Atomistry » Cadmium » PDB 3umi-3zi7 » 3x1y
Atomistry »
  Cadmium »
    PDB 3umi-3zi7 »
      3x1y »

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

Protein crystallography data

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

Other elements in 3x1y:

The structure of Ras-Related Protein RAP1B(L9V) 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(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 3x1y

Go back to Cadmium Binding Sites List in 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

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: Sun Jan 24 09:56:22 2021

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy