Cadmium in PDB 3x1y: Ras-Related Protein RAP1B(L9V) with Gppnhp

The structure of Ras-Related Protein RAP1B(L9V) with Gppnhp, PDB code: 3x1y 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)	35.42 / 1.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.600, 52.600, 60.720, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.9

The structure of Ras-Related Protein RAP1B(L9V) with Gppnhp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Cadmium atom in the Ras-Related Protein RAP1B(L9V) with Gppnhp (pdb code 3x1y). 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(L9V) with Gppnhp, PDB code: 3x1y:

Cadmium binding site 1 out of 1 in the Ras-Related Protein RAP1B(L9V) 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(L9V) with Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:9.7 occ:1.00 OE2 A:GLU156 2.3 11.1 1.0 O A:HOH318 2.4 15.0 1.0 OD2 A:ASP160 2.5 9.1 1.0 OD1 A:ASP160 2.5 8.7 1.0 O A:HOH325 2.5 15.0 1.0 CG A:ASP160 2.8 8.4 1.0 CD A:GLU156 3.3 10.1 1.0 CG A:GLU156 3.6 8.8 1.0 NH2 A:ARG163 3.9 12.3 1.0 O A:HOH448 3.9 30.2 1.0 O A:HOH482 4.2 29.2 1.0 CB A:ASP160 4.3 8.3 1.0 OE1 A:GLU156 4.4 10.8 1.0 O A:HOH402 4.5 22.6 1.0 O A:HOH324 4.6 12.9 1.0 CZ A:ARG163 4.8 12.1 1.0

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