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Cadmium in PDB 1y7m: Crystal Structure of the B. Subtilis Ykud Protein at 2 A Resolution

Protein crystallography data

The structure of Crystal Structure of the B. Subtilis Ykud Protein at 2 A Resolution, PDB code: 1y7m was solved by J.A.Bielnicki, Y.Devedjiev, U.Derewenda, Z.Dauter, A.Joachimiak, Z.S.Derewenda, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.276, 63.910, 93.679, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 27

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the B. Subtilis Ykud Protein at 2 A Resolution (pdb code 1y7m). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of the B. Subtilis Ykud Protein at 2 A Resolution, PDB code: 1y7m:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1y7m

Go back to Cadmium Binding Sites List in 1y7m
Cadmium binding site 1 out of 2 in the Crystal Structure of the B. Subtilis Ykud Protein at 2 A Resolution


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 B. Subtilis Ykud Protein at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:37.0
occ:1.00
SG A:CYS139 2.3 19.1 1.0
O2 A:SO4203 2.6 25.1 1.0
O A:HOH204 2.7 13.2 1.0
O4 A:SO4203 2.8 32.6 1.0
S A:SO4203 3.1 27.2 1.0
CB A:CYS139 3.2 18.4 1.0
O A:HIS119 3.8 18.5 1.0
N A:CYS139 3.9 18.5 1.0
O3 A:SO4203 3.9 29.8 1.0
CA A:CYS139 4.1 18.6 1.0
O1 A:SO4203 4.4 27.6 1.0
CH2 A:TRP112 4.4 21.8 1.0
NE2 A:HIS123 4.4 21.7 1.0
CZ3 A:TRP112 4.5 22.6 1.0
ND1 A:HIS119 4.5 18.3 1.0
CD2 A:HIS123 4.7 22.8 1.0
CE1 A:HIS119 4.8 17.9 1.0
CB A:LYS137 4.8 19.5 1.0
N A:GLY138 5.0 18.0 1.0
C A:GLY138 5.0 18.2 1.0

Cadmium binding site 2 out of 2 in 1y7m

Go back to Cadmium Binding Sites List in 1y7m
Cadmium binding site 2 out of 2 in the Crystal Structure of the B. Subtilis Ykud Protein at 2 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the B. Subtilis Ykud Protein at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:39.3
occ:1.00
SG B:CYS139 2.3 23.1 1.0
O3 B:SO4204 2.5 33.1 1.0
O B:HOH207 2.6 14.1 1.0
O1 B:SO4204 2.7 28.8 1.0
S B:SO4204 3.1 34.5 1.0
CB B:CYS139 3.3 21.6 1.0
O B:HIS119 3.9 19.8 1.0
O4 B:SO4204 3.9 32.0 1.0
N B:CYS139 3.9 20.6 1.0
CA B:CYS139 4.2 21.5 1.0
NE2 B:HIS123 4.3 21.4 1.0
O2 B:SO4204 4.4 33.6 1.0
CH2 B:TRP112 4.4 23.3 1.0
CZ3 B:TRP112 4.4 24.3 1.0
ND1 B:HIS119 4.6 19.8 1.0
CD2 B:HIS123 4.7 21.1 1.0
CB B:LYS137 4.8 21.5 1.0
CE1 B:HIS119 4.9 17.1 1.0
C B:GLY138 5.0 20.4 1.0
CE2 B:PHE108 5.0 28.8 1.0

Reference:

J.Bielnicki, Y.Devedjiev, U.Derewenda, Z.Dauter, A.Joachimiak, Z.S.Derewenda. B. Subtilis Ykud Protein at 2.0 A Resolution: Insights Into the Structure and Function of A Novel, Ubiquitous Family of Bacterial Enzymes. Proteins V. 62 144 2006.
ISSN: ISSN 0887-3585
PubMed: 16287140
DOI: 10.1002/PROT.20702
Page generated: Fri Aug 28 12:40:01 2020
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