.1;

Protein crystallography data

The structure of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator, PDB code: 3ml1 was solved by C.Coelho, J.Trincao, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.48 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.202, 82.384, 96.837, 90.00, 100.72, 90.00
R / Rfree (%) 15.7 / 19

Other elements in 3ml1:

The structure of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator (pdb code 3ml1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator, PDB code: 3ml1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3ml1

Go back to Iron Binding Sites List in 3ml1
Iron binding site 1 out of 6 in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:9.3
occ:1.00
FE1 A:SF41801 0.0 9.3 1.0
S2 A:SF41801 2.2 8.8 1.0
S4 A:SF41801 2.3 8.6 1.0
S3 A:SF41801 2.3 8.7 1.0
SG A:CYS22 2.3 7.5 1.0
FE3 A:SF41801 2.7 9.0 1.0
FE4 A:SF41801 2.7 9.5 1.0
FE2 A:SF41801 2.7 10.0 1.0
CB A:CYS22 3.5 6.9 1.0
N A:CYS22 3.6 7.9 1.0
S1 A:SF41801 3.8 9.0 1.0
CA A:CYS22 3.9 6.3 1.0
O A:HOH803 3.9 7.3 1.0
CB A:THR24 4.0 7.3 1.0
O A:CYS22 4.1 6.9 1.0
OG1 A:THR24 4.2 7.3 1.0
C A:CYS22 4.3 7.7 1.0
CD A:PRO194 4.6 5.8 1.0
SG A:CYS54 4.7 7.6 1.0
SG A:CYS26 4.7 9.0 1.0
SG A:CYS19 4.7 8.7 1.0
C A:PHE21 4.8 8.6 1.0
N A:THR24 4.8 6.5 1.0
CG2 A:THR24 4.9 9.7 1.0
CB A:PHE21 5.0 8.9 1.0
CA A:THR24 5.0 6.6 1.0
N A:GLY25 5.0 8.3 1.0

Iron binding site 2 out of 6 in 3ml1

Go back to Iron Binding Sites List in 3ml1
Iron binding site 2 out of 6 in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:10.0
occ:1.00
FE2 A:SF41801 0.0 10.0 1.0
S1 A:SF41801 2.2 9.0 1.0
S4 A:SF41801 2.3 8.6 1.0
S3 A:SF41801 2.3 8.7 1.0
SG A:CYS54 2.4 7.6 1.0
FE4 A:SF41801 2.7 9.5 1.0
FE3 A:SF41801 2.7 9.0 1.0
FE1 A:SF41801 2.7 9.3 1.0
CB A:CYS54 3.5 8.1 1.0
N A:CYS54 3.7 8.7 1.0
S2 A:SF41801 3.8 8.8 1.0
CA A:CYS54 4.1 8.8 1.0
N A:GLY57 4.4 7.4 1.0
O A:HOH803 4.5 7.3 1.0
NZ A:LYS56 4.5 7.6 1.0
CG A:PRO194 4.6 7.0 1.0
CD A:PRO194 4.6 5.8 1.0
C A:CYS54 4.6 8.3 1.0
SG A:CYS22 4.7 7.5 1.0
O A:CYS54 4.7 8.3 1.0
C A:ASN53 4.8 8.1 1.0
SG A:CYS26 4.8 9.0 1.0
CA A:GLY57 4.8 7.8 1.0
SG A:CYS19 4.9 8.7 1.0
CB A:PRO194 4.9 6.9 1.0
CE A:LYS56 4.9 9.4 1.0

Iron binding site 3 out of 6 in 3ml1

Go back to Iron Binding Sites List in 3ml1
Iron binding site 3 out of 6 in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:9.0
occ:1.00
FE3 A:SF41801 0.0 9.0 1.0
S4 A:SF41801 2.2 8.6 1.0
S2 A:SF41801 2.2 8.8 1.0
S1 A:SF41801 2.3 9.0 1.0
SG A:CYS26 2.3 9.0 1.0
FE4 A:SF41801 2.6 9.5 1.0
FE1 A:SF41801 2.7 9.3 1.0
FE2 A:SF41801 2.7 10.0 1.0
CB A:CYS26 3.3 7.9 1.0
S3 A:SF41801 3.8 8.7 1.0
N A:CYS26 4.1 8.5 1.0
CA A:CYS26 4.3 7.8 1.0
CG1 A:ILE195 4.3 14.2 1.0
CB A:THR24 4.4 7.3 1.0
CG2 A:THR24 4.4 9.7 1.0
CB A:ILE195 4.5 7.1 1.0
SG A:CYS19 4.7 8.7 1.0
CB A:CYS19 4.7 8.5 1.0
SG A:CYS22 4.7 7.5 1.0
N A:CYS54 4.7 8.7 1.0
ND2 A:ASN53 4.7 14.2 1.0
SG A:CYS54 4.9 7.6 1.0
CA A:ASN53 5.0 7.9 1.0

Iron binding site 4 out of 6 in 3ml1

Go back to Iron Binding Sites List in 3ml1
Iron binding site 4 out of 6 in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:9.5
occ:1.00
FE4 A:SF41801 0.0 9.5 1.0
S3 A:SF41801 2.2 8.7 1.0
S2 A:SF41801 2.3 8.8 1.0
S1 A:SF41801 2.3 9.0 1.0
SG A:CYS19 2.4 8.7 1.0
FE3 A:SF41801 2.6 9.0 1.0
FE2 A:SF41801 2.7 10.0 1.0
FE1 A:SF41801 2.7 9.3 1.0
CB A:CYS19 3.2 8.5 1.0
S4 A:SF41801 3.8 8.6 1.0
CB A:PHE21 4.2 8.9 1.0
N A:CYS22 4.3 7.9 1.0
CA A:GLY57 4.4 7.8 1.0
N A:GLY57 4.5 7.4 1.0
SG A:CYS26 4.6 9.0 1.0
CB A:CYS26 4.7 7.9 1.0
SG A:CYS54 4.7 7.6 1.0
CA A:CYS19 4.7 8.6 1.0
N A:PHE21 4.8 7.1 1.0
CA A:PHE21 4.8 7.5 1.0
C A:PHE21 4.8 8.6 1.0
SG A:CYS22 4.8 7.5 1.0
CD1 A:PHE21 4.9 8.0 1.0

