Copper in PDB 2c9v: Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase

All present enzymatic activity of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase:
1.15.1.1;

The structure of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase, PDB code: 2c9v was solved by R.W.Strange, S.V.Antonyuk, M.A.Hough, P.A.Doucette, J.S.Valentine, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.00 / 1.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.605, 67.368, 52.532, 90.00, 106.54, 90.00
R / Rfree (%)	13.1 / 15.8

The structure of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Copper atom in the Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase (pdb code 2c9v). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase, PDB code: 2c9v:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu154 b:8.3 occ:0.90 CU A:CU154 0.0 8.3 0.9 CU A:CU154 1.3 12.0 0.1 NE2 A:HIS48 2.0 8.2 1.0 ND1 A:HIS46 2.0 8.3 1.0 NE2 A:HIS120 2.0 8.2 1.0 CE1 A:HIS48 2.9 8.0 1.0 CE1 A:HIS46 3.0 8.6 1.0 CD2 A:HIS120 3.0 7.7 1.0 CG A:HIS46 3.0 7.3 1.0 CD2 A:HIS48 3.0 7.8 1.0 CE1 A:HIS120 3.0 8.3 1.0 CB A:HIS46 3.4 8.0 1.0 O A:HOH2127 3.4 16.4 0.5 NE2 A:HIS63 3.5 10.2 1.0 O A:HOH2254 3.7 12.0 1.0 CD2 A:HIS63 3.8 9.9 1.0 CB A:VAL118 4.0 7.6 1.0 ND1 A:HIS48 4.1 7.5 1.0 NE2 A:HIS46 4.1 8.2 1.0 CG A:HIS48 4.1 7.0 1.0 ND1 A:HIS120 4.1 8.5 1.0 CG1 A:VAL118 4.1 8.9 1.0 CD2 A:HIS46 4.1 8.8 1.0 CG A:HIS120 4.1 7.7 1.0 N A:HIS46 4.2 7.2 1.0 CA A:HIS46 4.3 7.2 1.0 O A:HOH2262 4.3 12.2 0.5 CE1 A:HIS63 4.4 9.1 1.0 O A:VAL118 4.5 8.0 1.0 O A:HIS46 4.5 7.3 1.0 CG2 A:VAL118 4.7 8.0 1.0 C A:HIS46 4.7 6.9 1.0 CG A:HIS63 4.8 8.2 1.0 C A:VAL118 5.0 6.8 1.0

Copper binding site 2 out of 4 in the Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu154 b:12.0 occ:0.10 CU A:CU154 0.0 12.0 0.1 CU A:CU154 1.3 8.3 0.9 ND1 A:HIS46 2.1 8.3 1.0 NE2 A:HIS63 2.2 10.2 1.0 O A:HOH2127 2.4 16.4 0.5 NE2 A:HIS48 2.5 8.2 1.0 NE2 A:HIS120 2.5 8.2 1.0 O A:HOH2254 2.6 12.0 1.0 CE1 A:HIS46 2.7 8.6 1.0 CD2 A:HIS63 2.8 9.9 1.0 CE1 A:HIS48 3.0 8.0 1.0 CE1 A:HIS120 3.1 8.3 1.0 CG A:HIS46 3.2 7.3 1.0 CE1 A:HIS63 3.3 9.1 1.0 CD2 A:HIS120 3.5 7.7 1.0 O A:HOH2262 3.6 12.2 0.5 CD2 A:HIS48 3.7 7.8 1.0 CB A:HIS46 3.8 8.0 1.0 NE2 A:HIS46 3.8 8.2 1.0 CG A:HIS63 3.9 8.2 1.0 CD2 A:HIS46 4.1 8.8 1.0 ND1 A:HIS63 4.1 7.8 1.0 ND1 A:HIS48 4.2 7.5 1.0 ND1 A:HIS120 4.3 8.5 1.0 O A:HOH2129 4.5 16.3 1.0 CG A:HIS120 4.5 7.7 1.0 CG A:HIS48 4.6 7.0 1.0 O A:HOH2280 4.6 12.1 1.0 O A:THR137 4.9 10.7 1.0

