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Cadmium in PDB 2enr: Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site

Protein crystallography data

The structure of Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site, PDB code: 2enr was solved by J.Bouckaert, R.Loris, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.35
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 63.200, 87.690, 89.230, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / n/a

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site (pdb code 2enr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site, PDB code: 2enr:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 2enr

Go back to Cadmium Binding Sites List in 2enr
Cadmium binding site 1 out of 2 in the Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd241

b:28.7
occ:1.00
H2 A:HOH246 2.0 0.0 1.0
O A:HOH243 2.3 23.4 1.0
OD2 A:ASP10 2.3 26.7 1.0
NE2 A:HIS24 2.3 20.9 1.0
OE2 A:GLU8 2.5 16.6 1.0
H1 A:HOH243 2.5 0.0 1.0
O A:HOH246 2.6 30.5 1.0
H2 A:HOH243 2.7 0.0 1.0
OD1 A:ASP19 2.8 32.7 1.0
CD2 A:HIS24 3.1 17.2 1.0
CG A:ASP19 3.3 30.9 1.0
H1 A:HOH246 3.3 0.0 1.0
CG A:ASP10 3.3 22.8 1.0
CE1 A:HIS24 3.4 19.0 1.0
OD2 A:ASP19 3.4 28.1 1.0
CD A:GLU8 3.5 13.4 1.0
H1 A:HOH266 3.5 0.0 1.0
OE1 A:GLU8 3.7 16.8 1.0
CB A:ASP10 3.8 19.0 1.0
HG A:SER34 4.1 0.0 1.0
O A:HOH266 4.1 43.5 1.0
OG A:SER34 4.1 20.0 1.0
O A:HOH244 4.2 29.3 1.0
CD A:CD242 4.2 32.1 1.0
CB A:ASP19 4.3 30.3 1.0
OD1 A:ASP10 4.3 23.1 1.0
CG A:HIS24 4.3 15.6 1.0
ND1 A:HIS24 4.4 23.3 1.0
O A:VAL32 4.6 20.4 1.0
CA A:ASP19 4.6 34.8 1.0
H1 A:HOH244 4.6 0.0 1.0
H A:SER34 4.7 0.0 1.0
H2 A:HOH266 4.8 0.0 1.0
CG A:GLU8 4.8 15.4 1.0
H2 A:HOH244 4.9 0.0 1.0

Cadmium binding site 2 out of 2 in 2enr

Go back to Cadmium Binding Sites List in 2enr
Cadmium binding site 2 out of 2 in the Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Co-Crystals of Demetallized Concanavalin A with Cadmium Having A Cadmium Ion Bound in Both the S1 Site and the S2 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd242

b:32.1
occ:1.00
OD2 A:ASP19 2.4 28.1 1.0
OD1 A:ASP10 2.4 23.1 1.0
O A:TYR12 2.4 31.9 1.0
H1 A:HOH244 2.5 0.0 1.0
OD2 A:ASP10 2.7 26.7 1.0
O A:HOH245 2.7 34.3 1.0
O A:HOH244 2.8 29.3 1.0
CG A:ASP10 2.9 22.8 1.0
H2 A:HOH245 2.9 0.0 1.0
H1 A:HOH245 2.9 0.0 1.0
H A:ASN14 3.0 0.0 1.0
OD1 A:ASN14 3.1 31.7 1.0
H2 A:HOH244 3.4 0.0 1.0
CG A:ASP19 3.5 30.9 1.0
C A:TYR12 3.6 31.2 1.0
H2 A:HOH243 3.6 0.0 1.0
H A:TYR12 3.7 0.0 1.0
OD1 A:ASP19 3.9 32.7 1.0
N A:ASN14 4.0 32.8 1.0
CG A:ASN14 4.1 31.2 1.0
CD A:CD241 4.2 28.7 1.0
CB A:ASN14 4.3 26.2 1.0
N A:TYR12 4.4 27.7 1.0
CA A:TYR12 4.4 28.4 1.0
O A:HOH243 4.4 23.4 1.0
CB A:ASP10 4.4 19.0 1.0
CB A:TYR12 4.4 26.6 1.0
N A:PRO13 4.6 35.1 1.0
H1 A:HOH243 4.6 0.0 1.0
CE1 A:HIS24 4.6 19.0 1.0
CA A:PRO13 4.7 34.6 1.0
CB A:ASP19 4.7 30.3 1.0
CA A:ASN14 4.8 28.5 1.0
O A:ASP208 4.8 20.4 1.0
C A:PRO13 4.8 34.5 1.0
NE2 A:HIS24 4.8 20.9 1.0
OD1 A:ASP208 4.9 24.8 1.0
O A:ARG228 5.0 19.5 1.0

Reference:

J.Bouckaert, R.Loris, L.Wyns. Zinc/Calcium- and Cadmium/Cadmium-Substituted Concanavalin A: Interplay of Metal Binding, pH and Molecular Packing. Acta Crystallogr.,Sect.D V. 56 1569 2000.
ISSN: ISSN 0907-4449
PubMed: 11092923
DOI: 10.1107/S0907444900013342
Page generated: Sat Dec 12 08:16:59 2020

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