Zinc in PDB 2wyz: L38V SOD1 Mutant Complexed with Ump

All present enzymatic activity of L38V SOD1 Mutant Complexed with Ump:
1.15.1.1;

The structure of L38V SOD1 Mutant Complexed with Ump, PDB code: 2wyz was solved by S.V.Antonyuk, R.W.Strange, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.717, 67.589, 50.777, 90.00, 105.98, 90.00
R / Rfree (%)	17.6 / 23.9

The structure of L38V SOD1 Mutant Complexed with Ump also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Zinc atom in the L38V SOD1 Mutant Complexed with Ump (pdb code 2wyz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the L38V SOD1 Mutant Complexed with Ump, PDB code: 2wyz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the L38V SOD1 Mutant Complexed with Ump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of L38V SOD1 Mutant Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn154 b:19.2 occ:0.50 CU A:CU154 1.1 14.6 0.5 NE2 A:HIS120 1.9 11.5 1.0 O4 A:SO4156 2.1 13.9 0.5 NE2 A:HIS48 2.1 8.9 1.0 ND1 A:HIS46 2.5 13.0 1.0 O A:HOH2184 2.5 11.2 0.5 CE1 A:HIS120 2.7 13.0 1.0 CE1 A:HIS48 2.7 10.0 1.0 NE2 A:HIS63 3.0 15.0 1.0 CD2 A:HIS120 3.0 10.6 1.0 CE1 A:HIS46 3.3 16.6 1.0 S A:SO4156 3.4 16.1 0.5 CD2 A:HIS48 3.4 12.5 1.0 CD2 A:HIS63 3.4 13.8 1.0 CG A:HIS46 3.5 9.1 1.0 O2 A:SO4156 3.7 17.1 0.5 ND1 A:HIS120 3.8 9.5 1.0 CB A:HIS46 3.9 9.8 1.0 CE1 A:HIS63 4.0 13.5 1.0 ND1 A:HIS48 4.0 8.1 1.0 CG A:HIS120 4.0 10.1 1.0 O1 A:SO4156 4.1 19.1 0.5 CG A:HIS48 4.3 7.8 1.0 O3 A:SO4156 4.4 15.6 0.5 NE2 A:HIS46 4.4 11.7 1.0 O A:HOH2183 4.4 6.8 0.5 CG A:HIS63 4.6 11.1 1.0 CD2 A:HIS46 4.6 12.3 1.0 CG1 A:VAL118 4.6 6.0 1.0 CB A:VAL118 4.7 6.2 1.0 ND1 A:HIS63 4.8 10.0 1.0 O A:HOH2186 5.0 22.4 1.0

Zinc binding site 2 out of 4 in the L38V SOD1 Mutant Complexed with Ump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of L38V SOD1 Mutant Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn155 b:9.9 occ:1.00 ND1 A:HIS80 1.9 10.0 1.0 OD1 A:ASP83 2.0 10.9 1.0 ND1 A:HIS63 2.0 10.0 1.0 ND1 A:HIS71 2.1 10.7 1.0 CG A:ASP83 2.8 10.1 1.0 CE1 A:HIS80 2.8 11.2 1.0 OD2 A:ASP83 2.8 8.8 1.0 CE1 A:HIS63 2.9 13.5 1.0 CE1 A:HIS71 2.9 11.8 1.0 CG A:HIS63 3.0 11.1 1.0 CG A:HIS80 3.0 7.1 1.0 CG A:HIS71 3.2 12.7 1.0 CB A:HIS63 3.4 9.3 1.0 CB A:HIS80 3.5 7.8 1.0 CB A:HIS71 3.7 12.9 1.0 NE2 A:HIS80 4.0 12.2 1.0 O A:LYS136 4.0 16.4 1.0 CA A:HIS71 4.0 12.7 1.0 NE2 A:HIS63 4.1 15.0 1.0 CD2 A:HIS80 4.1 10.2 1.0 NE2 A:HIS71 4.1 12.1 1.0 CD2 A:HIS63 4.1 13.8 1.0 CB A:ASP83 4.2 8.2 1.0 CD2 A:HIS71 4.3 12.9 1.0 CA A:ASP83 4.7 7.8 1.0 N A:HIS80 4.7 8.2 1.0 O A:HOH2165 4.7 11.9 1.0 N A:GLY72 4.7 11.8 1.0 CA A:HIS80 4.8 7.6 1.0 C A:LYS136 4.9 17.6 1.0 C A:HIS71 4.9 12.9 1.0 CA A:HIS63 5.0 8.3 1.0 N A:ASP83 5.0 8.5 1.0 N A:HIS71 5.0 13.0 1.0

