Copper in PDB 1zxi: Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans

All present enzymatic activity of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans:
1.2.99.2;

The structure of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans, PDB code: 1zxi was solved by M.Resch, H.Dobbek, O.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.840, 131.320, 159.990, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.4

The structure of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Iron	(Fe)	8 atoms

The binding sites of Copper atom in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans (pdb code 1zxi). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans, PDB code: 1zxi:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu3910 b:14.7 occ:0.20 OE2 B:GLU763 1.9 16.4 1.0 N B:SER389 2.0 12.7 1.0 CU B:CUM3920 2.2 15.7 0.6 OM2 B:CUM3920 2.7 15.3 1.0 N B:CYS388 2.8 13.3 1.0 CA B:SER389 2.8 13.4 1.0 CD B:GLU763 2.9 13.3 1.0 C B:CYS388 3.0 14.1 1.0 S B:CUM3920 3.2 17.0 0.8 CA B:CYS388 3.3 14.2 1.0 OE1 B:GLU763 3.4 14.9 1.0 C B:ARG387 3.5 12.8 1.0 SG B:CYS388 3.5 16.2 1.0 MO B:CUM3920 3.5 13.0 1.0 N B:PHE390 3.6 13.5 1.0 C B:SER389 3.7 14.5 1.0 CA B:ARG387 3.9 12.3 1.0 CB B:CYS388 3.9 14.1 1.0 CB B:SER389 4.0 14.4 1.0 O B:CYS388 4.1 13.5 1.0 OG B:SER389 4.1 14.0 1.0 CG B:GLU763 4.2 13.1 1.0 N B:GLY569 4.2 12.1 1.0 O B:ARG387 4.3 12.4 1.0 CA B:GLY569 4.3 12.2 1.0 N B:ARG387 4.3 12.6 1.0 S8' B:MCN3921 4.5 13.3 1.0 O B:SER389 4.9 16.1 1.0 S7' B:MCN3921 4.9 12.8 1.0 CA B:PHE390 5.0 13.7 1.0 CB B:GLU763 5.0 9.0 1.0

Copper binding site 2 out of 4 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu3920 b:15.7 occ:0.60 CU B:CUM3920 0.0 15.7 0.6 CU B:CU3910 2.2 14.7 0.2 S B:CUM3920 2.3 17.0 0.8 SG B:CYS388 2.4 16.2 1.0 N B:CYS388 3.1 13.3 1.0 OM2 B:CUM3920 3.3 15.3 1.0 CB B:CYS388 3.4 14.1 1.0 N B:ALA385 3.4 11.7 1.0 CA B:ALA385 3.5 11.2 1.0 N B:SER389 3.5 12.7 1.0 CA B:CYS388 3.6 14.2 1.0 C B:ALA385 3.6 11.2 1.0 O B:ALA385 3.7 11.9 1.0 OE2 B:GLU763 3.7 16.4 1.0 CG1 B:VAL384 3.8 17.1 1.0 MO B:CUM3920 3.8 13.0 1.0 C B:CYS388 3.9 14.1 1.0 C B:VAL384 4.0 13.6 1.0 N B:PHE390 4.2 13.5 1.0 C B:ARG387 4.2 12.8 1.0 N B:ARG387 4.2 12.6 1.0 N B:TYR386 4.2 12.0 1.0 CA B:ARG387 4.5 12.3 1.0 CA B:SER389 4.5 13.4 1.0 CA B:VAL384 4.6 13.2 1.0 O B:VAL384 4.6 13.5 1.0 O B:HOH4672 4.7 39.5 1.0 C B:TYR386 4.8 12.8 1.0 CB B:VAL384 4.8 15.8 1.0 C B:SER389 4.9 14.5 1.0 OM1 B:CUM3920 4.9 16.0 1.0 CD B:GLU763 5.0 13.3 1.0 O B:CYS388 5.0 13.5 1.0 CB B:ALA385 5.0 12.9 1.0

