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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the 1.0 A Resolution Structure of L38V SOD1 Mutant, PDB code: 2wyt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2wyt

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Zinc 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 Zinc with other atoms in the Zn 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:Zn154

b:6.6
occ:0.20
CU A:CU154 1.0 8.6 0.1
CU A:CU154 1.1 7.1 0.8
HE2 A:HIS120 1.2 7.2 1.0
HE2 A:HIS48 1.6 6.8 1.0
NE2 A:HIS120 1.8 7.7 1.0
HD1 A:HIS46 1.9 7.7 1.0
O1 A:SO4161 2.1 6.7 0.2
NE2 A:HIS48 2.2 7.3 1.0
CE1 A:HIS120 2.4 7.6 1.0
HE1 A:HIS120 2.5 7.3 1.0
HE2 A:HIS63 2.5 8.0 1.0
HE1 A:HIS48 2.5 6.6 1.0
ND1 A:HIS46 2.6 8.0 1.0
CE1 A:HIS48 2.7 7.0 1.0
O A:HOH2319 2.8 5.9 0.5
CD2 A:HIS120 3.0 6.8 1.0
HE1 A:HIS46 3.1 8.1 1.0
NE2 A:HIS63 3.1 8.5 1.0
CE1 A:HIS46 3.2 8.9 1.0
S A:SO4161 3.2 11.1 0.2
O A:HOH2320 3.4 6.1 0.2
O2 A:SO4161 3.4 12.0 0.2
HD2 A:HIS120 3.4 6.7 1.0
HD2 A:HIS63 3.5 8.2 1.0
CD2 A:HIS48 3.5 6.8 1.0
CD2 A:HIS63 3.6 8.9 1.0
HB2 A:HIS46 3.6 6.7 1.0
ND1 A:HIS120 3.6 7.3 1.0
CG A:HIS46 3.7 7.1 1.0
HB A:VAL118 3.8 5.9 1.0
CG A:HIS120 3.9 6.4 1.0
HD2 A:HIS48 4.0 6.6 1.0
ND1 A:HIS48 4.0 6.4 1.0
O4 A:SO4161 4.1 12.8 0.2
O3 A:SO4161 4.1 9.7 0.2
CE1 A:HIS63 4.2 7.1 1.0
HG12 A:VAL118 4.2 6.5 1.0
CB A:HIS46 4.2 8.2 1.0
HG13 A:VAL118 4.2 6.7 1.0
O A:HOH2317 4.3 8.3 0.7
HD1 A:HIS120 4.3 7.0 1.0
CG A:HIS48 4.4 6.1 1.0
O A:HOH2276 4.4 11.1 0.2
NE2 A:HIS46 4.4 7.7 1.0
HG2 A:ARG143 4.5 6.7 1.0
HE1 A:HIS63 4.5 6.9 1.0
CG1 A:VAL118 4.5 7.3 1.0
HE A:ARG143 4.5 6.6 1.0
HB3 A:ALA140 4.6 8.3 1.0
CB A:VAL118 4.6 5.9 1.0
HD1 A:HIS48 4.6 6.2 1.0
CD2 A:HIS46 4.7 8.0 1.0
O A:HOH2316 4.7 17.0 1.0
HG23 A:VAL118 4.7 6.1 1.0
CG A:HIS63 4.8 7.0 1.0
HB3 A:HIS46 4.8 7.0 1.0
HH21 A:ARG143 4.9 6.4 1.0
NE A:ARG143 4.9 7.0 1.0
H A:HIS46 5.0 5.7 1.0

