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Cadmium in PDB 1w1b: Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase.

Protein crystallography data

The structure of Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase., PDB code: 1w1b was solved by D.E.Blair, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 2.10
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 87.824, 87.824, 120.562, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 22.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase. (pdb code 1w1b). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase., PDB code: 1w1b:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1w1b

Go back to Cadmium Binding Sites List in 1w1b
Cadmium binding site 1 out of 4 in the Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd1259

b:24.0
occ:0.50
O 1:HOH2116 2.4 21.8 1.0
NE2 1:HIS128 2.4 31.7 1.0
O 1:HOH2083 2.4 28.1 1.0
NE2 1:HIS124 2.4 23.2 1.0
O 1:HOH2041 2.7 25.9 1.0
CE1 1:HIS128 3.2 29.7 1.0
CD2 1:HIS124 3.3 22.7 1.0
CE1 1:HIS124 3.4 23.6 1.0
CD2 1:HIS128 3.4 30.6 1.0
O 1:HOH2039 4.1 28.6 1.0
OD2 1:ASP73 4.1 27.2 1.0
N 1:ARG166 4.4 39.0 1.0
ND1 1:HIS128 4.4 30.0 1.0
CG 1:HIS128 4.5 29.6 1.0
ND1 1:HIS124 4.5 20.7 1.0
CG 1:HIS124 4.5 21.5 1.0
CB 1:ASP73 4.5 22.1 1.0
O 1:HOH2023 4.5 40.7 1.0
CG 1:ASP73 4.6 24.5 1.0
CA 1:PRO165 4.9 32.4 1.0

Cadmium binding site 2 out of 4 in 1w1b

Go back to Cadmium Binding Sites List in 1w1b
Cadmium binding site 2 out of 4 in the Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd1260

b:32.2
occ:0.50
NE2 1:HIS127 2.6 29.0 1.0
O 1:HOH2065 2.7 46.1 1.0
O 1:HOH2030 3.0 46.1 1.0
CE1 1:HIS127 3.4 28.5 1.0
O 1:HOH2084 3.4 38.0 1.0
CD2 1:HIS127 3.6 28.3 1.0
CE1 1:PHE126 4.2 32.3 1.0
ND1 1:HIS127 4.6 28.5 1.0
CD1 1:PHE126 4.6 30.4 1.0
CG 1:HIS127 4.7 28.2 1.0

Cadmium binding site 3 out of 4 in 1w1b

Go back to Cadmium Binding Sites List in 1w1b
Cadmium binding site 3 out of 4 in the Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd1259

b:24.7
occ:0.50
O 2:HOH2109 2.4 21.7 1.0
NE2 2:HIS128 2.4 33.6 1.0
NE2 2:HIS124 2.5 25.5 1.0
O 2:HOH2036 2.5 20.4 1.0
O 2:HOH2033 2.6 34.8 1.0
CE1 2:HIS128 3.1 32.1 1.0
CD2 2:HIS124 3.3 22.1 1.0
CD2 2:HIS128 3.4 33.4 1.0
CE1 2:HIS124 3.4 22.5 1.0
OD2 2:ASP73 4.0 22.9 1.0
O 2:HOH2034 4.2 27.7 1.0
N 2:ARG166 4.2 38.9 1.0
ND1 2:HIS128 4.2 33.3 1.0
CG 2:HIS128 4.4 32.9 1.0
CB 2:ASP73 4.5 20.8 1.0
CG 2:HIS124 4.5 22.6 1.0
ND1 2:HIS124 4.5 21.9 1.0
CG 2:ASP73 4.5 23.2 1.0
CA 2:ARG166 4.8 40.5 1.0

Cadmium binding site 4 out of 4 in 1w1b

Go back to Cadmium Binding Sites List in 1w1b
Cadmium binding site 4 out of 4 in the Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Bacillus Subtilis Pdaa with Cadmium, A Family 4 Carbohydrate Esterase. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd1260

b:35.0
occ:0.50
NE2 2:HIS127 2.7 25.1 1.0
CE1 2:HIS127 3.5 26.1 1.0
CD2 2:HIS127 3.7 24.6 1.0
CE1 2:PHE126 4.4 29.7 1.0
ND1 2:HIS127 4.7 26.3 1.0
CD1 2:PHE126 4.8 24.7 1.0
CG 2:HIS127 4.8 27.3 1.0

Reference:

D.E.Blair, D.M.Van Aalten. Structures of Bacillus Subtilis Pdaa, A Family 4 Carbohydrate Esterase, and A Complex with N-Acetyl-Glucosamine. Febs Lett. V. 570 13 2004.
ISSN: ISSN 0014-5793
PubMed: 15251431
DOI: 10.1016/J.FEBSLET.2004.06.013
Page generated: Fri Aug 28 12:34:27 2020
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