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Cadmium in PDB 3po0: Crystal Structure of SAMP1 From Haloferax Volcanii

Protein crystallography data

The structure of Crystal Structure of SAMP1 From Haloferax Volcanii, PDB code: 3po0 was solved by Y.J.Jeong, B.-C.Jeong, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.19 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.881, 42.251, 43.568, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.3

Other elements in 3po0:

The structure of Crystal Structure of SAMP1 From Haloferax Volcanii also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of SAMP1 From Haloferax Volcanii (pdb code 3po0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of SAMP1 From Haloferax Volcanii, PDB code: 3po0:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3po0

Go back to Cadmium Binding Sites List in 3po0
Cadmium binding site 1 out of 2 in the Crystal Structure of SAMP1 From Haloferax Volcanii


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 SAMP1 From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd89

b:16.9
occ:1.00
OD1 A:ASP55 2.3 18.1 1.0
ND1 A:HIS56 2.4 19.6 1.0
CE1 A:HIS56 3.3 18.9 1.0
CG A:ASP55 3.4 21.6 1.0
CG A:HIS56 3.5 19.1 1.0
OD2 A:ASP55 3.7 24.2 1.0
CB A:HIS56 3.8 17.8 1.0
N A:HIS56 4.2 16.9 1.0
O A:HOH112 4.3 25.6 1.0
NE2 A:HIS56 4.4 19.4 1.0
CD2 A:HIS56 4.6 18.9 1.0
CA A:HIS56 4.6 17.4 1.0
N A:ASP55 4.7 19.6 1.0
CB A:ASP55 4.8 19.1 1.0
C A:ASP55 4.9 21.4 1.0

Cadmium binding site 2 out of 2 in 3po0

Go back to Cadmium Binding Sites List in 3po0
Cadmium binding site 2 out of 2 in the Crystal Structure of SAMP1 From Haloferax Volcanii


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 SAMP1 From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd90

b:61.1
occ:1.00
OD2 A:ASP30 2.4 25.0 1.0
OD1 A:ASP30 2.5 25.1 1.0
CG A:ASP30 2.8 25.8 1.0
OG1 A:THR27 4.2 22.6 1.0
CB A:ASP30 4.3 21.5 1.0
O A:HOH99 4.4 29.0 1.0
O A:HOH153 4.4 38.9 1.0
CG2 A:THR27 4.7 27.3 1.0

Reference:

Y.J.Jeong, B.-C.Jeong, H.K.Song. Crystal Structure of Ubiquitin-Like Small Archaeal Modifier Protein 1 (SAMP1) From Haloferax Volcanii. Biochem.Biophys.Res.Commun. V. 405 112 2011.
ISSN: ISSN 0006-291X
PubMed: 21216237
DOI: 10.1016/J.BBRC.2011.01.004
Page generated: Sat Dec 12 08:22:55 2020

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