Iron in PDB 1ogy: Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides

All present enzymatic activity of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides:
1.7.99.4;

The structure of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides, PDB code: 1ogy was solved by P.Arnoux, M.Sabaty, J.Alric, B.Frangioni, B.Guigliarelli, J.-M.Adriano, D.Pignol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	123.000, 225.200, 154.600, 90.00, 92.10, 90.00
R / Rfree (%)	25 / 26.9

The structure of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides also contains other interesting chemical elements:

Molybdenum

(Mo)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides (pdb code 1ogy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides, PDB code: 1ogy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


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 Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1801 b:10.0 occ:1.00 FE1 A:SF41801 0.0 10.0 1.0 CB A:CYS22 2.1 10.0 1.0 S4 A:SF41801 2.2 10.5 1.0 S3 A:SF41801 2.2 10.2 1.0 S2 A:SF41801 2.3 12.0 1.0 SG A:CYS22 2.3 12.5 1.0 FE4 A:SF41801 2.6 10.0 1.0 FE2 A:SF41801 2.7 10.0 1.0 FE3 A:SF41801 2.7 10.5 1.0 CA A:CYS22 3.6 10.0 1.0 S1 A:SF41801 3.8 10.0 1.0 N A:CYS22 4.0 11.0 1.0 CB A:THR24 4.1 10.0 1.0 OG1 A:THR24 4.2 10.0 1.0 C A:CYS22 4.4 11.2 1.0 SG A:CYS19 4.6 10.0 1.0 SG A:CYS26 4.7 11.1 1.0 SG A:CYS54 4.7 11.4 1.0 CD A:PRO194 4.8 13.6 1.0 O A:CYS22 4.8 13.2 1.0 N A:THR24 4.9 10.0 1.0

Iron binding site 2 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


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 Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides 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 S3 A:SF41801 2.2 10.2 1.0 S4 A:SF41801 2.2 10.5 1.0 SG A:CYS54 2.3 11.4 1.0 S1 A:SF41801 2.3 10.0 1.0 FE4 A:SF41801 2.7 10.0 1.0 FE3 A:SF41801 2.7 10.5 1.0 FE1 A:SF41801 2.7 10.0 1.0 CB A:CYS54 3.3 10.0 1.0 N A:CYS54 3.8 10.9 1.0 S2 A:SF41801 3.8 12.0 1.0 CA A:CYS54 4.1 10.3 1.0 N A:GLY57 4.5 10.9 1.0 CD A:PRO194 4.6 13.6 1.0 CB A:CYS22 4.7 10.0 1.0 SG A:CYS26 4.7 11.1 1.0 C A:ASN53 4.7 10.4 1.0 SG A:CYS22 4.7 12.5 1.0 SG A:CYS19 4.7 10.0 1.0 CG1 A:ILE195 4.8 11.5 1.0 CA A:GLY57 4.8 10.7 1.0 C A:CYS54 4.8 10.3 1.0 CG A:PRO194 4.8 14.3 1.0 NZ A:LYS56 4.9 11.0 1.0 CB A:PRO194 5.0 14.0 1.0 CA A:ASN53 5.0 10.7 1.0

Iron binding site 3 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


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 Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1801 b:10.5 occ:1.00 FE3 A:SF41801 0.0 10.5 1.0 SG A:CYS26 2.2 11.1 1.0 S1 A:SF41801 2.2 10.0 1.0 S2 A:SF41801 2.3 12.0 1.0 S4 A:SF41801 2.3 10.5 1.0 FE2 A:SF41801 2.7 10.0 1.0 FE4 A:SF41801 2.7 10.0 1.0 FE1 A:SF41801 2.7 10.0 1.0 CB A:CYS26 3.0 10.0 1.0 S3 A:SF41801 3.8 10.2 1.0 CG1 A:ILE195 4.0 11.5 1.0 N A:CYS26 4.1 10.2 1.0 CA A:CYS26 4.2 10.0 1.0 CB A:ILE195 4.4 12.4 1.0 CB A:THR24 4.6 10.0 1.0 CB A:CYS22 4.6 10.0 1.0 SG A:CYS19 4.6 10.0 1.0 CG2 A:THR24 4.6 10.6 1.0 CB A:CYS19 4.7 10.0 1.0 SG A:CYS22 4.7 12.5 1.0 CA A:ASN53 4.8 10.7 1.0 SG A:CYS54 4.9 11.4 1.0 N A:CYS54 4.9 10.9 1.0