Zinc binding site 3 out of 4 in the L38V SOD1 Mutant Complexed with Ump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of L38V SOD1 Mutant Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn154 b:16.8 occ:0.50 CU F:CU154 1.1 15.5 0.5 NE2 F:HIS120 1.9 10.3 1.0 NE2 F:HIS48 2.2 10.2 1.0 O2 F:SO4156 2.2 13.0 0.5 ND1 F:HIS46 2.3 12.4 1.0 CE1 F:HIS120 2.7 9.8 1.0 CE1 F:HIS48 2.8 10.7 1.0 CD2 F:HIS120 2.9 9.9 1.0 NE2 F:HIS63 3.1 15.7 1.0 O F:HOH2196 3.2 30.2 1.0 CE1 F:HIS46 3.3 11.7 1.0 CG F:HIS46 3.4 10.8 1.0 CD2 F:HIS48 3.4 10.7 1.0 S F:SO4156 3.5 13.5 0.5 CD2 F:HIS63 3.5 13.1 1.0 CB F:HIS46 3.7 10.7 1.0 O1 F:SO4156 3.8 14.4 0.5 ND1 F:HIS120 3.9 7.5 1.0 CG F:HIS120 4.0 7.7 1.0 CE1 F:HIS63 4.1 13.2 1.0 ND1 F:HIS48 4.1 8.5 1.0 O4 F:SO4156 4.4 18.4 0.5 CG F:HIS48 4.4 8.1 1.0 O3 F:SO4156 4.4 13.3 0.5 NE2 F:HIS46 4.4 12.5 1.0 O F:HOH2200 4.4 6.7 0.5 CD2 F:HIS46 4.5 12.5 1.0 CG1 F:VAL118 4.5 7.6 1.0 CB F:VAL118 4.6 6.2 1.0 CG F:HIS63 4.7 10.4 1.0 O F:HOH2198 4.8 19.1 1.0 ND1 F:HIS63 4.9 12.2 1.0 CA F:HIS46 5.0 7.6 1.0

Zinc binding site 4 out of 4 in the L38V SOD1 Mutant Complexed with Ump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of L38V SOD1 Mutant Complexed with Ump within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn155 b:9.3 occ:1.00 ND1 F:HIS80 1.9 8.9 1.0 ND1 F:HIS63 2.0 12.2 1.0 OD1 F:ASP83 2.0 9.8 1.0 ND1 F:HIS71 2.1 7.5 1.0 CG F:ASP83 2.8 9.1 1.0 CE1 F:HIS80 2.8 9.1 1.0 OD2 F:ASP83 2.8 10.9 1.0 CE1 F:HIS71 2.9 9.5 1.0 CE1 F:HIS63 2.9 13.2 1.0 CG F:HIS63 3.0 10.4 1.0 CG F:HIS80 3.0 8.2 1.0 CG F:HIS71 3.3 12.3 1.0 CB F:HIS63 3.4 8.2 1.0 CB F:HIS80 3.5 7.5 1.0 CB F:HIS71 3.7 11.5 1.0 O F:LYS136 3.9 18.9 1.0 NE2 F:HIS80 4.0 10.0 1.0 CA F:HIS71 4.0 11.6 1.0 NE2 F:HIS63 4.0 15.7 1.0 CD2 F:HIS80 4.1 9.4 1.0 NE2 F:HIS71 4.1 10.4 1.0 CD2 F:HIS63 4.1 13.1 1.0 CB F:ASP83 4.2 7.7 1.0 CD2 F:HIS71 4.3 11.3 1.0 N F:GLY72 4.7 11.7 1.0 N F:HIS80 4.7 9.7 1.0 CA F:ASP83 4.7 7.7 1.0 CA F:HIS80 4.8 8.1 1.0 O F:HOH2090 4.9 14.8 1.0 C F:LYS136 4.9 17.3 1.0 C F:HIS71 4.9 12.2 1.0 N F:HIS71 4.9 11.9 1.0 CA F:HIS63 4.9 7.9 1.0 N F:ASP83 5.0 7.1 1.0

S.V.Antonyuk, R.W.Strange, S.S.Hasnain. Structural Discovery of Small Molecule Binding Sites in Cu-Zn Human Superoxide Dismutase Familial Amyotrophic Lateral Sclerosis Mutants Provides Insights For Lead Optimization. J.Med.Chem. V. 53 1402 2010.
ISSN: ISSN 0022-2623
PubMed: 20067275
DOI: 10.1021/JM9017948