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Cadmium in PDB 2nne: The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor

Protein crystallography data

The structure of The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor, PDB code: 2nne was solved by C.Redondo, R.J.Bingham, M.Vouropoulou, S.W.Homans, J.B.Findlay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.00 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.777, 53.777, 137.596, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor (pdb code 2nne). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor, PDB code: 2nne:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 2nne

Go back to Cadmium Binding Sites List in 2nne
Cadmium binding site 1 out of 4 in the The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd167

b:20.3
occ:1.00
O A:HOH431 2.3 15.4 1.0
O A:HOH484 2.3 17.9 1.0
ND1 A:HIS108 2.3 13.2 1.0
O A:HOH526 2.6 8.6 1.0
CE1 A:HIS108 3.0 12.0 1.0
CG A:HIS108 3.3 8.7 1.0
CD A:CD373 3.7 24.1 1.0
OG1 A:THR95 3.8 10.4 1.0
CB A:HIS108 3.8 7.6 1.0
NE2 A:HIS108 4.1 9.3 1.0
O A:HOH520 4.3 39.0 1.0
CD2 A:HIS108 4.3 9.3 1.0
O A:HOH401 4.4 30.9 1.0
CE1 A:HIS145 4.5 14.7 1.0
O A:HIS108 4.7 8.9 1.0
C A:HIS108 5.0 8.0 1.0
CB A:THR95 5.0 11.2 1.0

Cadmium binding site 2 out of 4 in 2nne

Go back to Cadmium Binding Sites List in 2nne
Cadmium binding site 2 out of 4 in the The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd200

b:10.3
occ:1.00
OE1 A:GLU143 2.3 11.0 1.0
O A:HOH548 2.5 11.3 1.0
O A:HOH381 2.5 12.3 1.0
OE2 A:GLU143 2.5 8.3 1.0
CD A:GLU143 2.7 9.2 1.0
NE2 A:GLN140 4.2 8.0 1.0
CG A:GLU143 4.3 9.3 1.0
O A:HOH444 4.4 21.2 1.0
O A:HOH419 4.5 21.4 1.0
OE1 A:GLN140 4.5 13.2 1.0
CD A:GLN140 4.8 8.2 1.0
O A:HOH483 5.0 21.4 1.0

Cadmium binding site 3 out of 4 in 2nne

Go back to Cadmium Binding Sites List in 2nne
Cadmium binding site 3 out of 4 in the The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:21.3
occ:1.00
O A:HOH446 1.9 29.4 1.0
OE1 A:GLU13 2.3 17.9 1.0
O A:HOH434 2.3 18.5 1.0
O A:HOH432 2.4 18.5 1.0
OE2 A:GLU13 2.7 22.1 1.0
CD A:GLU13 2.8 18.3 1.0
CG A:GLU13 4.3 16.2 1.0
O A:HOH531 4.6 30.6 1.0
O A:HOH411 4.9 40.0 1.0

Cadmium binding site 4 out of 4 in 2nne

Go back to Cadmium Binding Sites List in 2nne
Cadmium binding site 4 out of 4 in the The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The Structural Identification of the Interaction Site and Functional State of Rbp For Its Membrane Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd373

b:24.1
occ:1.00
O A:HOH478 2.4 22.1 1.0
CE1 A:HIS145 2.4 14.7 1.0
O A:HOH526 2.6 8.6 1.0
NE2 A:HIS145 3.0 16.6 1.0
ND1 A:HIS145 3.6 14.2 1.0
CD A:CD167 3.7 20.3 1.0
O A:HOH383 3.8 8.4 1.0
CD2 A:HIS145 4.3 12.6 1.0
O A:HOH511 4.5 34.8 1.0
CG A:HIS145 4.6 12.8 1.0
ND1 A:HIS108 4.7 13.2 1.0

Reference:

C.Redondo, M.Vouropoulou, J.Evans, J.B.Findlay. Identification of the Retinol-Binding Protein (Rbp) Interaction Site and Functional State of Rbps For the Membrane Receptor. Faseb J. V. 22 1043 2008.
ISSN: ISSN 0892-6638
PubMed: 17991731
DOI: 10.1096/FJ.07-8939COM
Page generated: Wed Oct 28 09:59:54 2020
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