Copper in PDB 2wyt: 1.0 A Resolution Structure of L38V SOD1 Mutant

All present enzymatic activity of 1.0 A Resolution Structure of L38V SOD1 Mutant:
1.15.1.1;

The structure of 1.0 A Resolution Structure of L38V SOD1 Mutant, PDB code: 2wyt 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 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.690, 67.345, 52.577, 90.00, 106.57, 90.00
R / Rfree (%)	12.4 / 14.7

The structure of 1.0 A Resolution Structure of L38V SOD1 Mutant also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Copper atom in the 1.0 A Resolution Structure of L38V SOD1 Mutant (pdb code 2wyt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the 1.0 A Resolution Structure of L38V SOD1 Mutant, PDB code: 2wyt:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the 1.0 A Resolution Structure of L38V SOD1 Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of 1.0 A Resolution Structure of L38V SOD1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu154 b:7.1 occ:0.75 CU A:CU154 0.0 7.1 0.8 ZN A:ZN154A 1.1 6.6 0.2 HE2 A:HIS48 1.1 6.8 1.0 HD1 A:HIS46 1.2 7.7 1.0 CU A:CU154 1.2 8.6 0.1 HE2 A:HIS120 1.3 7.2 1.0 NE2 A:HIS48 1.9 7.3 1.0 ND1 A:HIS46 2.0 8.0 1.0 NE2 A:HIS120 2.0 7.7 1.0 HB2 A:HIS46 2.7 6.7 1.0 CE1 A:HIS48 2.9 7.0 1.0 CD2 A:HIS120 3.0 6.8 1.0 CE1 A:HIS46 3.0 8.9 1.0 CG A:HIS46 3.0 7.1 1.0 CD2 A:HIS48 3.0 6.8 1.0 HD2 A:HIS120 3.1 6.7 1.0 CE1 A:HIS120 3.1 7.6 1.0 HE2 A:HIS63 3.1 8.0 1.0 HB A:VAL118 3.1 5.9 1.0 HE1 A:HIS48 3.1 6.6 1.0 O1 A:SO4161 3.1 6.7 0.2 HE1 A:HIS46 3.1 8.1 1.0 HD2 A:HIS48 3.2 6.6 1.0 CB A:HIS46 3.3 8.2 1.0 HE1 A:HIS120 3.3 7.3 1.0 NE2 A:HIS63 3.5 8.5 1.0 O A:HOH2319 3.7 5.9 0.5 HD2 A:HIS63 3.7 8.2 1.0 CD2 A:HIS63 3.8 8.9 1.0 H A:HIS46 3.9 5.7 1.0 HG13 A:VAL118 3.9 6.7 1.0 HB3 A:HIS46 4.0 7.0 1.0 CB A:VAL118 4.0 5.9 1.0 ND1 A:HIS48 4.1 6.4 1.0 NE2 A:HIS46 4.1 7.7 1.0 CD2 A:HIS46 4.1 8.0 1.0 HG12 A:VAL118 4.1 6.5 1.0 CG A:HIS48 4.1 6.1 1.0 CG A:HIS120 4.1 6.4 1.0 ND1 A:HIS120 4.2 7.3 1.0 CA A:HIS46 4.2 6.0 1.0 N A:HIS46 4.2 5.7 1.0 CG1 A:VAL118 4.2 7.3 1.0 S A:SO4161 4.3 11.1 0.2 CE1 A:HIS63 4.4 7.1 1.0 O A:HOH2320 4.4 6.1 0.2 HG23 A:VAL118 4.4 6.1 1.0 O2 A:SO4161 4.5 12.0 0.2 O A:VAL118 4.5 6.2 1.0 O A:HIS46 4.5 6.0 1.0 C A:HIS46 4.6 5.4 1.0 CG2 A:VAL118 4.7 6.5 1.0 HE1 A:HIS63 4.7 6.9 1.0 HG22 A:VAL118 4.8 6.3 1.0 HD1 A:HIS48 4.8 6.2 1.0 CG A:HIS63 4.9 7.0 1.0 HE2 A:HIS46 4.9 7.5 1.0 HG2 A:ARG143 4.9 6.7 1.0 HD2 A:HIS46 4.9 7.4 1.0 HD1 A:HIS120 4.9 7.0 1.0 C A:VAL118 5.0 5.5 1.0

