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Cadmium in PDB 1ee3: Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form

Enzymatic activity of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form

All present enzymatic activity of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form:
3.4.17.1;

Protein crystallography data

The structure of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form, PDB code: 1ee3 was solved by F.Jensen, T.Bukrinsky, J.Bjerrum, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.178, 60.205, 51.715, 90.00, 97.46, 90.00
R / Rfree (%) 17.4 / 19.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form (pdb code 1ee3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form, PDB code: 1ee3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1ee3

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Cadmium binding site 1 out of 5 in the Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd350

b:13.9
occ:1.00
 ND1 P:HIS196 2.3 9.2 1.0
ND1 P:HIS69 2.3 8.0 1.0
OE2 P:GLU72 2.4 10.6 1.0
O P:HOH401 2.5 20.5 1.0
OE1 P:GLU72 2.6 11.3 1.0
O P:HOH550 2.7 27.6 1.0
CD P:GLU72 2.8 10.6 1.0
CE1 P:HIS69 3.2 10.1 1.0
CG P:HIS196 3.2 8.3 1.0
CE1 P:HIS196 3.3 8.8 1.0
CG P:HIS69 3.3 9.2 1.0
CB P:HIS196 3.5 9.2 1.0
CB P:HIS69 3.6 9.3 1.0
O P:SER197 4.1 8.8 1.0
O P:HOH402 4.1 20.6 1.0
OE2 P:GLU270 4.2 15.4 1.0
CG P:GLU72 4.3 9.9 1.0
O P:HOH403 4.3 11.4 1.0
NE2 P:HIS69 4.4 7.9 1.0
CD2 P:HIS196 4.4 8.0 1.0
CA P:HIS196 4.4 9.0 1.0
NE2 P:HIS196 4.4 10.2 1.0
CD2 P:HIS69 4.4 7.8 1.0
N P:SER197 4.5 7.9 1.0
NH2 P:ARG127 4.5 20.7 1.0
OE1 P:GLU270 4.7 14.6 1.0
O P:HOH595 4.8 28.9 1.0
O P:HOH606 4.8 28.5 1.0
CD P:GLU270 4.9 13.9 1.0

Cadmium binding site 2 out of 5 in 1ee3

Go back to Cadmium Binding Sites List in 1ee3
Cadmium binding site 2 out of 5 in the Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd351

b:15.6
occ:0.15
 CD P:CD351 0.0 15.6 0.1
CE1 P:HIS303 1.2 16.6 0.5
ND1 P:HIS303 1.5 17.7 0.5
NE2 P:HIS303 1.9 17.2 0.5
CG P:HIS303 2.2 17.4 0.5
ND1 P:HIS303 2.3 17.5 0.5
CD2 P:HIS303 2.4 17.5 0.5
O P:HOH495 2.4 24.9 1.0
CG P:HIS303 3.1 17.2 0.5
CE1 P:HIS303 3.1 17.0 0.5
CD P:CD351 3.2 13.1 0.1
CB P:HIS303 3.5 18.6 0.5
CB P:HIS303 3.5 17.5 0.5
CD2 P:HIS303 4.1 17.6 0.5
NE2 P:HIS303 4.1 17.0 0.5
CA P:HIS303 4.3 18.7 1.0
CG2 P:VAL222 4.6 12.1 1.0
N P:HIS303 4.9 18.0 1.0

Cadmium binding site 3 out of 5 in 1ee3

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Cadmium binding site 3 out of 5 in the Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd351

b:13.1
occ:0.15
 CD P:CD351 0.0 13.1 0.1
CE1 P:HIS303 0.3 17.0 0.5
NE2 P:HIS303 1.2 17.0 0.5
ND1 P:HIS303 1.4 17.5 0.5
CD2 P:HIS303 2.0 17.6 0.5
CG P:HIS303 2.1 17.2 0.5
ND1 P:HIS303 3.0 17.7 0.5
CD P:CD351 3.2 15.6 0.1
CG P:HIS303 3.5 17.4 0.5
CB P:HIS303 3.5 18.6 0.5
CB P:HIS303 3.6 17.5 0.5
OE2 P:GLU218 3.6 22.4 1.0
CE1 P:HIS303 3.9 16.6 0.5
CA P:HIS303 4.4 18.7 1.0
CG2 P:VAL222 4.4 12.1 1.0
O P:HIS303 4.5 21.6 1.0
CD P:GLU218 4.6 21.1 1.0
CD2 P:HIS303 4.6 17.5 0.5
OH P:TYR265 4.7 18.9 1.0
CG P:GLU218 4.8 18.5 1.0
NE2 P:HIS303 4.8 17.2 0.5
C P:HIS303 4.9 19.9 1.0
O P:HOH495 4.9 24.9 1.0

Cadmium binding site 4 out of 5 in 1ee3

Go back to Cadmium Binding Sites List in 1ee3
Cadmium binding site 4 out of 5 in the Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd353

b:18.0
occ:0.10
 O P:HOH590 2.1 24.6 1.0
O P:HOH540 2.4 24.7 1.0
NE2 P:HIS29 2.4 18.4 1.0
CE1 P:HIS29 2.6 18.8 1.0
NZ P:LYS84 3.6 15.7 1.0
CD2 P:HIS29 3.8 17.8 1.0
ND1 P:HIS29 4.0 18.2 1.0
OG1 P:THR87 4.4 16.6 1.0
CG P:HIS29 4.5 17.1 1.0
OE1 P:GLU28 4.8 18.7 1.0
CB P:THR87 4.9 14.7 1.0
CE P:LYS84 4.9 13.3 1.0
O P:THR87 4.9 16.8 1.0

Cadmium binding site 5 out of 5 in 1ee3

Go back to Cadmium Binding Sites List in 1ee3
Cadmium binding site 5 out of 5 in the Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cadmium-Substituted Bovine Pancreatic Carboxypeptidase A (Alfa-Form) at pH 7.5 and 2 Mm Chloride in Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd354

b:18.4
occ:0.15
 O P:HOH680 2.1 32.6 1.0
OE1 P:GLU17 2.4 17.9 1.0
ND1 P:HIS13 2.7 15.5 1.0
OE2 P:GLU17 2.8 20.0 1.0
CD P:GLU17 3.0 17.8 1.0
CE1 P:HIS13 3.2 15.6 1.0
CG P:HIS13 3.8 14.5 1.0
O P:TYR12 4.0 14.5 1.0
CA P:HIS13 4.3 13.0 1.0
CB P:HIS13 4.3 13.6 1.0
NE2 P:HIS13 4.4 14.0 1.0
CG P:GLU17 4.4 15.2 1.0
CD2 P:HIS13 4.7 14.0 1.0
O P:HOH416 4.8 19.9 1.0
O P:HOH527 4.8 29.8 1.0
CG2 P:THR11 4.8 15.4 1.0
C P:TYR12 4.9 12.8 1.0
CB P:GLU17 4.9 13.2 1.0

Reference:

F.Jensen, T.Bukrinsky, J.Bjerrum, S.Larsen. Three High-Resolution Crystal Structures of Cadmium-Substituted Carboxypeptidase A Provide Insight Into the Enzymatic Function J.Biol.Inorg.Chem. V. 7 490 2002.
ISSN: ISSN 0949-8257
PubMed: 11941507
DOI: 10.1007/S00775-001-0324-0
Page generated: Sun Jan 24 09:41:33 2021

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