Copper binding site 3 out of 4 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu3911 b:15.0 occ:0.20 OE2 E:GLU763 1.8 14.7 1.0 N E:SER389 2.2 13.1 1.0 CU E:CUM3922 2.2 17.3 0.6 OM2 E:CUM3922 2.3 14.7 1.0 N E:CYS388 2.9 13.8 1.0 CA E:SER389 2.9 13.9 1.0 CD E:GLU763 3.0 13.1 1.0 S E:CUM3922 3.1 16.7 0.8 C E:CYS388 3.1 14.2 1.0 MO E:CUM3922 3.3 14.8 1.0 CA E:CYS388 3.4 14.8 1.0 OE1 E:GLU763 3.4 12.3 1.0 SG E:CYS388 3.6 19.4 1.0 C E:ARG387 3.6 13.9 1.0 N E:PHE390 3.7 15.7 1.0 C E:SER389 3.8 14.3 1.0 CA E:ARG387 4.0 13.2 1.0 CB E:CYS388 4.0 13.9 1.0 N E:GLY569 4.1 11.1 1.0 CB E:SER389 4.2 14.5 1.0 CA E:GLY569 4.2 11.5 1.0 CG E:GLU763 4.2 12.8 1.0 OG E:SER389 4.2 14.7 1.0 O E:CYS388 4.3 13.6 1.0 S8' E:MCN3923 4.3 13.0 1.0 N E:ARG387 4.4 12.1 1.0 O E:ARG387 4.5 13.7 1.0 OM1 E:CUM3922 4.8 16.3 1.0 S7' E:MCN3923 4.8 13.2 1.0 O E:SER389 5.0 16.6 1.0

Copper binding site 4 out of 4 in the Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Reconstituted Co Dehydrogenase From Oligotropha Carboxidovorans within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu3922 b:17.3 occ:0.60 CU E:CUM3922 0.0 17.3 0.6 CU E:CU3911 2.2 15.0 0.2 S E:CUM3922 2.3 16.7 0.8 SG E:CYS388 2.4 19.4 1.0 N E:CYS388 3.1 13.8 1.0 OM2 E:CUM3922 3.3 14.7 1.0 N E:ALA385 3.3 14.3 1.0 CB E:CYS388 3.3 13.9 1.0 CA E:ALA385 3.4 14.1 1.0 C E:ALA385 3.5 12.8 1.0 N E:SER389 3.5 13.1 1.0 CA E:CYS388 3.6 14.8 1.0 O E:ALA385 3.7 12.6 1.0 CG1 E:VAL384 3.7 15.8 1.0 OE2 E:GLU763 3.7 14.7 1.0 MO E:CUM3922 3.8 14.8 1.0 C E:CYS388 3.9 14.2 1.0 C E:VAL384 4.0 15.7 1.0 N E:ARG387 4.2 12.1 1.0 N E:TYR386 4.2 12.9 1.0 C E:ARG387 4.2 13.9 1.0 N E:PHE390 4.2 15.7 1.0 CA E:ARG387 4.5 13.2 1.0 CA E:SER389 4.6 13.9 1.0 CA E:VAL384 4.6 15.3 1.0 O E:VAL384 4.6 15.8 1.0 C E:TYR386 4.7 13.0 1.0 CB E:VAL384 4.8 15.8 1.0 OM1 E:CUM3922 4.9 16.3 1.0 CB E:ALA385 4.9 13.3 1.0 O E:CYS388 4.9 13.6 1.0 CD E:GLU763 4.9 13.1 1.0 C E:SER389 5.0 14.3 1.0

M.Resch, H.Dobbek, O.Meyer. Structural and Functional Reconstruction in Situ of the [Cusmoo(2)] Active Site of Carbon Monoxide Dehydrogenase From the Carbon Monoxide Oxidizing Eubacterium Oligotropha Carboxidovorans J.Biol.Inorg.Chem. V. 10 518 2005.
ISSN: ISSN 0949-8257
PubMed: 16091936
DOI: 10.1007/S00775-005-0006-4