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Cadmium in PDB 4g1a: Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster

Protein crystallography data

The structure of Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster, PDB code: 4g1a was solved by S.Ni, M.A.Kennedy, M.Y.Ogawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.05 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 30.762, 35.204, 64.123, 90.00, 97.49, 90.00
R / Rfree (%) 19.1 / 25.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster (pdb code 4g1a). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster, PDB code: 4g1a:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 4g1a

Go back to Cadmium Binding Sites List in 4g1a
Cadmium binding site 1 out of 4 in the Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:12.7
occ:1.00
OE1 A:GLU20 1.9 14.0 1.0
SG A:CYS19 2.5 25.2 1.0
SG B:CYS16 2.6 14.0 1.0
CD A:GLU20 2.7 13.4 1.0
SG B:CYS19 2.7 23.6 1.0
OE2 A:GLU20 2.7 14.6 1.0
CB A:CYS19 3.3 17.6 1.0
CB B:CYS16 3.4 12.9 1.0
CB B:CYS19 3.5 17.7 1.0
CA B:CYS16 3.8 13.8 1.0
CD C:CD101 3.9 13.4 1.0
CD B:CD101 4.0 13.1 1.0
CD A:CD102 4.0 13.3 1.0
CG A:GLU20 4.2 12.8 1.0
N A:GLU20 4.3 15.7 1.0
CB A:CYS16 4.4 14.3 1.0
SG C:CYS19 4.4 25.9 1.0
C A:CYS19 4.5 16.1 1.0
O B:LYS15 4.5 14.2 1.0
CA A:CYS19 4.5 16.9 1.0
SG A:CYS16 4.5 12.9 1.0
N B:CYS16 4.6 13.6 1.0
CD1 A:ILE23 4.8 13.5 1.0
C B:LYS15 4.8 14.4 1.0
CA B:CYS19 4.9 16.6 1.0
C B:CYS16 4.9 14.2 1.0
SG C:CYS16 4.9 13.0 1.0
CA A:GLU20 4.9 14.3 1.0
O A:CYS16 5.0 13.9 1.0

Cadmium binding site 2 out of 4 in 4g1a

Go back to Cadmium Binding Sites List in 4g1a
Cadmium binding site 2 out of 4 in the Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:13.3
occ:1.00
SG A:CYS16 2.4 12.9 1.0
SG B:CYS16 2.4 14.0 1.0
O A:HOH202 2.5 8.9 1.0
SG C:CYS16 2.5 13.0 1.0
CB A:CYS16 3.3 14.3 1.0
CB B:CYS16 3.3 12.9 1.0
CB C:CYS16 3.4 15.5 1.0
CD A:CD101 4.0 12.7 1.0
CD C:CD101 4.0 13.4 1.0
CD B:CD101 4.0 13.1 1.0
CA A:CYS16 4.8 13.8 1.0
CA B:CYS16 4.8 13.8 1.0
CA C:CYS16 4.8 15.9 1.0
SG C:CYS19 4.8 25.9 1.0
SG B:CYS19 4.9 23.6 1.0

Cadmium binding site 3 out of 4 in 4g1a

Go back to Cadmium Binding Sites List in 4g1a
Cadmium binding site 3 out of 4 in the Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd101

b:13.1
occ:1.00
OE1 B:GLU20 2.1 16.5 1.0
SG B:CYS19 2.4 23.6 1.0
SG C:CYS19 2.5 25.9 1.0
OE2 B:GLU20 2.5 14.2 1.0
CD B:GLU20 2.6 13.5 1.0
SG C:CYS16 2.6 13.0 1.0
CB C:CYS16 3.4 15.5 1.0
CB C:CYS19 3.5 18.3 1.0
CA C:CYS16 3.8 15.9 1.0
CD A:CD101 4.0 12.7 1.0
CD C:CD101 4.0 13.4 1.0
CD A:CD102 4.0 13.3 1.0
CB B:CYS19 4.0 17.7 1.0
CG B:GLU20 4.2 13.7 1.0
N B:GLU20 4.2 13.2 1.0
CB B:CYS16 4.5 12.9 1.0
CA C:CYS19 4.5 16.9 1.0
O C:LYS15 4.5 17.9 1.0
SG A:CYS19 4.6 25.2 1.0
N C:CYS16 4.6 15.9 1.0
C B:CYS19 4.6 15.2 1.0
SG B:CYS16 4.6 14.0 1.0
CD1 B:ILE23 4.8 12.9 1.0
CA B:CYS19 4.8 16.6 1.0
SG A:CYS16 4.8 12.9 1.0
C C:LYS15 4.8 16.7 1.0
O B:HOH201 4.9 24.4 1.0
CA B:GLU20 4.9 12.9 1.0
C C:CYS16 5.0 16.3 1.0

Cadmium binding site 4 out of 4 in 4g1a

Go back to Cadmium Binding Sites List in 4g1a
Cadmium binding site 4 out of 4 in the Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Metal-Binding Properties of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolated Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd101

b:13.4
occ:1.00
OE2 C:GLU20 2.2 16.9 1.0
SG C:CYS19 2.4 25.9 1.0
SG A:CYS19 2.6 25.2 1.0
SG A:CYS16 2.6 12.9 1.0
OE1 C:GLU20 2.6 16.8 1.0
CD C:GLU20 2.7 14.8 1.0
CB C:CYS19 3.2 18.3 1.0
CB A:CYS16 3.3 14.3 1.0
CB A:CYS19 3.4 17.6 1.0
CA A:CYS16 3.8 13.8 1.0
CD A:CD101 3.9 12.7 1.0
CD B:CD101 4.0 13.1 1.0
CD A:CD102 4.0 13.3 1.0
CG C:GLU20 4.2 13.2 1.0
N C:GLU20 4.2 14.9 1.0
CA C:CYS19 4.4 16.9 1.0
C C:CYS19 4.4 15.8 1.0
O A:LYS15 4.5 13.7 1.0
CB C:CYS16 4.6 15.5 1.0
CA A:CYS19 4.6 16.9 1.0
N A:CYS16 4.6 13.7 1.0
SG C:CYS16 4.7 13.0 1.0
SG B:CYS19 4.8 23.6 1.0
SG B:CYS16 4.8 14.0 1.0
C A:LYS15 4.8 14.1 1.0
CA C:GLU20 4.9 14.4 1.0
CD1 C:ILE23 4.9 10.9 1.0
C A:CYS16 4.9 14.1 1.0
CB C:GLU20 5.0 14.2 1.0

Reference:

D.V.Zaytsev, V.A.Morozov, J.Fan, X.Zhu, M.Mukherjee, S.Ni, M.A.Kennedy, M.Y.Ogawa. Metal-Binding Properties and Structural Characterization of A Self-Assembled Coiled Coil: Formation of A Polynuclear Cd-Thiolate Cluster. J.Inorg.Biochem. V.119C 1 2012.
ISSN: ISSN 0162-0134
PubMed: 23160144
DOI: 10.1016/J.JINORGBIO.2012.10.010
Page generated: Sat Dec 12 08:24:34 2020

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