Iron binding site 5 out of 6 in 3ml1

Go back to Iron Binding Sites List in 3ml1
Iron binding site 5 out of 6 in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1128

b:12.0
occ:1.00
FE B:HEC1128 0.0 12.0 1.0
NA B:HEC1128 2.0 11.8 1.0
NB B:HEC1128 2.0 9.3 1.0
NC B:HEC1128 2.0 9.9 1.0
ND B:HEC1128 2.1 11.4 1.0
NE2 B:HIS62 2.1 11.2 1.0
NE2 B:HIS44 2.1 12.1 1.0
C4A B:HEC1128 3.0 13.3 1.0
CE1 B:HIS62 3.0 11.5 1.0
C1D B:HEC1128 3.0 15.8 1.0
C1A B:HEC1128 3.0 13.3 1.0
C1B B:HEC1128 3.0 12.4 1.0
CE1 B:HIS44 3.1 12.0 1.0
C4B B:HEC1128 3.1 9.9 1.0
C4D B:HEC1128 3.1 12.7 1.0
C4C B:HEC1128 3.1 16.3 1.0
C1C B:HEC1128 3.1 11.1 1.0
CD2 B:HIS44 3.1 13.1 1.0
CD2 B:HIS62 3.1 10.8 1.0
CHB B:HEC1128 3.4 11.0 1.0
CHD B:HEC1128 3.4 15.8 1.0
CHA B:HEC1128 3.4 15.6 1.0
CHC B:HEC1128 3.5 11.0 1.0
ND1 B:HIS62 4.2 11.3 1.0
ND1 B:HIS44 4.2 13.5 1.0
C3A B:HEC1128 4.2 12.7 1.0
CG B:HIS44 4.2 13.6 1.0
C2A B:HEC1128 4.2 14.5 1.0
CG B:HIS62 4.3 10.9 1.0
C2D B:HEC1128 4.3 16.4 1.0
C2B B:HEC1128 4.3 10.8 1.0
C3B B:HEC1128 4.3 10.2 1.0
C3C B:HEC1128 4.3 13.3 1.0
C3D B:HEC1128 4.3 15.9 1.0
C2C B:HEC1128 4.3 12.1 1.0
CG2 B:ILE42 4.6 10.6 1.0

Iron binding site 6 out of 6 in 3ml1

Go back to Iron Binding Sites List in 3ml1
Iron binding site 6 out of 6 in the Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Periplasmic Nitrate Reductase From Cupriavidus Necator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1129

b:9.0
occ:1.00
FE B:HEC1129 0.0 9.0 1.0
NC B:HEC1129 2.0 7.0 1.0
NB B:HEC1129 2.0 6.0 1.0
NE2 B:HIS102 2.0 8.1 1.0
NE2 B:HIS79 2.0 8.7 1.0
NA B:HEC1129 2.1 9.5 1.0
ND B:HEC1129 2.1 9.1 1.0
CD2 B:HIS102 3.0 7.7 1.0
CE1 B:HIS79 3.0 13.0 1.0
C1D B:HEC1129 3.0 8.6 1.0
C1B B:HEC1129 3.0 8.4 1.0
CE1 B:HIS102 3.0 8.6 1.0
C4B B:HEC1129 3.0 9.4 1.0
C4C B:HEC1129 3.0 9.1 1.0
C4A B:HEC1129 3.0 10.3 1.0
C1A B:HEC1129 3.1 11.0 1.0
CD2 B:HIS79 3.1 8.5 1.0
C1C B:HEC1129 3.1 7.5 1.0
C4D B:HEC1129 3.1 9.9 1.0
CHB B:HEC1129 3.4 9.2 1.0
CHD B:HEC1129 3.4 8.8 1.0
CHA B:HEC1129 3.5 10.6 1.0
CHC B:HEC1129 3.5 8.0 1.0
ND1 B:HIS102 4.1 8.4 1.0
ND1 B:HIS79 4.1 10.9 1.0
CG B:HIS102 4.1 7.9 1.0
CG B:HIS79 4.2 9.8 1.0
C2B B:HEC1129 4.2 8.4 1.0
C3C B:HEC1129 4.2 7.2 1.0
C2D B:HEC1129 4.2 9.3 1.0
C2C B:HEC1129 4.2 7.8 1.0
C2A B:HEC1129 4.3 10.7 1.0
C3B B:HEC1129 4.3 8.6 1.0
C3A B:HEC1129 4.3 12.0 1.0
C3D B:HEC1129 4.3 7.4 1.0
NH1 B:ARG95 4.5 17.5 1.0

Reference:

C.Coelho, P.J.Gonzalez, J.J.G.Moura, I.Moura, J.Trincao, M.J.Romao. The Crystal Structure of Cupriavidus Necator Nitrate Reductase in Oxidized and Partially Reduced States J.Mol.Biol. V. 408 932 2011.
ISSN: ISSN 0022-2836
PubMed: 21419779
DOI: 10.1016/J.JMB.2011.03.016
Page generated: Sun Dec 13 15:12:26 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy