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Cadmium in PDB 2dvz: Structure of A Periplasmic Transporter

Protein crystallography data

The structure of Structure of A Periplasmic Transporter, PDB code: 2dvz was solved by I.Huvent, H.Belrhali, R.Antoine, C.Bompard, C.Locht, F.Jacob-Dubuisson, V.Villeret, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 53.829, 53.829, 422.660, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 24.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of A Periplasmic Transporter (pdb code 2dvz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of A Periplasmic Transporter, PDB code: 2dvz:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 2dvz

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Cadmium binding site 1 out of 5 in the Structure of A Periplasmic Transporter


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of A Periplasmic Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:17.6
occ:1.00
O A:HOH1153 1.9 2.0 1.0
OD2 A:ASP225 2.3 14.3 1.0
O A:HOH1255 2.5 14.7 1.0
OD1 A:ASP225 2.6 18.5 1.0
CG A:ASP225 2.8 13.3 1.0
CB A:ASP225 4.3 11.8 1.0

Cadmium binding site 2 out of 5 in 2dvz

Go back to Cadmium Binding Sites List in 2dvz
Cadmium binding site 2 out of 5 in the Structure of A Periplasmic Transporter


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of A Periplasmic Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:22.3
occ:1.00
O A:HOH1147 2.2 2.0 1.0
OD2 A:ASP129 2.2 17.7 1.0
OD1 A:ASP129 2.4 17.0 1.0
O A:HOH1148 2.5 6.5 1.0
CG A:ASP129 2.7 16.5 1.0
O A:HOH1146 2.7 2.0 1.0
O A:HOH1185 4.0 23.9 1.0
N A:GLY132 4.2 13.6 1.0
CB A:ASP129 4.2 16.0 1.0
CA A:GLY132 4.4 13.2 1.0
CD A:CD1003 4.4 34.5 1.0
CG A:LYS128 4.5 24.0 1.0
CE A:LYS128 4.6 26.6 1.0
O A:HOH1162 4.6 19.7 1.0
CB A:LYS131 4.7 16.7 1.0
N A:ASP129 4.7 17.8 1.0
CA A:ASP129 5.0 16.7 1.0

Cadmium binding site 3 out of 5 in 2dvz

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Cadmium binding site 3 out of 5 in the Structure of A Periplasmic Transporter


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of A Periplasmic Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:34.5
occ:1.00
OE1 A:GLU135 2.4 19.4 1.0
O A:HOH1147 2.6 2.0 1.0
O A:HOH1149 2.8 15.2 1.0
CD A:GLU135 3.5 18.8 1.0
OE2 A:GLU135 3.8 21.4 1.0
NZ A:LYS131 4.2 22.8 1.0
O A:HOH1064 4.3 16.7 1.0
CA A:GLY132 4.3 13.2 1.0
CD A:CD1002 4.4 22.3 1.0
O A:HOH1148 4.5 6.5 1.0
CG A:GLU135 4.8 16.7 1.0
O A:HOH1146 4.8 2.0 1.0
N A:GLY132 5.0 13.6 1.0

Cadmium binding site 4 out of 5 in 2dvz

Go back to Cadmium Binding Sites List in 2dvz
Cadmium binding site 4 out of 5 in the Structure of A Periplasmic Transporter


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of A Periplasmic Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:23.8
occ:1.00
O A:HOH1124 2.3 20.7 1.0
OE1 A:GLU136 2.3 20.7 1.0
O A:HOH1151 2.5 2.0 1.0
O A:HOH1150 2.8 13.6 1.0
CD A:GLU136 3.3 19.8 1.0
OE2 A:GLU136 3.6 20.2 1.0
O A:HOH1113 3.9 17.4 1.0
ND2 A:ASN140 4.3 14.2 1.0
CG A:PRO126 4.6 13.4 1.0
CG A:GLU136 4.7 15.9 1.0

Cadmium binding site 5 out of 5 in 2dvz

Go back to Cadmium Binding Sites List in 2dvz
Cadmium binding site 5 out of 5 in the Structure of A Periplasmic Transporter


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of A Periplasmic Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:18.6
occ:0.50
OD2 A:ASP221 2.2 22.0 1.0
O A:HOH1152 2.3 10.7 1.0
OD1 A:ASP221 2.7 19.3 1.0
CG A:ASP221 2.8 19.0 1.0
NZ A:LYS224 3.8 22.1 1.0
CB A:ASP221 4.2 17.3 1.0
CE A:LYS224 4.8 21.0 1.0

Reference:

I.Huvent, H.Belrhali, R.Antoine, C.Bompard, C.Locht, F.Jacob-Dubuisson, V.Villeret. Structural Analysis of Bordetella Pertussis Buge Solute Receptor in A Bound Conformation Acta Crystallogr.,Sect.D V. 62 1375 2006.
ISSN: ISSN 0907-4449
PubMed: 17057341
DOI: 10.1107/S0907444906032653
Page generated: Sat Dec 12 08:16:48 2020

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