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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

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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

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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

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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

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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

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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

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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 Aug 4 14:51:24 2024

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