Copper binding site 2 out of 4 in the 1.0 A Resolution Structure of L38V SOD1 Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of 1.0 A Resolution Structure of L38V SOD1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu154 b:8.6 occ:0.05 CU A:CU154 0.0 8.6 0.1 ZN A:ZN154A 1.0 6.6 0.2 CU A:CU154 1.2 7.1 0.8 HD1 A:HIS46 1.4 7.7 1.0 ND1 A:HIS46 1.9 8.0 1.0 HE2 A:HIS63 1.9 8.0 1.0 HE2 A:HIS48 1.9 6.8 1.0 HE2 A:HIS120 1.9 7.2 1.0 O1 A:SO4161 2.2 6.7 0.2 NE2 A:HIS63 2.4 8.5 1.0 NE2 A:HIS120 2.5 7.7 1.0 CE1 A:HIS46 2.5 8.9 1.0 NE2 A:HIS48 2.5 7.3 1.0 HE1 A:HIS46 2.6 8.1 1.0 O A:HOH2319 2.6 5.9 0.5 CG A:HIS46 2.9 7.1 1.0 CD2 A:HIS63 3.0 8.9 1.0 HE1 A:HIS48 3.0 6.6 1.0 HD2 A:HIS63 3.1 8.2 1.0 HB2 A:HIS46 3.1 6.7 1.0 CE1 A:HIS48 3.1 7.0 1.0 CE1 A:HIS120 3.2 7.6 1.0 CE1 A:HIS63 3.3 7.1 1.0 HE1 A:HIS120 3.4 7.3 1.0 CD2 A:HIS120 3.4 6.8 1.0 CB A:HIS46 3.5 8.2 1.0 HE1 A:HIS63 3.6 6.9 1.0 NE2 A:HIS46 3.6 7.7 1.0 S A:SO4161 3.6 11.1 0.2 CD2 A:HIS48 3.7 6.8 1.0 HD2 A:HIS120 3.7 6.7 1.0 CD2 A:HIS46 3.8 8.0 1.0 O A:HOH2320 3.9 6.1 0.2 HD2 A:HIS48 4.0 6.6 1.0 CG A:HIS63 4.0 7.0 1.0 HB3 A:HIS46 4.1 7.0 1.0 O2 A:SO4161 4.1 12.0 0.2 ND1 A:HIS63 4.2 6.3 1.0 O A:HOH2276 4.3 11.1 0.2 ND1 A:HIS48 4.3 6.4 1.0 HE2 A:HIS46 4.3 7.5 1.0 ND1 A:HIS120 4.3 7.3 1.0 O4 A:SO4161 4.3 12.8 0.2 HB A:VAL118 4.3 5.9 1.0 O3 A:SO4161 4.4 9.7 0.2 CG A:HIS120 4.5 6.4 1.0 CG A:HIS48 4.6 6.1 1.0 HB3 A:ALA140 4.6 8.3 1.0 HD2 A:HIS46 4.7 7.4 1.0 O A:HOH2317 4.7 8.3 0.7 CA A:HIS46 4.8 6.0 1.0 O A:HOH2316 4.8 17.0 1.0 H A:HIS46 4.8 5.7 1.0 O A:THR137 4.9 9.6 1.0 HD1 A:HIS63 4.9 6.5 1.0 N A:HIS46 4.9 5.7 1.0 HD1 A:HIS48 5.0 6.2 1.0 HG13 A:VAL118 5.0 6.7 1.0

Copper binding site 3 out of 4 in the 1.0 A Resolution Structure of L38V SOD1 Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of 1.0 A Resolution Structure of L38V SOD1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu154 b:5.3 occ:0.55 CU F:CU154 0.0 5.3 0.6 CU F:CU154 0.9 12.1 0.1 HE2 F:HIS48 1.1 6.7 1.0 ZN F:ZN154A 1.2 6.9 0.2 HD1 F:HIS46 1.2 7.5 1.0 HE2 F:HIS120 1.3 6.8 1.0 NE2 F:HIS48 1.9 6.9 1.0 NE2 F:HIS120 2.0 7.1 1.0 ND1 F:HIS46 2.0 7.9 1.0 HB2 F:HIS46 2.7 6.5 1.0 CE1 F:HIS48 2.9 7.0 1.0 CD2 F:HIS120 2.9 6.9 1.0 CD2 F:HIS48 2.9 7.0 1.0 CG F:HIS46 3.0 7.1 1.0 CE1 F:HIS46 3.0 8.2 1.0 HB F:VAL118 3.0 5.4 1.0 HD2 F:HIS120 3.1 6.6 1.0 CE1 F:HIS120 3.1 7.2 1.0 HE1 F:HIS48 3.1 6.5 1.0 HE2 F:HIS63 3.1 8.6 1.0 HD2 F:HIS48 3.2 6.7 1.0 O1 F:SO4156 3.2 6.8 0.2 HE1 F:HIS46 3.2 7.7 1.0 CB F:HIS46 3.3 7.6 1.0 HE1 F:HIS120 3.3 7.0 1.0 NE2 F:HIS63 3.5 9.1 1.0 HD2 F:HIS63 3.6 8.7 1.0 O F:HOH2294 3.7 8.6 0.7 CD2 F:HIS63 3.8 9.7 1.0 HG13 F:VAL118 3.8 6.5 1.0 O F:HOH2297 3.8 15.8 0.5 CB F:VAL118 3.9 5.5 1.0 H F:HIS46 3.9 5.6 1.0 HB3 F:HIS46 4.0 6.6 1.0 HG12 F:VAL118 4.0 6.3 1.0 ND1 F:HIS48 4.1 6.2 1.0 CG F:HIS48 4.1 6.4 1.0 CG F:HIS120 4.1 6.7 1.0 CG1 F:VAL118 4.1 7.0 1.0 NE2 F:HIS46 4.1 7.7 1.0 CD2 F:HIS46 4.1 7.6 1.0 ND1 F:HIS120 4.1 7.0 1.0 CA F:HIS46 4.2 5.9 1.0 N F:HIS46 4.2 5.8 1.0 HG23 F:VAL118 4.4 5.9 1.0 S F:SO4156 4.4 9.3 0.2 CE1 F:HIS63 4.4 7.1 1.0 O F:VAL118 4.4 6.0 1.0 O F:HOH2296 4.5 10.2 0.5 O2 F:SO4156 4.5 9.7 0.2 O F:HIS46 4.5 5.5 1.0 C F:HIS46 4.6 5.5 1.0 CG2 F:VAL118 4.6 6.4 1.0 HG22 F:VAL118 4.8 6.0 1.0 HE1 F:HIS63 4.8 7.2 1.0 CG F:HIS63 4.8 7.2 1.0 HD1 F:HIS48 4.8 6.2 1.0 HG2 F:ARG143 4.9 6.7 1.0 HE2 F:HIS46 4.9 7.4 1.0 C F:VAL118 4.9 5.3 1.0 HD1 F:HIS120 4.9 6.7 1.0 HD2 F:HIS46 5.0 7.1 1.0