Iron binding site 4 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


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 Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1801 b:10.0 occ:1.00 FE4 A:SF41801 0.0 10.0 1.0 S2 A:SF41801 2.1 12.0 1.0 S1 A:SF41801 2.1 10.0 1.0 S3 A:SF41801 2.1 10.2 1.0 SG A:CYS19 2.2 10.0 1.0 FE1 A:SF41801 2.6 10.0 1.0 FE2 A:SF41801 2.7 10.0 1.0 FE3 A:SF41801 2.7 10.5 1.0 CB A:CYS19 3.1 10.0 1.0 S4 A:SF41801 3.7 10.5 1.0 CB A:CYS22 3.8 10.0 1.0 CB A:PHE21 4.4 10.0 1.0 CA A:GLY57 4.4 10.7 1.0 SG A:CYS54 4.5 11.4 1.0 CB A:CYS26 4.5 10.0 1.0 N A:CYS22 4.6 11.0 1.0 SG A:CYS26 4.6 11.1 1.0 CA A:CYS19 4.6 10.0 1.0 N A:GLY57 4.7 10.9 1.0 SG A:CYS22 4.8 12.5 1.0 CD1 A:PHE21 4.9 10.8 1.0 CA A:CYS22 4.9 10.0 1.0 N A:PHE21 5.0 10.0 1.0

Iron binding site 5 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


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 Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1128 b:15.9 occ:1.00 FE B:HEC1128 0.0 15.9 1.0 ND B:HEC1128 1.9 19.4 1.0 NE2 B:HIS44 1.9 20.9 1.0 NE2 B:HIS62 2.0 11.5 1.0 NB B:HEC1128 2.0 15.2 1.0 NC B:HEC1128 2.0 16.6 1.0 NA B:HEC1128 2.0 15.7 1.0 CE1 B:HIS44 2.8 24.4 1.0 CE1 B:HIS62 2.9 10.7 1.0 C4D B:HEC1128 3.0 22.1 1.0 C1D B:HEC1128 3.0 21.6 1.0 C4A B:HEC1128 3.0 14.7 1.0 C4B B:HEC1128 3.0 14.7 1.0 C4C B:HEC1128 3.0 17.2 1.0 C1C B:HEC1128 3.0 16.3 1.0 C1A B:HEC1128 3.0 16.4 1.0 C1B B:HEC1128 3.0 13.5 1.0 CD2 B:HIS44 3.1 26.5 1.0 CD2 B:HIS62 3.1 10.0 1.0 CHB B:HEC1128 3.4 14.1 1.0 CHD B:HEC1128 3.4 18.9 1.0 CHA B:HEC1128 3.4 19.6 1.0 CHC B:HEC1128 3.4 16.4 1.0 ND1 B:HIS44 4.0 27.3 1.0 ND1 B:HIS62 4.1 11.8 1.0 CG B:HIS44 4.1 28.6 1.0 CG B:HIS62 4.2 11.2 1.0 C2B B:HEC1128 4.2 12.2 1.0 C2D B:HEC1128 4.2 25.2 1.0 C3B B:HEC1128 4.2 12.7 1.0 C2C B:HEC1128 4.3 14.6 1.0 C3C B:HEC1128 4.3 16.6 1.0 C3D B:HEC1128 4.3 26.1 1.0 C3A B:HEC1128 4.3 15.5 1.0 C2A B:HEC1128 4.3 15.9 1.0

