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Iron in PDB 3o5a: Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids

Enzymatic activity of Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids

All present enzymatic activity of Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids:
1.7.99.4; 1.9.6.1;

Protein crystallography data

The structure of Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids, PDB code: 3o5a 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) 27.63 / 1.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.400, 71.410, 128.410, 90.00, 121.04, 90.00
R / Rfree (%) 14.3 / 18.1

Other elements in 3o5a:

The structure of Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids (pdb code 3o5a). 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 Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids, PDB code: 3o5a:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3o5a

Go back to Iron Binding Sites List in 3o5a
Iron binding site 1 out of 6 in the Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids


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 Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:7.1
occ:1.00
 FE1 A:SF41801 0.0 7.1 1.0
S2 A:SF41801 2.2 5.5 1.0
S4 A:SF41801 2.2 7.3 1.0
S3 A:SF41801 2.3 5.8 1.0
SG A:CYS22 2.3 6.8 1.0
FE4 A:SF41801 2.6 6.5 1.0
FE3 A:SF41801 2.6 7.0 1.0
FE2 A:SF41801 2.7 7.7 1.0
CB A:CYS22 3.5 3.4 1.0
N A:CYS22 3.7 3.9 1.0
S1 A:SF41801 3.8 6.0 1.0
O A:HOH940 3.9 7.6 1.0
CA A:CYS22 3.9 5.1 1.0
CB A:THR24 4.0 5.0 1.0
O A:CYS22 4.2 5.6 1.0
OG1 A:THR24 4.2 8.8 1.0
C A:CYS22 4.3 4.5 1.0
CD A:PRO194 4.6 5.3 1.0
SG A:CYS26 4.7 7.0 1.0
SG A:CYS54 4.7 7.0 1.0
SG A:CYS19 4.8 5.6 1.0
C A:PHE21 4.8 5.8 1.0
CG2 A:THR24 4.8 5.6 1.0
N A:THR24 4.9 5.9 1.0
CA A:THR24 5.0 5.1 1.0
N A:GLY25 5.0 5.2 1.0
CB A:PHE21 5.0 5.2 1.0

Iron binding site 2 out of 6 in 3o5a

Go back to Iron Binding Sites List in 3o5a
Iron binding site 2 out of 6 in the Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids


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 Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:7.7
occ:1.00
 FE2 A:SF41801 0.0 7.7 1.0
S1 A:SF41801 2.2 6.0 1.0
S3 A:SF41801 2.2 5.8 1.0
S4 A:SF41801 2.3 7.3 1.0
SG A:CYS54 2.4 7.0 1.0
FE4 A:SF41801 2.7 6.5 1.0
FE1 A:SF41801 2.7 7.1 1.0
FE3 A:SF41801 2.7 7.0 1.0
CB A:CYS54 3.4 2.7 1.0
N A:CYS54 3.6 4.7 1.0
S2 A:SF41801 3.8 5.5 1.0
CA A:CYS54 4.1 4.1 1.0
N A:GLY57 4.3 5.1 1.0
O A:HOH940 4.4 7.6 1.0
NZ A:LYS56 4.5 4.8 1.0
CD A:PRO194 4.6 5.3 1.0
C A:CYS54 4.6 4.8 1.0
O A:CYS54 4.7 6.7 1.0
CG A:PRO194 4.7 9.7 1.0
SG A:CYS22 4.7 6.8 1.0
C A:ASN53 4.7 6.3 1.0
CB A:PRO194 4.8 7.2 1.0
CA A:GLY57 4.8 3.9 1.0
SG A:CYS26 4.8 7.0 1.0
SG A:CYS19 4.9 5.6 1.0
CB A:LYS56 4.9 5.0 1.0
CD1 A:ILE195 5.0 9.4 1.0

Iron binding site 3 out of 6 in 3o5a

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Iron binding site 3 out of 6 in the Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids


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 Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:7.0
occ:1.00
 FE3 A:SF41801 0.0 7.0 1.0
S4 A:SF41801 2.2 7.3 1.0
S2 A:SF41801 2.2 5.5 1.0
S1 A:SF41801 2.3 6.0 1.0
SG A:CYS26 2.3 7.0 1.0
FE4 A:SF41801 2.6 6.5 1.0
FE1 A:SF41801 2.6 7.1 1.0
FE2 A:SF41801 2.7 7.7 1.0
CB A:CYS26 3.2 6.5 1.0
S3 A:SF41801 3.8 5.8 1.0
N A:CYS26 4.1 6.5 1.0
CA A:CYS26 4.2 6.7 1.0
CG2 A:THR24 4.4 5.6 1.0
CD1 A:ILE195 4.4 9.4 1.0
CB A:THR24 4.4 5.0 1.0
CB A:ILE195 4.5 7.5 1.0
CG1 A:ILE195 4.5 8.7 1.0
SG A:CYS19 4.7 5.6 1.0
CB A:CYS19 4.7 3.5 1.0
ND2 A:ASN53 4.7 10.2 1.0
N A:CYS54 4.7 4.7 1.0
SG A:CYS22 4.7 6.8 1.0
CA A:ASN53 4.9 6.6 1.0
SG A:CYS54 4.9 7.0 1.0

Iron binding site 4 out of 6 in 3o5a

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Iron binding site 4 out of 6 in the Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids


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 Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:6.5
occ:1.00
 FE4 A:SF41801 0.0 6.5 1.0
S3 A:SF41801 2.2 5.8 1.0
S2 A:SF41801 2.2 5.5 1.0
S1 A:SF41801 2.3 6.0 1.0
SG A:CYS19 2.4 5.6 1.0
FE3 A:SF41801 2.6 7.0 1.0
FE1 A:SF41801 2.6 7.1 1.0
FE2 A:SF41801 2.7 7.7 1.0
CB A:CYS19 3.2 3.5 1.0
S4 A:SF41801 3.8 7.3 1.0
N A:CYS22 4.2 3.9 1.0
CB A:PHE21 4.2 5.2 1.0
CA A:GLY57 4.5 3.9 1.0
N A:GLY57 4.5 5.1 1.0
CB A:CYS26 4.6 6.5 1.0
SG A:CYS26 4.6 7.0 1.0
CA A:CYS19 4.7 5.3 1.0
SG A:CYS54 4.7 7.0 1.0
N A:PHE21 4.7 4.7 1.0
SG A:CYS22 4.8 6.8 1.0
C A:PHE21 4.8 5.8 1.0
CA A:PHE21 4.8 5.7 1.0
CD2 A:PHE21 4.9 5.8 1.0

Iron binding site 5 out of 6 in 3o5a

Go back to Iron Binding Sites List in 3o5a
Iron binding site 5 out of 6 in the Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids


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 Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1128

b:16.8
occ:1.00
 FE B:HEC1128 0.0 16.8 1.0
NE2 B:HIS62 2.0 9.9 1.0
NA B:HEC1128 2.0 12.7 1.0
NC B:HEC1128 2.0 16.1 1.0
NB B:HEC1128 2.0 15.3 1.0
ND B:HEC1128 2.1 16.7 1.0
NE2 B:HIS44 2.1 16.2 1.0
CE1 B:HIS62 2.9 9.6 1.0
CD2 B:HIS62 3.0 12.5 1.0
C1B B:HEC1128 3.0 12.7 1.0
C4A B:HEC1128 3.0 13.2 1.0
C1D B:HEC1128 3.0 19.3 1.0
C1A B:HEC1128 3.0 12.5 1.0
CE1 B:HIS44 3.1 17.5 1.0
C4C B:HEC1128 3.1 16.2 1.0
C4B B:HEC1128 3.1 13.3 1.0
C1C B:HEC1128 3.1 11.1 1.0
C4D B:HEC1128 3.1 16.7 1.0
CD2 B:HIS44 3.2 16.2 1.0
CHB B:HEC1128 3.3 12.0 1.0
CHD B:HEC1128 3.4 16.5 1.0
CHA B:HEC1128 3.5 14.1 1.0
CHC B:HEC1128 3.5 16.7 1.0
ND1 B:HIS62 4.1 12.3 1.0
CG B:HIS62 4.1 14.9 1.0
C2B B:HEC1128 4.2 12.7 1.0
ND1 B:HIS44 4.2 16.6 1.0
C3A B:HEC1128 4.2 12.7 1.0
C2A B:HEC1128 4.3 13.0 1.0
C2D B:HEC1128 4.3 19.1 1.0
C3B B:HEC1128 4.3 12.6 1.0
CG B:HIS44 4.3 19.6 1.0
C2C B:HEC1128 4.3 15.0 1.0
C3C B:HEC1128 4.3 16.9 1.0
C3D B:HEC1128 4.3 19.7 1.0
CG2 B:ILE42 4.6 12.5 1.0

Iron binding site 6 out of 6 in 3o5a

Go back to Iron Binding Sites List in 3o5a
Iron binding site 6 out of 6 in the Crystal Structure of Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids


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 Partially Reduced Periplasmic Nitrate Reductase From Cupriavidus Necator Using Ionic Liquids within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1129

b:9.5
occ:1.00
 FE B:HEC1129 0.0 9.5 1.0
NB B:HEC1129 1.9 7.9 1.0
NE2 B:HIS79 2.0 10.0 1.0
ND B:HEC1129 2.0 9.6 1.0
NE2 B:HIS102 2.0 8.1 1.0
NC B:HEC1129 2.0 7.3 1.0
NA B:HEC1129 2.0 6.5 1.0
C1B B:HEC1129 2.9 10.6 1.0
CE1 B:HIS79 2.9 12.5 1.0
CD2 B:HIS102 3.0 8.6 1.0
C4A B:HEC1129 3.0 9.8 1.0
C4C B:HEC1129 3.0 9.9 1.0
C4B B:HEC1129 3.0 5.9 1.0
CE1 B:HIS102 3.0 11.1 1.0
CD2 B:HIS79 3.0 11.9 1.0
C1D B:HEC1129 3.0 9.2 1.0
C4D B:HEC1129 3.0 5.9 1.0
C1A B:HEC1129 3.0 9.2 1.0
C1C B:HEC1129 3.1 3.5 1.0
CHB B:HEC1129 3.3 10.6 1.0
CHD B:HEC1129 3.4 8.9 1.0
CHA B:HEC1129 3.5 8.5 1.0
CHC B:HEC1129 3.5 5.8 1.0
ND1 B:HIS79 4.1 14.8 1.0
CG B:HIS102 4.1 7.6 1.0
ND1 B:HIS102 4.1 10.4 1.0
CG B:HIS79 4.1 10.5 1.0
C2B B:HEC1129 4.2 7.5 1.0
C3B B:HEC1129 4.2 5.9 1.0
C3A B:HEC1129 4.2 9.3 1.0
C3C B:HEC1129 4.2 8.8 1.0
C2A B:HEC1129 4.2 9.9 1.0
C2D B:HEC1129 4.3 8.7 1.0
C2C B:HEC1129 4.3 9.1 1.0
C3D B:HEC1129 4.3 9.6 1.0
NH1 B:ARG95 4.6 22.1 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 15:15:30 2020

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