Copper binding site 4 out of 4 in the 1.0 A Resolution Structure of L38V SOD1 Mutant


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of 1.0 A Resolution Structure of L38V SOD1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu154 b:12.1 occ:0.15 CU F:CU154 0.0 12.1 0.1 ZN F:ZN154A 0.8 6.9 0.2 CU F:CU154 0.9 5.3 0.6 HD1 F:HIS46 1.4 7.5 1.0 HE2 F:HIS120 1.6 6.8 1.0 HE2 F:HIS48 1.6 6.7 1.0 ND1 F:HIS46 2.0 7.9 1.0 HE2 F:HIS63 2.2 8.6 1.0 NE2 F:HIS120 2.2 7.1 1.0 NE2 F:HIS48 2.3 6.9 1.0 O1 F:SO4156 2.4 6.8 0.2 NE2 F:HIS63 2.7 9.1 1.0 CE1 F:HIS46 2.7 8.2 1.0 HE1 F:HIS46 2.8 7.7 1.0 O F:HOH2294 2.9 8.6 0.7 HE1 F:HIS48 2.9 6.5 1.0 CE1 F:HIS48 2.9 7.0 1.0 CE1 F:HIS120 3.0 7.2 1.0 O F:HOH2297 3.1 15.8 0.5 HB2 F:HIS46 3.1 6.5 1.0 CG F:HIS46 3.1 7.1 1.0 HD2 F:HIS63 3.1 8.7 1.0 CD2 F:HIS63 3.1 9.7 1.0 HE1 F:HIS120 3.2 7.0 1.0 CD2 F:HIS120 3.2 6.9 1.0 CD2 F:HIS48 3.4 7.0 1.0 HD2 F:HIS120 3.5 6.6 1.0 CB F:HIS46 3.6 7.6 1.0 CE1 F:HIS63 3.6 7.1 1.0 S F:SO4156 3.7 9.3 0.2 HD2 F:HIS48 3.8 6.7 1.0 NE2 F:HIS46 3.9 7.7 1.0 O F:HOH2296 3.9 10.2 0.5 HB F:VAL118 4.0 5.4 1.0 HE1 F:HIS63 4.0 7.2 1.0 CD2 F:HIS46 4.0 7.6 1.0 O2 F:SO4156 4.0 9.7 0.2 ND1 F:HIS120 4.1 7.0 1.0 ND1 F:HIS48 4.1 6.2 1.0 HB3 F:HIS46 4.2 6.6 1.0 CG F:HIS63 4.2 7.2 1.0 CG F:HIS120 4.2 6.7 1.0 CG F:HIS48 4.4 6.4 1.0 ND1 F:HIS63 4.5 6.5 1.0 O4 F:SO4156 4.5 13.4 0.2 HG13 F:VAL118 4.5 6.5 1.0 HE2 F:HIS46 4.6 7.4 1.0 O3 F:SO4156 4.6 11.1 0.2 HB2 F:ALA140 4.7 8.8 1.0 HG12 F:VAL118 4.7 6.3 1.0 H F:HIS46 4.7 5.6 1.0 CA F:HIS46 4.7 5.9 1.0 CB F:VAL118 4.8 5.5 1.0 HD1 F:HIS120 4.8 6.7 1.0 N F:HIS46 4.8 5.8 1.0 HD1 F:HIS48 4.8 6.2 1.0 O F:HOH2290 4.8 10.2 0.8 CG1 F:VAL118 4.9 7.0 1.0 HD2 F:HIS46 4.9 7.1 1.0 O F:HOH2295 4.9 17.6 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