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Zinc in PDB 2pj4: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex

Enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex

All present enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex:
3.4.17.2;

Protein crystallography data

The structure of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex, PDB code: 2pj4 was solved by M.Adler, M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.92 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 90.069, 90.069, 173.666, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex (pdb code 2pj4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex, PDB code: 2pj4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2pj4

Go back to Zinc Binding Sites List in 2pj4
Zinc binding site 1 out of 2 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:13.6
occ:1.00
 ND1 A:HIS196 2.0 8.9 1.0
OE1 A:GLU72 2.1 14.5 1.0
ND1 A:HIS69 2.1 5.2 1.0
O35 A:414401 2.4 17.2 1.0
OE2 A:GLU72 2.6 13.9 1.0
O34 A:414401 2.7 13.4 1.0
CD A:GLU72 2.7 14.4 1.0
P24 A:414401 2.9 15.6 1.0
CE1 A:HIS196 3.0 10.5 1.0
CE1 A:HIS69 3.1 8.5 1.0
CG A:HIS196 3.1 9.1 1.0
CG A:HIS69 3.2 7.3 1.0
CB A:HIS196 3.5 8.6 1.0
CB A:HIS69 3.6 8.0 1.0
O23 A:414401 4.0 13.9 1.0
C1 A:414401 4.0 16.8 1.0
O A:HOH470 4.1 5.7 1.0
NE2 A:HIS196 4.2 12.2 1.0
CG A:GLU72 4.2 13.8 1.0
CD2 A:HIS196 4.2 10.5 1.0
NH1 A:ARG127 4.2 14.1 1.0
C25 A:414401 4.3 11.9 1.0
NE2 A:HIS69 4.3 7.9 1.0
O A:HOH402 4.3 5.7 1.0
O A:SER197 4.3 9.7 1.0
CD2 A:HIS69 4.3 6.2 1.0
C2 A:414401 4.5 15.7 1.0
CA A:HIS196 4.5 8.4 1.0
O14 A:414401 4.6 13.8 1.0
N A:SER197 4.8 9.0 1.0
CA A:HIS69 4.9 8.1 1.0
OE2 A:GLU270 5.0 23.8 1.0

Zinc binding site 2 out of 2 in 2pj4

Go back to Zinc Binding Sites List in 2pj4
Zinc binding site 2 out of 2 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-Benzyloxycarbonylamino-Cyclohexyl- Methyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:14.1
occ:1.00
 ND1 B:HIS196 2.1 14.3 1.0
OE1 B:GLU72 2.1 12.4 1.0
ND1 B:HIS69 2.1 9.6 1.0
O35 B:414501 2.4 16.9 1.0
OE2 B:GLU72 2.4 14.5 1.0
CD B:GLU72 2.6 15.6 1.0
O34 B:414501 2.7 13.8 1.0
P24 B:414501 2.9 15.3 1.0
CE1 B:HIS69 3.0 10.0 1.0
CE1 B:HIS196 3.1 16.7 1.0
CG B:HIS196 3.2 14.6 1.0
CG B:HIS69 3.2 10.8 1.0
CB B:HIS196 3.5 13.1 1.0
CB B:HIS69 3.6 8.6 1.0
O23 B:414501 4.1 14.7 1.0
C1 B:414501 4.1 14.6 1.0
CG B:GLU72 4.1 12.0 1.0
NH1 B:ARG127 4.1 6.0 1.0
O B:HOH503 4.2 9.3 1.0
O B:HOH510 4.2 10.0 1.0
NE2 B:HIS69 4.2 11.7 1.0
NE2 B:HIS196 4.3 17.5 1.0
C25 B:414501 4.3 15.8 1.0
CD2 B:HIS196 4.3 15.6 1.0
CD2 B:HIS69 4.3 11.7 1.0
O B:SER197 4.4 12.3 1.0
CA B:HIS196 4.5 11.0 1.0
C2 B:414501 4.6 14.5 1.0
O14 B:414501 4.6 13.3 1.0
N B:SER197 4.9 12.0 1.0
CA B:HIS69 4.9 10.2 1.0
N B:HIS69 4.9 12.7 1.0

Reference:

M.Adler, B.Buckman, J.Bryant, Z.Chang, K.Chu, K.Emayan, P.Hrvatin, I.Islam, J.Morser, D.Sukovich, C.West, S.Yuan, M.Whitlow. Structures of Potent Selective Peptide Mimetics Bound to Carboxypeptidase B. Acta Crystallogr.,Sect.D V. 64 149 2008.
ISSN: ISSN 0907-4449
PubMed: 18219114
DOI: 10.1107/S0907444907057228
Page generated: Thu Oct 17 03:03:26 2024

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