Atomistry » Copper » PDB 2vr7-2xv0 » 2wyt
Atomistry »
  Copper »
    PDB 2vr7-2xv0 »
      2wyt »

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

Other elements in 2wyt:

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

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

Go back to Copper Binding Sites List in 2wyt
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

Go back to Copper Binding Sites List in 2wyt
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

Go back to Copper Binding Sites List in 2wyt
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: Sun Dec 13 11:07:27 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy