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

Enzymatic activity of 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;

Protein crystallography data

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

Copper Binding Sites:

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 2wyt

Go back to Copper Binding Sites List in 2wyt
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 2wyt

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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 2wyt

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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 2wyt

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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

Reference:

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
Page generated: Thu Sep 3 16:53:13 2020
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