Copper in PDB 2v0a: Atomic Resolution Crystal Structure of Human Superoxide Dismutase

All present enzymatic activity of Atomic Resolution Crystal Structure of Human Superoxide Dismutase:
1.15.1.1;

The structure of Atomic Resolution Crystal Structure of Human Superoxide Dismutase, PDB code: 2v0a was solved by R.W.Strange, S.Antonyuk, C.W.Yong, W.Smith, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.50 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.545, 68.220, 50.306, 90.00, 105.14, 90.00
R / Rfree (%)	15.5 / 20.6

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

Zinc

(Zn)

2 atoms

The binding sites of Copper atom in the Atomic Resolution Crystal Structure of Human Superoxide Dismutase (pdb code 2v0a). 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 Crystal Structure of Human Superoxide Dismutase, PDB code: 2v0a:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Atomic Resolution Crystal Structure of 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 Crystal Structure of Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1154 b:10.8 occ:0.88 CU A:CU1154 0.0 10.8 0.9 CU A:CU1154 1.1 9.9 0.1 NE2 A:HIS48 2.0 9.1 1.0 NE2 A:HIS120 2.0 11.5 1.0 ND1 A:HIS46 2.0 10.8 1.0 CD2 A:HIS120 2.9 10.7 1.0 CE1 A:HIS48 2.9 10.4 1.0 CD2 A:HIS48 3.0 10.6 1.0 CG A:HIS46 3.0 10.3 1.0 CE1 A:HIS46 3.1 11.8 1.0 CE1 A:HIS120 3.1 10.4 1.0 CB A:HIS46 3.3 10.6 1.0 NE2 A:HIS63 3.4 13.1 1.0 O A:HOH2114 3.6 11.7 0.2 CD2 A:HIS63 3.7 13.3 1.0 O A:HOH2231 3.8 17.0 1.0 CB A:VAL118 3.9 9.2 1.0 CG1 A:VAL118 4.1 11.6 1.0 ND1 A:HIS48 4.1 10.5 1.0 CG A:HIS48 4.1 10.4 1.0 CG A:HIS120 4.1 9.8 1.0 N A:HIS46 4.1 9.1 1.0 ND1 A:HIS120 4.2 10.4 1.0 NE2 A:HIS46 4.2 12.1 1.0 CA A:HIS46 4.2 8.5 1.0 CD2 A:HIS46 4.2 13.7 1.0 CE1 A:HIS63 4.3 11.9 1.0 O A:HOH2238 4.4 18.3 0.8 O A:HIS46 4.4 9.7 1.0 O A:VAL118 4.5 9.5 1.0 C A:HIS46 4.6 8.4 1.0 CG2 A:VAL118 4.6 9.2 1.0 CG A:HIS63 4.7 10.9 1.0 C A:VAL118 4.9 8.3 1.0 CA A:VAL118 5.0 9.7 1.0 C A:PHE45 5.0 10.7 1.0

Copper binding site 2 out of 4 in the Atomic Resolution Crystal Structure of 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 Crystal Structure of Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1154 b:9.9 occ:0.12 CU A:CU1154 0.0 9.9 0.1 CU A:CU1154 1.1 10.8 0.9 ND1 A:HIS46 1.9 10.8 1.0 NE2 A:HIS120 2.3 11.5 1.0 NE2 A:HIS48 2.4 9.1 1.0 NE2 A:HIS63 2.5 13.1 1.0 CE1 A:HIS46 2.6 11.8 1.0 O A:HOH2114 2.8 11.7 0.2 O A:HOH2231 2.9 17.0 1.0 CD2 A:HIS63 3.0 13.3 1.0 CG A:HIS46 3.0 10.3 1.0 CE1 A:HIS48 3.0 10.4 1.0 CE1 A:HIS120 3.1 10.4 1.0 CD2 A:HIS120 3.3 10.7 1.0 CE1 A:HIS63 3.4 11.9 1.0 CB A:HIS46 3.5 10.6 1.0 CD2 A:HIS48 3.6 10.6 1.0 O A:HOH2238 3.8 18.3 0.8 NE2 A:HIS46 3.8 12.1 1.0 CD2 A:HIS46 4.0 13.7 1.0 CG A:HIS63 4.1 10.9 1.0 ND1 A:HIS120 4.2 10.4 1.0 ND1 A:HIS48 4.2 10.5 1.0 ND1 A:HIS63 4.3 10.8 1.0 CG A:HIS120 4.3 9.8 1.0 CG A:HIS48 4.5 10.4 1.0 CA A:HIS46 4.7 8.5 1.0 N A:HIS46 4.7 9.1 1.0 O A:HOH2115 4.8 19.3 1.0 O A:HOH2265 4.9 17.6 1.0 CB A:VAL118 4.9 9.2 1.0 CG1 A:VAL118 5.0 11.6 1.0