Zinc binding site 2 out of 4 in 2wyt

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Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:5.7
occ:1.00
HD1 A:HIS71 1.2 5.7 1.0
HD1 A:HIS63 1.2 6.5 1.0
HD1 A:HIS80 1.3 5.9 1.0
OD1 A:ASP83 2.0 5.6 1.0
ND1 A:HIS80 2.0 6.0 1.0
ND1 A:HIS71 2.0 5.8 1.0
ND1 A:HIS63 2.0 6.3 1.0
CG A:ASP83 2.7 6.2 1.0
OD2 A:ASP83 2.8 6.0 1.0
CE1 A:HIS80 2.9 6.4 1.0
CE1 A:HIS71 2.9 5.9 1.0
CE1 A:HIS63 3.0 7.1 1.0
HE1 A:HIS71 3.0 5.7 1.0
HB2 A:HIS80 3.0 5.6 1.0
HE1 A:HIS80 3.0 6.2 1.0
CG A:HIS80 3.1 5.8 1.0
CG A:HIS63 3.1 7.0 1.0
HE1 A:HIS63 3.1 6.9 1.0
CG A:HIS71 3.2 6.5 1.0
HA A:HIS71 3.3 6.4 1.0
HB3 A:HIS63 3.3 6.3 1.0
HB2 A:HIS63 3.3 6.2 1.0
HB2 A:HIS71 3.4 6.3 1.0
CB A:HIS63 3.5 6.8 1.0
CB A:HIS80 3.5 5.8 1.0
CB A:HIS71 3.6 6.8 1.0
O A:LYS136 3.9 9.7 1.0
CA A:HIS71 4.0 6.5 1.0
NE2 A:HIS80 4.0 7.0 1.0
HB3 A:HIS80 4.0 5.6 1.0
H A:HIS80 4.0 5.7 1.0
NE2 A:HIS71 4.1 6.0 1.0
NE2 A:HIS63 4.1 8.5 1.0
CD2 A:HIS80 4.1 6.6 1.0
CB A:ASP83 4.2 6.1 1.0
CD2 A:HIS63 4.2 8.9 1.0
H A:GLY72 4.2 6.3 1.0
CD2 A:HIS71 4.2 6.9 1.0
HA A:ASP83 4.3 5.9 1.0
HB3 A:ASP83 4.6 5.9 1.0
HB3 A:HIS71 4.6 6.3 1.0
HA A:THR137 4.7 8.2 1.0
CA A:ASP83 4.7 6.1 1.0
HB2 A:ASP83 4.7 5.9 1.0
N A:HIS80 4.7 5.9 1.0
HE2 A:HIS80 4.8 6.6 1.0
CA A:HIS80 4.8 5.8 1.0
N A:GLY72 4.8 6.5 1.0
HD2 A:HIS46 4.8 7.4 1.0
HE2 A:HIS71 4.8 5.8 1.0
HE2 A:HIS63 4.9 8.0 1.0
C A:LYS136 4.9 8.2 1.0
O A:HOH2149 4.9 4.9 0.3
C A:HIS71 4.9 6.4 1.0
N A:ASP83 4.9 5.7 1.0
N A:HIS71 4.9 6.9 1.0
CD2 A:HIS46 5.0 8.0 1.0
HD2 A:HIS80 5.0 6.3 1.0
HB3 A:HIS46 5.0 7.0 1.0

Zinc binding site 3 out of 4 in 2wyt

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Zinc 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 Zinc with other atoms in the Zn 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:Zn154

b:6.9
occ:0.20
CU F:CU154 0.8 12.1 0.1
CU F:CU154 1.2 5.3 0.6
HE2 F:HIS120 1.2 6.8 1.0
HE2 F:HIS48 1.6 6.7 1.0
NE2 F:HIS120 1.8 7.1 1.0
O1 F:SO4156 2.1 6.8 0.2
HD1 F:HIS46 2.1 7.5 1.0
NE2 F:HIS48 2.2 6.9 1.0
CE1 F:HIS120 2.3 7.2 1.0
HE1 F:HIS120 2.4 7.0 1.0
HE1 F:HIS48 2.5 6.5 1.0
HE2 F:HIS63 2.5 8.6 1.0
CE1 F:HIS48 2.6 7.0 1.0
O F:HOH2297 2.6 15.8 0.5
ND1 F:HIS46 2.7 7.9 1.0
O F:HOH2294 2.9 8.6 0.7
CD2 F:HIS120 3.0 6.9 1.0
NE2 F:HIS63 3.1 9.1 1.0
S F:SO4156 3.2 9.3 0.2
HE1 F:HIS46 3.2 7.7 1.0
O F:HOH2296 3.3 10.2 0.5
CE1 F:HIS46 3.3 8.2 1.0
O2 F:SO4156 3.3 9.7 0.2
HD2 F:HIS63 3.4 8.7 1.0
HD2 F:HIS120 3.5 6.6 1.0
CD2 F:HIS48 3.5 7.0 1.0
CD2 F:HIS63 3.5 9.7 1.0
ND1 F:HIS120 3.6 7.0 1.0
HB2 F:HIS46 3.7 6.5 1.0
HB F:VAL118 3.8 5.4 1.0
CG F:HIS46 3.9 7.1 1.0
CG F:HIS120 3.9 6.7 1.0
ND1 F:HIS48 3.9 6.2 1.0
HD2 F:HIS48 4.0 6.7 1.0
O4 F:SO4156 4.1 13.4 0.2
HG13 F:VAL118 4.1 6.5 1.0
HG12 F:VAL118 4.1 6.3 1.0
O3 F:SO4156 4.2 11.1 0.2
CE1 F:HIS63 4.2 7.1 1.0
HD1 F:HIS120 4.2 6.7 1.0
CB F:HIS46 4.3 7.6 1.0
HG2 F:ARG143 4.3 6.7 1.0
O F:HOH2290 4.4 10.2 0.8
CG F:HIS48 4.4 6.4 1.0
CG1 F:VAL118 4.4 7.0 1.0
NE2 F:HIS46 4.5 7.7 1.0
HE1 F:HIS63 4.5 7.2 1.0
CB F:VAL118 4.5 5.5 1.0
HD1 F:HIS48 4.6 6.2 1.0
HB2 F:ALA140 4.6 8.8 1.0
HG23 F:VAL118 4.7 5.9 1.0
HE F:ARG143 4.7 7.0 1.0
O F:HOH2292 4.7 18.0 0.5
O F:HOH2295 4.7 17.6 1.0
CG F:HIS63 4.7 7.2 1.0
CD2 F:HIS46 4.8 7.6 1.0
HH21 F:ARG143 4.8 6.7 1.0
NE F:ARG143 4.9 7.7 1.0
HB3 F:HIS46 4.9 6.6 1.0