Iron binding site 6 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


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 Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1129 b:15.4 occ:1.00 FE B:HEC1129 0.0 15.4 1.0 NE2 B:HIS102 2.0 10.5 1.0 NE2 B:HIS79 2.0 10.2 1.0 NA B:HEC1129 2.0 15.4 1.0 NB B:HEC1129 2.0 14.0 1.0 ND B:HEC1129 2.0 16.7 1.0 NC B:HEC1129 2.0 16.8 1.0 CE1 B:HIS79 2.8 10.0 1.0 CE1 B:HIS102 2.8 10.6 1.0 C1A B:HEC1129 3.0 17.3 1.0 C4A B:HEC1129 3.0 14.2 1.0 C4B B:HEC1129 3.0 14.0 1.0 C1D B:HEC1129 3.0 18.3 1.0 C4D B:HEC1129 3.0 19.2 1.0 C1B B:HEC1129 3.1 13.6 1.0 C1C B:HEC1129 3.1 17.2 1.0 C4C B:HEC1129 3.1 17.3 1.0 CD2 B:HIS102 3.1 10.0 1.0 CD2 B:HIS79 3.2 11.1 1.0 CHB B:HEC1129 3.4 13.2 1.0 CHA B:HEC1129 3.4 18.8 1.0 CHD B:HEC1129 3.4 18.3 1.0 CHC B:HEC1129 3.4 16.1 1.0 ND1 B:HIS102 4.0 11.6 1.0 ND1 B:HIS79 4.0 10.1 1.0 CG B:HIS102 4.2 10.4 1.0 CG B:HIS79 4.2 11.7 1.0 C2A B:HEC1129 4.2 16.8 1.0 C2B B:HEC1129 4.3 13.8 1.0 C3B B:HEC1129 4.3 13.3 1.0 C3A B:HEC1129 4.3 14.6 1.0 C2D B:HEC1129 4.3 20.2 1.0 C2C B:HEC1129 4.3 17.0 1.0 C3C B:HEC1129 4.3 16.9 1.0 C3D B:HEC1129 4.3 22.5 1.0 NH1 B:ARG95 4.8 12.6 1.0

Iron binding site 7 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1801 b:10.0 occ:1.00 FE1 C:SF41801 0.0 10.0 1.0 S4 C:SF41801 2.1 11.4 1.0 S2 C:SF41801 2.2 12.3 1.0 CB C:CYS22 2.2 24.8 1.0 S3 C:SF41801 2.3 10.0 1.0 SG C:CYS22 2.5 27.4 1.0 FE4 C:SF41801 2.6 10.0 1.0 FE3 C:SF41801 2.7 10.0 1.0 FE2 C:SF41801 2.7 10.3 1.0 CA C:CYS22 3.7 23.7 1.0 S1 C:SF41801 3.8 11.8 1.0 CB C:THR24 4.1 21.3 1.0 N C:CYS22 4.1 23.1 1.0 OG1 C:THR24 4.2 21.7 1.0 C C:CYS22 4.4 24.6 1.0 SG C:CYS19 4.5 18.3 1.0 SG C:CYS26 4.6 19.9 1.0 O C:CYS22 4.7 25.1 1.0 SG C:CYS54 4.7 22.3 1.0 CD C:PRO194 4.7 23.3 1.0 N C:THR24 4.8 23.0 1.0 CG2 C:THR24 4.9 21.3 1.0 N C:GLY25 4.9 22.0 1.0

Iron binding site 8 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1801 b:10.3 occ:1.00 FE2 C:SF41801 0.0 10.3 1.0 S3 C:SF41801 2.2 10.0 1.0 S4 C:SF41801 2.3 11.4 1.0 SG C:CYS54 2.3 22.3 1.0 S1 C:SF41801 2.3 11.8 1.0 FE4 C:SF41801 2.7 10.0 1.0 FE3 C:SF41801 2.7 10.0 1.0 FE1 C:SF41801 2.7 10.0 1.0 CB C:CYS54 3.5 21.8 1.0 N C:CYS54 3.7 22.7 1.0 S2 C:SF41801 3.8 12.3 1.0 CA C:CYS54 4.2 21.2 1.0 N C:GLY57 4.5 14.5 1.0 CD C:PRO194 4.5 23.3 1.0 C C:ASN53 4.6 23.8 1.0 SG C:CYS22 4.7 27.4 1.0 CB C:CYS22 4.7 24.8 1.0 SG C:CYS26 4.8 19.9 1.0 CA C:GLY57 4.8 14.9 1.0 CG C:PRO194 4.8 23.1 1.0 CG1 C:ILE195 4.8 19.6 1.0 C C:CYS54 4.9 19.7 1.0 SG C:CYS19 4.9 18.3 1.0 NZ C:LYS56 4.9 10.0 1.0 CA C:ASN53 5.0 24.2 1.0

Iron binding site 9 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1801 b:10.0 occ:1.00 FE3 C:SF41801 0.0 10.0 1.0 SG C:CYS26 2.2 19.9 1.0 S2 C:SF41801 2.2 12.3 1.0 S1 C:SF41801 2.3 11.8 1.0 S4 C:SF41801 2.3 11.4 1.0 FE4 C:SF41801 2.7 10.0 1.0 FE1 C:SF41801 2.7 10.0 1.0 FE2 C:SF41801 2.7 10.3 1.0 CB C:CYS26 3.0 19.5 1.0 S3 C:SF41801 3.8 10.0 1.0 CG1 C:ILE195 4.0 19.6 1.0 N C:CYS26 4.0 19.2 1.0 CA C:CYS26 4.1 19.3 1.0 CB C:ILE195 4.4 18.4 1.0 CB C:THR24 4.6 21.3 1.0 CG2 C:THR24 4.6 21.3 1.0 CB C:CYS19 4.7 15.1 1.0 SG C:CYS19 4.7 18.3 1.0 CA C:ASN53 4.8 24.2 1.0 CB C:CYS22 4.8 24.8 1.0 SG C:CYS54 4.9 22.3 1.0 N C:CYS54 4.9 22.7 1.0

Iron binding site 10 out of 48 in the Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1801 b:10.0 occ:1.00 FE4 C:SF41801 0.0 10.0 1.0 S2 C:SF41801 2.1 12.3 1.0 S3 C:SF41801 2.1 10.0 1.0 S1 C:SF41801 2.2 11.8 1.0 SG C:CYS19 2.3 18.3 1.0 FE1 C:SF41801 2.6 10.0 1.0 FE2 C:SF41801 2.7 10.3 1.0 FE3 C:SF41801 2.7 10.0 1.0 CB C:CYS19 3.1 15.1 1.0 S4 C:SF41801 3.7 11.4 1.0 CB C:CYS22 4.0 24.8 1.0 CB C:PHE21 4.4 18.2 1.0 CA C:GLY57 4.5 14.9 1.0 CB C:CYS26 4.5 19.5 1.0 CA C:CYS19 4.5 14.9 1.0 N C:CYS22 4.6 23.1 1.0 SG C:CYS26 4.6 19.9 1.0 SG C:CYS54 4.7 22.3 1.0 N C:GLY57 4.8 14.5 1.0 CD1 C:PHE21 4.9 15.7 1.0 SG C:CYS22 4.9 27.4 1.0 N C:PHE21 4.9 16.9 1.0 CA C:CYS22 5.0 23.7 1.0

P.Arnoux, M.Sabaty, J.Alric, B.Frangioni, B.Guigliarelli, J.-M.Adriano, D.Pignol. Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase Nat.Struct.Biol. V. 10 928 2003.
ISSN: ISSN 1072-8368
PubMed: 14528294
DOI: 10.1038/NSB994