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Cadmium in PDB 3kxd: Crystal Structure of the Mthk Rck in Complex with Cadmium

Protein crystallography data

The structure of Crystal Structure of the Mthk Rck in Complex with Cadmium, PDB code: 3kxd was solved by H.Dvir, S.Choe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.83 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.022, 38.293, 96.634, 90.00, 95.10, 90.00
R / Rfree (%) 18.4 / 25.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Mthk Rck in Complex with Cadmium (pdb code 3kxd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of the Mthk Rck in Complex with Cadmium, PDB code: 3kxd:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3kxd

Go back to Cadmium Binding Sites List in 3kxd
Cadmium binding site 1 out of 4 in the Crystal Structure of the Mthk Rck in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Mthk Rck in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:95.2
occ:1.00
OD2 A:ASP184 2.6 25.3 1.0
OD1 A:ASP184 2.6 22.1 1.0
OE2 A:GLU210 2.7 41.7 1.0
CG A:ASP184 3.0 20.9 1.0
CD A:GLU210 3.1 38.0 1.0
OE2 A:GLU212 3.2 55.5 1.0
OE1 A:GLU210 3.2 42.5 1.0
OG A:SER124 3.8 31.3 1.0
CB A:SER124 3.9 26.2 1.0
O A:HOH4 4.1 11.4 1.0
CG A:GLU210 4.2 26.8 1.0
OG A:SER126 4.3 30.5 1.0
CD A:GLU212 4.3 56.3 1.0
CE1 B:PHE232 4.4 49.6 1.0
CB A:ASP184 4.5 20.6 1.0
CB A:GLU210 4.6 20.9 1.0
CG A:GLU212 4.6 45.3 1.0
CD1 B:PHE232 4.7 44.0 1.0
CB A:SER126 4.7 24.4 1.0

Cadmium binding site 2 out of 4 in 3kxd

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Cadmium binding site 2 out of 4 in the Crystal Structure of the Mthk Rck in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Mthk Rck in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:0.3
occ:1.00
NE2 A:HIS161 1.9 42.9 1.0
O A:GLU144 2.5 40.4 1.0
CE1 A:HIS161 2.6 42.8 1.0
OE1 A:GLU144 2.7 38.3 1.0
CD2 A:HIS161 3.1 37.0 1.0
C A:GLU144 3.4 36.0 1.0
CA A:GLU144 3.6 32.3 1.0
ND1 A:HIS161 3.7 42.3 1.0
CD A:GLU144 3.8 38.2 1.0
CG A:HIS161 4.0 36.9 1.0
CG A:GLU144 4.2 36.5 1.0
CB A:GLU144 4.3 33.6 1.0
N A:ASP145 4.6 37.9 1.0
N A:GLU146 4.7 47.3 1.0
OE2 A:GLU144 4.9 41.1 1.0
O A:ALA143 4.9 24.6 1.0
CA A:ASP145 5.0 42.6 1.0
N A:GLU144 5.0 27.4 1.0
CB A:GLU146 5.0 51.4 1.0

Cadmium binding site 3 out of 4 in 3kxd

Go back to Cadmium Binding Sites List in 3kxd
Cadmium binding site 3 out of 4 in the Crystal Structure of the Mthk Rck in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Mthk Rck in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:0.7
occ:1.00
OE1 A:GLU326 2.6 53.0 1.0
OD2 B:ASP305 2.7 70.5 1.0
OE2 A:GLU326 2.9 62.1 1.0
O A:GLY290 3.0 51.9 1.0
CD A:GLU326 3.1 57.0 1.0
CG B:ASP305 3.3 69.5 1.0
NE A:ARG262 3.4 68.5 1.0
OD1 B:ASP305 3.8 70.2 1.0
NH2 A:ARG262 3.9 77.2 1.0
C A:GLY290 4.0 52.5 1.0
CB B:ASP305 4.1 66.8 1.0
CZ A:ARG262 4.1 74.0 1.0
CD A:ARG262 4.3 65.9 1.0
CA A:GLY322 4.3 45.6 1.0
CA A:GLY290 4.5 56.6 1.0
CG A:GLU326 4.6 58.8 1.0
O A:ILE321 4.7 40.9 1.0
N A:LYS323 4.7 52.7 1.0
CE A:LYS323 5.0 69.9 1.0

Cadmium binding site 4 out of 4 in 3kxd

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Cadmium binding site 4 out of 4 in the Crystal Structure of the Mthk Rck in Complex with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Mthk Rck in Complex with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd601

b:71.9
occ:1.00
OE2 B:GLU210 2.5 42.9 1.0
OD2 B:ASP184 2.8 32.6 1.0
O B:HOH47 2.8 20.4 1.0
OD1 B:ASP184 2.8 29.2 1.0
CD B:GLU210 3.0 39.1 1.0
CG B:ASP184 3.2 29.3 1.0
OE1 B:GLU210 3.3 38.8 1.0
O B:HOH113 3.3 27.7 1.0
O B:HOH2 3.8 2.8 1.0
OG B:SER124 3.9 32.3 1.0
CE1 A:PHE232 3.9 49.4 1.0
CB B:SER124 4.1 34.1 1.0
OG B:SER126 4.1 38.5 1.0
CG B:GLU210 4.3 32.8 1.0
CD1 A:PHE232 4.3 46.5 1.0
CB B:SER126 4.4 29.7 1.0
CB B:ASP184 4.7 25.7 1.0
CZ A:PHE232 4.7 51.2 1.0
CB B:GLU210 5.0 26.2 1.0

Reference:

H.Dvir, E.Valera, S.Choe. Structure of the Mthk Rck in Complex with Cadmium. J.Struct.Biol. V. 171 231 2010.
ISSN: ISSN 1047-8477
PubMed: 20371380
DOI: 10.1016/J.JSB.2010.03.020
Page generated: Wed Oct 28 10:03:41 2020
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