Zinc binding site 4 out of 4 in 2wyt

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Zinc 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 Zinc with other atoms in the Zn 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:Zn155

b:5.7
occ:1.00
HD1 F:HIS63 1.2 6.6 1.0
HD1 F:HIS71 1.2 5.6 1.0
HD1 F:HIS80 1.3 5.7 1.0
OD1 F:ASP83 1.9 5.9 1.0
ND1 F:HIS63 2.0 6.5 1.0
ND1 F:HIS80 2.0 5.9 1.0
ND1 F:HIS71 2.1 6.0 1.0
CG F:ASP83 2.7 5.6 1.0
OD2 F:ASP83 2.9 6.2 1.0
CE1 F:HIS71 2.9 5.7 1.0
CE1 F:HIS80 2.9 6.2 1.0
CE1 F:HIS63 3.0 7.1 1.0
HE1 F:HIS71 3.0 5.7 1.0
HB2 F:HIS80 3.0 5.4 1.0
CG F:HIS63 3.1 7.2 1.0
HE1 F:HIS80 3.1 6.0 1.0
CG F:HIS80 3.1 5.7 1.0
HE1 F:HIS63 3.1 7.2 1.0
CG F:HIS71 3.2 6.1 1.0
HB3 F:HIS63 3.3 6.4 1.0
HA F:HIS71 3.3 6.5 1.0
HB2 F:HIS63 3.3 6.4 1.0
HB2 F:HIS71 3.4 6.3 1.0
CB F:HIS63 3.5 7.0 1.0
CB F:HIS80 3.5 5.6 1.0
CB F:HIS71 3.7 6.6 1.0
O F:LYS136 3.9 10.3 1.0
CA F:HIS71 4.0 6.8 1.0
NE2 F:HIS80 4.0 7.4 1.0
HB3 F:HIS80 4.0 5.4 1.0
H F:HIS80 4.1 5.6 1.0
NE2 F:HIS71 4.1 6.3 1.0
NE2 F:HIS63 4.1 9.1 1.0
CD2 F:HIS80 4.1 6.7 1.0
CD2 F:HIS63 4.2 9.7 1.0
CB F:ASP83 4.2 5.7 1.0
H F:GLY72 4.2 6.3 1.0
CD2 F:HIS71 4.2 6.3 1.0
HA F:ASP83 4.3 5.5 1.0
HB3 F:ASP83 4.5 5.3 1.0
HB3 F:HIS71 4.6 6.4 1.0
CA F:ASP83 4.7 5.5 1.0
HB2 F:ASP83 4.7 5.4 1.0
HD2 F:HIS46 4.7 7.1 1.0
HA F:THR137 4.7 8.8 1.0
HE2 F:HIS80 4.8 6.8 1.0
N F:HIS80 4.8 5.6 1.0
CA F:HIS80 4.8 5.5 1.0
N F:GLY72 4.8 6.5 1.0
O F:HOH2270 4.8 8.2 0.5
HE2 F:HIS71 4.8 6.0 1.0
HE2 F:HIS63 4.9 8.6 1.0
CD2 F:HIS46 4.9 7.6 1.0
C F:LYS136 4.9 8.9 1.0
N F:ASP83 4.9 5.6 1.0
C F:HIS71 4.9 6.5 1.0
HB3 F:HIS46 5.0 6.6 1.0
HD2 F:HIS80 5.0 6.5 1.0
CA F:HIS63 5.0 6.4 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: Sat Sep 26 04:28:54 2020
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