Copper binding site 3 out of 4 in the Atomic Resolution Crystal Structure of 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 Crystal Structure of Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu1156 b:9.9 occ:0.80 CU F:CU1156 0.0 9.9 0.8 CU F:CU1156 1.0 9.8 0.2 NE2 F:HIS48 1.9 11.3 1.0 NE2 F:HIS120 2.0 10.2 1.0 ND1 F:HIS46 2.0 10.3 1.0 CE1 F:HIS48 2.9 11.0 1.0 CD2 F:HIS120 3.0 11.2 1.0 CD2 F:HIS48 3.0 9.2 1.0 CE1 F:HIS120 3.0 11.3 1.0 CE1 F:HIS46 3.0 11.9 1.0 CG F:HIS46 3.0 9.6 1.0 CB F:HIS46 3.3 10.9 1.0 NE2 F:HIS63 3.3 12.2 1.0 CD2 F:HIS63 3.6 12.2 1.0 O F:HOH2276 3.7 14.9 1.0 O F:HOH2154 3.9 16.2 0.5 CB F:VAL118 3.9 9.5 1.0 ND1 F:HIS48 4.0 9.9 1.0 CG1 F:VAL118 4.1 10.9 1.0 CG F:HIS48 4.1 10.3 1.0 CG F:HIS120 4.1 9.7 1.0 ND1 F:HIS120 4.1 10.6 1.0 NE2 F:HIS46 4.2 12.6 1.0 CD2 F:HIS46 4.2 12.1 1.0 N F:HIS46 4.2 9.2 1.0 CA F:HIS46 4.3 8.9 1.0 CE1 F:HIS63 4.3 12.6 1.0 O F:HOH2281 4.4 14.7 0.5 O F:HIS46 4.5 9.2 1.0 O F:VAL118 4.6 9.9 1.0 CG2 F:VAL118 4.6 9.7 1.0 C F:HIS46 4.7 9.0 1.0 CG F:HIS63 4.7 9.6 1.0

Copper binding site 4 out of 4 in the Atomic Resolution Crystal Structure of 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 Crystal Structure of Human Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu1156 b:9.8 occ:0.20 CU F:CU1156 0.0 9.8 0.2 CU F:CU1156 1.0 9.9 0.8 ND1 F:HIS46 1.9 10.3 1.0 NE2 F:HIS120 2.2 10.2 1.0 NE2 F:HIS48 2.4 11.3 1.0 NE2 F:HIS63 2.4 12.2 1.0 CE1 F:HIS46 2.6 11.9 1.0 O F:HOH2276 2.8 14.9 1.0 CE1 F:HIS120 3.0 11.3 1.0 CD2 F:HIS63 3.0 12.2 1.0 CE1 F:HIS48 3.0 11.0 1.0 CG F:HIS46 3.0 9.6 1.0 O F:HOH2154 3.2 16.2 0.5 CD2 F:HIS120 3.2 11.2 1.0 CE1 F:HIS63 3.5 12.6 1.0 CB F:HIS46 3.6 10.9 1.0 CD2 F:HIS48 3.6 9.2 1.0 NE2 F:HIS46 3.8 12.6 1.0 O F:HOH2281 3.9 14.7 0.5 CD2 F:HIS46 4.0 12.1 1.0 CG F:HIS63 4.1 9.6 1.0 ND1 F:HIS120 4.1 10.6 1.0 CG F:HIS120 4.2 9.7 1.0 ND1 F:HIS48 4.3 9.9 1.0 ND1 F:HIS63 4.3 10.7 1.0 CG F:HIS48 4.5 10.3 1.0 CA F:HIS46 4.7 8.9 1.0 N F:HIS46 4.8 9.2 1.0 CB F:VAL118 4.9 9.5 1.0 CG1 F:VAL118 4.9 10.9 1.0 O F:HOH2155 4.9 18.2 1.0 O F:HOH2308 4.9 18.7 1.0

R.W.Strange, C.W.Yong, W.Smith, S.S.Hasnain. Molecular Dynamics Using Atomic-Resolution Structure Reveal Structural Fluctuations That May Lead to Polymerization of Human Cu-Zn Superoxide Dismutase. Proc.Natl.Acad.Sci.Usa V. 104 10040 2007.
ISSN: ISSN 0027-8424
PubMed: 17548825
DOI: 10.1073/PNAS.0703857104