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Cadmium in PDB 3x1x: Ras-Related Protein RAP1B with Gppnhp

Protein crystallography data

The structure of Ras-Related Protein RAP1B with Gppnhp, PDB code: 3x1x was solved by H.Noguchi, T.Ikegami, S.Y.Park, J.R.H.Tame, S.Unzai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.90 / 1.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.722, 52.460, 60.790, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 21.1

Other elements in 3x1x:

The structure of Ras-Related Protein RAP1B with Gppnhp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Ras-Related Protein RAP1B with Gppnhp (pdb code 3x1x). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Ras-Related Protein RAP1B with Gppnhp, PDB code: 3x1x:

Cadmium binding site 1 out of 1 in 3x1x

Go back to Cadmium Binding Sites List in 3x1x
Cadmium binding site 1 out of 1 in the Ras-Related Protein RAP1B with Gppnhp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Ras-Related Protein RAP1B with Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:10.5
occ:1.00
OE2 A:GLU156 2.4 11.9 1.0
OD1 A:ASP160 2.5 10.0 1.0
OD2 A:ASP160 2.5 10.2 1.0
O A:HOH367 2.5 14.1 1.0
O A:HOH366 2.5 13.5 1.0
CG A:ASP160 2.8 9.8 1.0
CD A:GLU156 3.3 11.2 1.0
CG A:GLU156 3.5 10.2 1.0
NH2 A:ARG163 3.9 12.8 1.0
O A:HOH402 4.0 24.6 1.0
O A:HOH365 4.3 16.4 1.0
CB A:ASP160 4.3 9.5 1.0
O A:HOH403 4.4 15.2 1.0
OE1 A:GLU156 4.4 11.7 1.0
O A:HOH401 4.6 18.8 1.0
O A:HOH332 4.6 14.1 1.0
O A:HOH436 4.6 30.7 1.0
CZ A:ARG163 4.8 12.8 1.0
O A:HOH407 4.9 25.9 1.0

Reference:

H.Noguchi, T.Ikegami, A.Nagadoi, Y.O.Kamatari, S.Y.Park, J.R.Tame, S.Unzai. The Structure and Conformational Switching of RAP1B Biochem.Biophys.Res.Commun. V. 462 46 2015.
ISSN: ISSN 0006-291X
PubMed: 25935485
DOI: 10.1016/J.BBRC.2015.04.103
Page generated: Sat Dec 12 08:23:45 2020

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