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Cadmium in PDB 1oee: Yoda From Escherichia Coli Crystallised with Cadmium Ions

Protein crystallography data

The structure of Yoda From Escherichia Coli Crystallised with Cadmium Ions, PDB code: 1oee was solved by G.David, K.Blondeau, M.Renouard, S.Penel, A.Lewit-Bentley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.45 / 2.1
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.470, 47.985, 42.493, 90.00, 92.77, 90.00
R / Rfree (%) 16.9 / 20.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Yoda From Escherichia Coli Crystallised with Cadmium Ions (pdb code 1oee). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Yoda From Escherichia Coli Crystallised with Cadmium Ions, PDB code: 1oee:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1oee

Go back to Cadmium Binding Sites List in 1oee
Cadmium binding site 1 out of 4 in the Yoda From Escherichia Coli Crystallised with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Yoda From Escherichia Coli Crystallised with Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1194

b:25.3
occ:1.00
NE2 A:HIS144 2.3 17.9 1.0
NE2 A:HIS155 2.4 13.9 1.0
NE2 A:HIS153 2.4 20.4 1.0
O A:HOH2142 2.4 31.4 1.0
O A:HOH2134 2.8 32.0 1.0
O A:HOH2163 2.8 24.4 1.0
CE1 A:HIS155 3.3 14.6 1.0
CD2 A:HIS153 3.3 16.8 1.0
CE1 A:HIS144 3.3 16.8 1.0
CD2 A:HIS144 3.3 15.4 1.0
CD2 A:HIS155 3.4 14.2 1.0
CE1 A:HIS153 3.5 18.1 1.0
O A:HOH2085 4.3 25.6 1.0
ND1 A:HIS144 4.4 15.2 1.0
ND1 A:HIS155 4.4 14.2 1.0
CG A:HIS144 4.4 15.5 1.0
CG A:HIS153 4.5 17.7 1.0
ND1 A:HIS153 4.5 18.6 1.0
CG A:HIS155 4.5 13.3 1.0

Cadmium binding site 2 out of 4 in 1oee

Go back to Cadmium Binding Sites List in 1oee
Cadmium binding site 2 out of 4 in the Yoda From Escherichia Coli Crystallised with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Yoda From Escherichia Coli Crystallised with Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1195

b:26.6
occ:1.00
O A:HOH2167 2.1 29.6 1.0
OE2 A:GLU185 2.3 24.9 1.0
O A:HOH2168 2.6 30.2 1.0
OE1 A:GLU185 2.7 22.7 1.0
CD A:GLU185 2.9 21.1 1.0
CG A:GLU185 4.4 18.8 1.0
O A:HOH2171 4.5 29.2 1.0
CG A:GLU188 4.6 27.8 1.0

Cadmium binding site 3 out of 4 in 1oee

Go back to Cadmium Binding Sites List in 1oee
Cadmium binding site 3 out of 4 in the Yoda From Escherichia Coli Crystallised with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Yoda From Escherichia Coli Crystallised with Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1196

b:19.3
occ:1.00
O A:HOH2160 2.1 15.1 1.0
O A:HOH2156 2.2 27.6 1.0
OE1 A:GLU169 2.3 18.7 1.0
OE2 A:GLU169 2.5 17.0 1.0
CD A:GLU169 2.8 16.3 1.0
OE1 A:GLU171 4.3 21.9 1.0
CG A:GLU169 4.3 16.5 1.0
CB A:GLU171 4.4 13.9 1.0
O A:HOH2154 4.6 24.8 1.0
O A:HOH2155 4.8 25.1 1.0
N A:ASN172 4.8 13.2 1.0
CD A:GLU171 4.9 19.1 1.0
CB A:ASN172 4.9 13.6 1.0
CB A:GLU169 5.0 15.7 1.0

Cadmium binding site 4 out of 4 in 1oee

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Cadmium binding site 4 out of 4 in the Yoda From Escherichia Coli Crystallised with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Yoda From Escherichia Coli Crystallised with Cadmium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1197

b:30.2
occ:0.50
O A:HOH2169 1.7 20.9 1.0
OE2 A:GLU188 2.3 36.1 1.0
OE1 A:GLU188 2.5 34.4 1.0
CD A:GLU188 2.7 32.1 1.0
O A:HOH2081 4.0 31.4 1.0
O A:HOH2170 4.1 32.2 1.0
CG A:GLU188 4.2 27.8 1.0

Reference:

G.David, K.Blondeau, M.Schiltz, S.Penel, A.Lewit-Bentley. Yoda From Escherichia Coli Is A Metal-Binding, Lipocalin-Like Protein J.Biol.Chem. V. 278 43728 2003.
ISSN: ISSN 0021-9258
PubMed: 12909634
DOI: 10.1074/JBC.M304484200
Page generated: Fri Aug 28 12:17:33 2020
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