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Cadmium in PDB 2zqo: Crystal Structure of the Earthworm R-Type Lectin C-Half in Complex with Galnac

Protein crystallography data

The structure of Crystal Structure of the Earthworm R-Type Lectin C-Half in Complex with Galnac, PDB code: 2zqo was solved by R.Suzuki, A.Kuno, T.Hasegawa, J.Hirabayashi, K.Kasai, M.Momma, Z.Fujimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.62 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.210, 34.747, 61.586, 90.00, 104.20, 90.00
R / Rfree (%) 19.2 / 26

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Earthworm R-Type Lectin C-Half in Complex with Galnac (pdb code 2zqo). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Crystal Structure of the Earthworm R-Type Lectin C-Half in Complex with Galnac, PDB code: 2zqo:

Cadmium binding site 1 out of 1 in 2zqo

Go back to Cadmium Binding Sites List in 2zqo
Cadmium binding site 1 out of 1 in the Crystal Structure of the Earthworm R-Type Lectin C-Half in Complex with Galnac


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Earthworm R-Type Lectin C-Half in Complex with Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:2.0
occ:0.50
NE2 A:HIS241 2.3 7.3 1.0
O A:HOH555 2.3 3.8 1.0
N1 A:IMD451 2.3 3.8 1.0
NE2 B:HIS241 2.3 10.1 1.0
O A:HOH557 2.5 11.3 1.0
O B:HOH516 2.5 10.2 1.0
C2 A:IMD451 3.2 7.6 1.0
CE1 A:HIS241 3.2 5.8 1.0
CE1 B:HIS241 3.3 6.1 1.0
CD2 A:HIS241 3.3 4.8 1.0
CD2 B:HIS241 3.3 8.3 1.0
C5 A:IMD451 3.3 9.2 1.0
O B:HOH470 4.2 13.2 1.0
OE1 B:GLU148 4.2 10.9 1.0
OE1 A:GLU148 4.2 10.8 1.0
O A:HOH469 4.2 12.9 1.0
ND1 A:HIS241 4.4 5.4 1.0
O A:GLY239 4.4 8.9 1.0
ND1 B:HIS241 4.4 6.6 1.0
N3 A:IMD451 4.4 11.3 1.0
CG A:HIS241 4.4 7.4 1.0
O B:GLY239 4.4 9.7 1.0
CG B:HIS241 4.4 10.4 1.0
C4 A:IMD451 4.5 9.4 1.0
OE2 A:GLU148 4.6 9.7 1.0
OE2 B:GLU148 4.6 8.9 1.0
CD A:GLU148 4.8 7.7 1.0
CD B:GLU148 4.9 8.5 1.0

Reference:

R.Suzuki, A.Kuno, T.Hasegawa, J.Hirabayashi, K.Kasai, M.Momma, Z.Fujimoto. Sugar-Complex Structures of the C-Half Domain of the Galactose-Binding Lectin EW29 From the Earthworm Lumbricus Terrestris Acta Crystallogr.,Sect.D V. 65 49 2009.
ISSN: ISSN 0907-4449
PubMed: 19153466
DOI: 10.1107/S0907444908037451
Page generated: Fri Aug 28 13:20:17 2020
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