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Cadmium in PDB 4bcy: Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F

Enzymatic activity of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F

All present enzymatic activity of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F:
1.15.1.1;

Protein crystallography data

The structure of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F, PDB code: 4bcy was solved by W.Awad, K.Saraboji, J.Danielsson, L.Lang, M.Kurnik, S.L.Marklund, M.Oliveberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.19 / 1.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.870, 47.910, 81.180, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 20.3

Other elements in 4bcy:

The structure of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F (pdb code 4bcy). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F, PDB code: 4bcy:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 4bcy

Go back to Cadmium Binding Sites List in 4bcy
Cadmium binding site 1 out of 6 in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1156

b:23.9
occ:0.30
 O A:ALA1 2.6 28.4 1.0
N A:ALA1 2.6 40.5 1.0
CA A:ALA1 3.2 28.8 1.0
C A:ALA1 3.3 28.6 1.0
CB A:ALA1 3.6 28.4 1.0
NZ A:LYS3 3.9 36.2 1.0
N A:THR2 4.6 24.2 1.0

Cadmium binding site 2 out of 6 in 4bcy

Go back to Cadmium Binding Sites List in 4bcy
Cadmium binding site 2 out of 6 in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1157

b:72.5
occ:0.61
 OE2 A:GLU78 2.5 29.9 1.0
CD A:GLU78 3.2 32.1 1.0
OE1 A:GLU78 3.3 34.5 1.0
CG A:GLU78 4.4 29.8 1.0
CD A:ARG69 4.7 28.8 0.7
N A:LYS70 4.7 23.1 1.0
CD A:ARG69 4.7 29.8 0.3
CG A:LYS70 4.7 31.5 1.0
CA A:ARG69 4.8 24.8 0.3
CA A:ARG69 4.8 25.0 0.7

Cadmium binding site 3 out of 6 in 4bcy

Go back to Cadmium Binding Sites List in 4bcy
Cadmium binding site 3 out of 6 in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1158

b:40.4
occ:0.58
 OD2 A:ASP90 2.5 44.8 0.5
OD2 A:ASP92 2.6 53.6 1.0
OD1 A:ASP92 2.7 58.1 1.0
CG A:ASP92 3.0 56.0 1.0
CG A:ASP90 3.3 44.3 0.5
CD A:CD1159 3.3 38.3 0.3
OD1 A:ASP90 3.5 43.0 0.5
O A:HOH2069 4.0 37.4 1.0
CB A:VAL94 4.3 34.8 1.0
CG2 A:VAL94 4.4 40.4 1.0
CB A:ASP92 4.5 53.9 1.0
CB A:ASP90 4.5 45.7 1.0

Cadmium binding site 4 out of 6 in 4bcy

Go back to Cadmium Binding Sites List in 4bcy
Cadmium binding site 4 out of 6 in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1159

b:38.3
occ:0.34
 OD2 A:ASP90 2.5 44.8 0.5
O A:HOH2069 2.6 37.4 1.0
CD A:CD1158 3.3 40.4 0.6
CG A:ASP90 3.7 44.3 0.5
CB A:ASP90 4.3 45.7 1.0
OD1 A:ASP90 4.6 43.0 0.5
O A:VAL94 4.7 34.6 1.0
OD2 A:ASP96 4.8 47.5 1.0

Cadmium binding site 5 out of 6 in 4bcy

Go back to Cadmium Binding Sites List in 4bcy
Cadmium binding site 5 out of 6 in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1160

b:29.5
occ:0.37
 NE2 A:HIS110 2.4 26.3 0.8
CD2 A:HIS110 3.4 22.9 0.8
CE1 A:HIS110 3.4 32.2 0.8
CG A:HIS110 4.5 23.0 0.8
ND1 A:HIS110 4.5 27.3 0.8
O A:PRO66 4.7 27.4 1.0
CB A:ASP109 5.0 28.6 1.0

Cadmium binding site 6 out of 6 in 4bcy

Go back to Cadmium Binding Sites List in 4bcy
Cadmium binding site 6 out of 6 in the Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Monomeric Human Cu,Zn Superoxide Dismutase, Mutation H43F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1161

b:24.3
occ:0.29
 O A:HOH2070 2.5 26.7 1.0
O A:GLN153 2.6 37.0 0.6
C A:GLN153 3.6 36.4 0.6
CB A:ALA152 4.8 29.7 1.0
O A:ALA152 4.8 31.9 1.0
C A:ALA152 4.9 30.4 1.0
CA A:GLN153 4.9 31.3 0.6
N A:GLN153 4.9 27.2 0.6

Reference:

J.Danielsson, W.Awad, K.Saraboji, M.Kurnik, L.Lang, L.Leinartaite, S.L.Marklund, D.T.Logan, M.Oliveberg. Global Structural Motions From the Strain of A Single Hydrogen Bond. Proc.Natl.Acad.Sci.Usa V. 110 3829 2013.
ISSN: ISSN 0027-8424
PubMed: 23431167
DOI: 10.1073/PNAS.1217306110
Page generated: Sat Dec 12 08:24:03 2020

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