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Cadmium in PDB 3v5s: Structure of Sodium/Calcium Exchanger From Methanococcus Jannaschii

Protein crystallography data

The structure of Structure of Sodium/Calcium Exchanger From Methanococcus Jannaschii, PDB code: 3v5s was solved by J.Liao, H.Li, W.Zeng, D.B.Sauer, R.Belmares, Y.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.20 / 3.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.990, 84.990, 181.634, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 30.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Sodium/Calcium Exchanger From Methanococcus Jannaschii (pdb code 3v5s). 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 Sodium/Calcium Exchanger From Methanococcus Jannaschii, PDB code: 3v5s:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3v5s

Go back to Cadmium Binding Sites List in 3v5s
Cadmium binding site 1 out of 2 in the Structure of Sodium/Calcium Exchanger From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Sodium/Calcium Exchanger From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd321

b:0.8
occ:0.50
CE1 A:HIS65 2.3 0.8 1.0
NE2 A:HIS65 3.2 0.4 1.0
ND1 A:HIS65 3.2 1.0 1.0
CD2 A:HIS65 4.3 0.9 1.0
CG A:HIS65 4.4 0.2 1.0
CE1 A:TYR63 4.7 1.0 1.0
O A:TYR63 4.7 0.1 1.0

Cadmium binding site 2 out of 2 in 3v5s

Go back to Cadmium Binding Sites List in 3v5s
Cadmium binding site 2 out of 2 in the Structure of Sodium/Calcium Exchanger From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Sodium/Calcium Exchanger From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd322

b:0.7
occ:1.00
OG A:SER77 2.3 1.0 1.0
OE2 A:GLU54 2.4 0.9 1.0
OD1 A:ASP240 2.5 0.6 1.0
OE1 A:GLU54 2.6 0.1 1.0
OG A:SER210 2.6 0.7 1.0
OD2 A:ASP240 2.7 0.9 1.0
CD A:GLU54 2.8 0.7 1.0
CG A:ASP240 2.9 0.3 1.0
OE2 A:GLU213 3.0 0.4 1.0
CD A:GLU213 3.2 0.1 1.0
OE1 A:GLU213 3.3 0.4 1.0
CB A:SER77 3.6 1.0 1.0
O A:SER77 3.9 0.2 1.0
OG A:SER51 3.9 0.2 1.0
CB A:SER210 4.0 0.7 1.0
CB A:SER51 4.1 0.9 1.0
CG A:GLU213 4.2 0.8 1.0
C A:SER77 4.3 0.8 1.0
OD1 A:ASN81 4.3 0.6 1.0
CG A:GLU54 4.3 0.4 1.0
CB A:ASP240 4.3 0.8 1.0
CA A:SER51 4.4 0.1 1.0
CB A:SER236 4.4 0.2 1.0
CA A:SER77 4.4 0.2 1.0
O A:SER236 4.5 0.8 1.0
CA A:SER210 4.6 0.4 1.0
CG A:ASN81 4.8 0.9 1.0
C A:SER236 4.8 0.7 1.0
ND2 A:ASN81 4.8 0.9 1.0
CB A:GLU213 4.9 0.8 1.0

Reference:

J.Liao, H.Li, W.Zeng, D.B.Sauer, R.Belmares, Y.Jiang. Structural Insight Into the Ion-Exchange Mechanism of the Sodium/Calcium Exchanger. Science V. 335 686 2012.
ISSN: ISSN 0036-8075
PubMed: 22323814
DOI: 10.1126/SCIENCE.1215759
Page generated: Sun Jan 24 09:56:06 2021

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