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Cadmium in PDB 5h4h: Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution

Protein crystallography data

The structure of Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution, PDB code: 5h4h was solved by A.Biswas, K.Hatti, N.Srinivasan, M.R.N.Murthy, K.Sekar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.85 / 2.23
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.970, 45.260, 53.620, 90.00, 104.75, 90.00
R / Rfree (%) 20.7 / 25.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution (pdb code 5h4h). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution, PDB code: 5h4h:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 5h4h

Go back to Cadmium Binding Sites List in 5h4h
Cadmium binding site 1 out of 2 in the Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:64.9
occ:1.00
OH A:TYR51 3.2 37.3 1.0
O B:LYS89 3.4 32.8 1.0
CA B:LYS89 3.8 35.3 1.0
C B:LYS89 4.0 35.2 1.0
CZ A:TYR51 4.4 38.5 1.0
OE1 B:GLU91 4.4 51.0 1.0
CB B:LYS89 4.5 34.1 1.0
CG B:LYS89 4.5 33.9 1.0
O B:ILE88 4.6 36.4 1.0
CE2 A:TYR51 4.9 37.3 1.0
N B:LYS89 4.9 34.4 1.0

Cadmium binding site 2 out of 2 in 5h4h

Go back to Cadmium Binding Sites List in 5h4h
Cadmium binding site 2 out of 2 in the Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Pin-Domain Protein (VAPC4 Toxin) From Pyrococcus Horikoshii Determined at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:59.5
occ:1.00
O B:PHE33 2.8 22.6 1.0
O B:LEU30 2.9 24.7 1.0
O B:ALA31 3.3 26.1 1.0
C B:PHE33 3.6 23.4 1.0
C B:ALA31 3.8 26.0 1.0
N B:PHE33 4.0 24.0 1.0
C B:LEU30 4.1 24.8 1.0
CA B:PHE33 4.4 23.7 1.0
CA B:ALA31 4.4 25.2 1.0
N B:THR34 4.4 23.4 1.0
N B:LYS32 4.4 25.8 1.0
C B:LYS32 4.5 24.9 1.0
N B:ALA31 4.7 25.5 1.0
OG1 B:THR34 4.7 25.3 1.0
CA B:THR34 4.7 24.2 1.0
CA B:LYS32 4.8 26.0 1.0

Reference:

K.Hatti, A.Biswas, S.Chaudhary, V.Dadireddy, K.Sekar, N.Srinivasan, M.R.N.Murthy. Structure Determination of Contaminant Proteins Using the Marathonmr Procedure J. Struct. Biol. V. 197 372 2017.
ISSN: ESSN 1095-8657
PubMed: 28167161
DOI: 10.1016/J.JSB.2017.01.005
Page generated: Sat Dec 12 08:26:45 2020

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