Copper binding site 3 out of 4 in the Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu154 b:8.2 occ:0.90 CU F:CU154 0.0 8.2 0.9 CU F:CU154 1.2 12.2 0.1 NE2 F:HIS48 1.9 7.7 1.0 ND1 F:HIS46 2.0 7.8 1.0 NE2 F:HIS120 2.0 8.7 1.0 CE1 F:HIS48 2.9 8.0 1.0 CD2 F:HIS120 3.0 7.8 1.0 CE1 F:HIS46 3.0 9.2 1.0 CD2 F:HIS48 3.0 7.9 1.0 CG F:HIS46 3.0 7.7 1.0 CE1 F:HIS120 3.1 8.1 1.0 CB F:HIS46 3.4 7.9 1.0 NE2 F:HIS63 3.5 10.1 1.0 O F:HOH2134 3.5 15.0 0.5 CD2 F:HIS63 3.7 9.9 1.0 O F:HOH2274 3.7 13.0 1.0 CB F:VAL118 4.0 7.7 1.0 ND1 F:HIS48 4.1 7.6 1.0 CG F:HIS48 4.1 7.7 1.0 NE2 F:HIS46 4.1 7.9 1.0 CG1 F:VAL118 4.1 8.5 1.0 CG F:HIS120 4.1 7.5 1.0 ND1 F:HIS120 4.2 8.2 1.0 CD2 F:HIS46 4.2 8.7 1.0 N F:HIS46 4.2 7.3 1.0 CA F:HIS46 4.3 7.0 1.0 O F:HOH2283 4.3 12.7 0.5 CE1 F:HIS63 4.4 9.0 1.0 O F:VAL118 4.5 7.9 1.0 O F:HIS46 4.6 7.7 1.0 CG2 F:VAL118 4.6 8.4 1.0 C F:HIS46 4.7 6.8 1.0 CG F:HIS63 4.7 8.3 1.0 C F:VAL118 5.0 7.5 1.0

Copper binding site 4 out of 4 in the Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu154 b:12.2 occ:0.10 CU F:CU154 0.0 12.2 0.1 CU F:CU154 1.2 8.2 0.9 ND1 F:HIS46 2.1 7.8 1.0 NE2 F:HIS63 2.3 10.1 1.0 NE2 F:HIS48 2.4 7.7 1.0 NE2 F:HIS120 2.4 8.7 1.0 O F:HOH2134 2.5 15.0 0.5 O F:HOH2274 2.7 13.0 1.0 CE1 F:HIS46 2.7 9.2 1.0 CD2 F:HIS63 2.8 9.9 1.0 CE1 F:HIS48 2.9 8.0 1.0 CE1 F:HIS120 3.1 8.1 1.0 CG F:HIS46 3.2 7.7 1.0 CE1 F:HIS63 3.3 9.0 1.0 CD2 F:HIS120 3.5 7.8 1.0 O F:HOH2283 3.5 12.7 0.5 CD2 F:HIS48 3.6 7.9 1.0 CB F:HIS46 3.8 7.9 1.0 NE2 F:HIS46 3.9 7.9 1.0 CG F:HIS63 3.9 8.3 1.0 CD2 F:HIS46 4.1 8.7 1.0 ND1 F:HIS48 4.2 7.6 1.0 ND1 F:HIS63 4.2 7.8 1.0 ND1 F:HIS120 4.2 8.2 1.0 CG F:HIS120 4.4 7.5 1.0 CG F:HIS48 4.5 7.7 1.0 O F:HOH2280 4.6 16.6 1.0 O F:HOH2299 4.7 12.5 1.0 CA F:HIS46 5.0 7.0 1.0

R.W.Strange, S.V.Antonyuk, M.A.Hough, P.A.Doucette, J.S.Valentine, S.S.Hasnain. Variable Metallation of Human Superoxide Dismutase: Atomic Resolution Crystal Structures of Cu-Zn, Zn-Zn and As-Isolated Wild-Type Enzymes. J.Mol.Biol. V. 356 1152 2006.
ISSN: ISSN 0022-2836
PubMed: 16406071
DOI: 10.1016/J.JMB.2005.11.081