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Zinc in PDB 2pj1: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex

Enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex

All present enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex:
3.4.17.2;

Protein crystallography data

The structure of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex, PDB code: 2pj1 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) 20.21 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.392, 96.152, 135.528, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex (pdb code 2pj1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex, PDB code: 2pj1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2pj1

Go back to Zinc Binding Sites List in 2pj1
Zinc binding site 1 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-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 (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:9.3
occ:1.00
 ND1 A:HIS196 2.0 7.0 1.0
OE1 A:GLU72 2.0 7.3 1.0
ND1 A:HIS69 2.0 8.7 1.0
O24 A:578401 2.4 12.2 1.0
O25 A:578401 2.4 11.9 1.0
OE2 A:GLU72 2.6 8.7 1.0
CD A:GLU72 2.6 8.8 1.0
P14 A:578401 2.8 10.2 1.0
CE1 A:HIS196 2.9 7.0 1.0
CE1 A:HIS69 3.0 8.7 1.0
CG A:HIS69 3.1 8.2 1.0
CG A:HIS196 3.1 7.3 1.0
CB A:HIS69 3.5 6.1 1.0
CB A:HIS196 3.6 6.6 1.0
O13 A:578401 4.0 10.8 1.0
O A:HOH420 4.0 8.8 1.0
CG A:GLU72 4.1 7.6 1.0
NE2 A:HIS196 4.1 8.1 1.0
C15 A:578401 4.1 10.7 1.0
C1 A:578401 4.1 9.7 1.0
NE2 A:HIS69 4.2 7.5 1.0
O A:SER197 4.2 6.8 1.0
O A:HOH432 4.2 10.0 1.0
CD2 A:HIS196 4.2 6.3 1.0
CD2 A:HIS69 4.2 8.4 1.0
NH1 A:ARG127 4.3 10.6 1.0
C2 A:578401 4.5 11.0 1.0
O12 A:578401 4.5 12.5 1.0
CA A:HIS196 4.5 6.3 1.0
N A:SER197 4.7 7.2 1.0
OE2 A:GLU270 4.8 12.4 1.0
CA A:HIS69 4.9 6.4 1.0
N A:HIS69 5.0 6.9 1.0

Zinc binding site 2 out of 3 in 2pj1

Go back to Zinc Binding Sites List in 2pj1
Zinc binding site 2 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-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 (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:8.8
occ:1.00
 OE1 B:GLU72 2.0 8.4 1.0
ND1 B:HIS196 2.0 7.5 1.0
ND1 B:HIS69 2.0 7.3 1.0
O24 B:578501 2.4 9.9 1.0
O25 B:578501 2.5 10.3 1.0
OE2 B:GLU72 2.6 8.4 1.0
CD B:GLU72 2.6 7.5 1.0
P14 B:578501 2.9 7.8 1.0
CE1 B:HIS196 2.9 8.8 1.0
CE1 B:HIS69 3.0 8.6 1.0
CG B:HIS196 3.1 7.0 1.0
CG B:HIS69 3.1 5.6 1.0
CB B:HIS196 3.5 6.6 1.0
CB B:HIS69 3.5 6.3 1.0
O13 B:578501 4.1 8.8 1.0
CG B:GLU72 4.1 8.0 1.0
O B:HOH565 4.1 9.9 1.0
NE2 B:HIS196 4.1 8.2 1.0
O B:SER197 4.2 7.0 1.0
NE2 B:HIS69 4.2 7.7 1.0
C1 B:578501 4.2 8.4 1.0
O B:HOH523 4.2 10.0 1.0
C15 B:578501 4.2 9.7 1.0
CD2 B:HIS196 4.2 7.0 1.0
CD2 B:HIS69 4.2 7.8 1.0
NH1 B:ARG127 4.3 11.0 1.0
CA B:HIS196 4.5 6.7 1.0
C2 B:578501 4.5 9.3 1.0
O12 B:578501 4.6 8.8 1.0
N B:SER197 4.7 7.3 1.0
OE2 B:GLU270 4.7 12.7 1.0
CA B:HIS69 4.9 5.3 1.0
N B:HIS69 5.0 7.0 1.0

Zinc binding site 3 out of 3 in 2pj1

Go back to Zinc Binding Sites List in 2pj1
Zinc binding site 3 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Aminomethyl-Phenyl)-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyloxy]-Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:7.4
occ:1.00
 ND1 C:HIS196 2.0 7.6 1.0
OE1 C:GLU72 2.0 7.2 1.0
ND1 C:HIS69 2.0 5.8 1.0
O25 C:578601 2.4 10.4 1.0
O24 C:578601 2.5 10.1 1.0
OE2 C:GLU72 2.6 7.6 1.0
CD C:GLU72 2.6 7.2 1.0
P14 C:578601 2.9 7.7 1.0
CE1 C:HIS196 2.9 8.1 1.0
CE1 C:HIS69 3.0 5.6 1.0
CG C:HIS196 3.1 5.9 1.0
CG C:HIS69 3.1 4.7 1.0
CB C:HIS196 3.5 6.4 1.0
CB C:HIS69 3.5 5.9 1.0
O13 C:578601 4.1 8.8 1.0
O C:HOH613 4.1 7.1 1.0
NE2 C:HIS196 4.1 7.1 1.0
CG C:GLU72 4.1 6.5 1.0
C1 C:578601 4.2 8.1 1.0
NE2 C:HIS69 4.2 6.5 1.0
CD2 C:HIS196 4.2 6.7 1.0
C15 C:578601 4.2 8.6 1.0
NH1 C:ARG127 4.2 8.4 1.0
O C:HOH622 4.2 8.8 1.0
O C:SER197 4.2 6.3 1.0
CD2 C:HIS69 4.2 6.4 1.0
C2 C:578601 4.4 7.6 1.0
CA C:HIS196 4.5 6.2 1.0
O12 C:578601 4.5 8.1 1.0
N C:SER197 4.7 7.0 1.0
CA C:HIS69 4.9 6.1 1.0
N C:HIS69 5.0 6.0 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 03:02:16 2024

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