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Cadmium in PDB 4q2l: Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain

Protein crystallography data

The structure of Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain, PDB code: 4q2l was solved by X.C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.04 / 1.07
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 34.970, 61.134, 70.391, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 19.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain (pdb code 4q2l). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain, PDB code: 4q2l:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 4q2l

Go back to Cadmium Binding Sites List in 4q2l
Cadmium binding site 1 out of 2 in the Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd103

b:19.0
occ:1.00
ND1 A:HIS44 2.3 18.6 1.0
O A:HOH1039 2.4 21.9 1.0
O A:HOH1040 2.5 27.1 1.0
O A:ACY101 2.6 31.7 1.0
OXT A:ACY101 2.7 30.5 1.0
C A:ACY101 3.0 30.1 1.0
CE1 A:HIS44 3.1 18.1 1.0
CG A:HIS44 3.4 17.4 1.0
CB A:HIS44 3.9 17.1 1.0
O A:HOH1017 4.2 34.4 1.0
O A:GLU41 4.2 22.2 1.0
O A:HOH1029 4.3 34.4 1.0
NE2 A:HIS44 4.3 18.7 1.0
O A:HOH1074 4.3 37.8 1.0
CA A:HIS44 4.4 17.2 1.0
CB A:ALA20 4.4 19.7 1.0
CD2 A:HIS44 4.5 18.4 1.0
CH3 A:ACY101 4.5 30.1 1.0
N A:ALA20 4.8 17.4 1.0
N A:HIS44 5.0 18.0 1.0

Cadmium binding site 2 out of 2 in 4q2l

Go back to Cadmium Binding Sites List in 4q2l
Cadmium binding site 2 out of 2 in the Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:20.0
occ:0.50
O A:GLU43 2.3 21.5 1.0
OE2 A:GLU13 2.5 26.1 0.6
O A:HOH1088 2.6 40.0 1.0
O A:HOH1035 2.6 35.0 1.0
OE1 A:GLU13 2.9 27.6 0.6
CD A:GLU13 3.0 25.4 0.6
C A:GLU43 3.3 17.7 1.0
CA A:GLU43 3.8 19.0 0.5
CB A:GLU43 3.8 19.6 0.5
CA A:GLU43 3.8 18.9 0.5
OG A:SER45 4.2 21.3 0.5
O A:HOH1051 4.3 34.5 1.0
CB A:GLU43 4.3 17.4 0.5
NH2 A:ARG11 4.3 30.9 1.0
N A:HIS44 4.4 18.0 1.0
O A:HOH1082 4.5 40.0 1.0
CG A:GLU13 4.5 25.3 0.4
CB A:HIS44 4.5 17.1 1.0
CG A:GLU13 4.5 24.3 0.6
O A:HIS44 4.7 17.3 1.0
OE2 A:GLU43 4.7 27.2 0.5
OE2 A:GLU13 4.7 27.6 0.4
C A:HIS44 4.7 15.9 1.0
CA A:HIS44 4.8 17.2 1.0
O A:HOH1021 4.8 36.4 1.0
CG A:GLU43 4.8 21.2 0.5
CG A:GLU43 4.8 21.6 0.5
CD A:GLU13 5.0 26.3 0.4

Reference:

D.Jiang, Y.Zhao, J.Fan, X.Liu, Y.Wu, W.Feng, X.C.Zhang. Atomic Resolution Structure of the E. Coli Yajr Transporter Yam Domain Biochem.Biophys.Res.Commun. 2014.
ISSN: ESSN 1090-2104
PubMed: 24952155
DOI: 10.1016/J.BBRC.2014.06.053
Page generated: Sat Dec 12 08:25:32 2020

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