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Zinc in PDB 2pj2: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic Acid Complex

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

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

Protein crystallography data

The structure of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic Acid Complex, PDB code: 2pj2 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) 21.09 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.547, 96.324, 135.769, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic Acid Complex (pdb code 2pj2). 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 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic Acid Complex, PDB code: 2pj2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2pj2

Go back to Zinc Binding Sites List in 2pj2
Zinc binding site 1 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic 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 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:16.4
occ:1.00
ND1 A:HIS69 2.1 12.7 1.0
OE1 A:GLU72 2.1 13.6 1.0
ND1 A:HIS196 2.2 13.0 1.0
O34 A:864401 2.4 21.0 1.0
O35 A:864401 2.4 18.9 1.0
OE2 A:GLU72 2.6 12.1 1.0
CD A:GLU72 2.6 13.2 1.0
P24 A:864401 2.9 20.2 1.0
CE1 A:HIS69 3.0 12.5 1.0
CE1 A:HIS196 3.1 13.0 1.0
CG A:HIS69 3.2 10.3 1.0
CG A:HIS196 3.2 11.6 1.0
CB A:HIS196 3.6 12.1 1.0
CB A:HIS69 3.6 9.6 1.0
O A:HOH412 4.0 12.8 1.0
CG A:GLU72 4.1 12.5 1.0
C25 A:864401 4.1 21.7 1.0
C15 A:864401 4.1 18.7 1.0
NE2 A:HIS69 4.2 11.1 1.0
O A:SER197 4.2 14.9 1.0
NH1 A:ARG127 4.2 13.3 1.0
CD2 A:HIS69 4.3 10.9 1.0
NE2 A:HIS196 4.3 15.6 1.0
C1 A:864401 4.3 17.6 1.0
O A:HOH407 4.3 11.6 1.0
CD2 A:HIS196 4.3 13.1 1.0
C2 A:864401 4.4 18.1 1.0
O14 A:864401 4.4 19.9 1.0
CA A:HIS196 4.5 13.4 1.0
N A:SER197 4.7 15.0 1.0
CA A:HIS69 4.9 12.5 1.0
N29 A:864401 4.9 23.4 1.0
N A:HIS69 5.0 12.7 1.0

Zinc binding site 2 out of 3 in 2pj2

Go back to Zinc Binding Sites List in 2pj2
Zinc binding site 2 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic 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 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:14.8
occ:1.00
OE1 B:GLU72 2.1 14.6 1.0
ND1 B:HIS196 2.1 10.5 1.0
ND1 B:HIS69 2.1 11.6 1.0
O34 B:864501 2.3 14.5 1.0
O35 B:864501 2.5 12.7 1.0
OE2 B:GLU72 2.5 12.7 1.0
CD B:GLU72 2.6 14.0 1.0
P24 B:864501 2.9 13.7 1.0
CE1 B:HIS196 3.1 12.1 1.0
CE1 B:HIS69 3.1 8.8 1.0
CG B:HIS196 3.2 11.1 1.0
CG B:HIS69 3.2 10.8 1.0
CB B:HIS196 3.5 10.7 1.0
CB B:HIS69 3.5 11.9 1.0
O B:HOH557 4.0 14.2 1.0
C25 B:864501 4.1 12.6 1.0
O B:SER197 4.1 13.6 1.0
C15 B:864501 4.1 11.7 1.0
CG B:GLU72 4.1 12.4 1.0
NH1 B:ARG127 4.2 13.5 1.0
O B:HOH558 4.2 10.3 1.0
NE2 B:HIS196 4.3 10.9 1.0
NE2 B:HIS69 4.3 8.2 1.0
CD2 B:HIS196 4.3 10.5 1.0
CD2 B:HIS69 4.3 7.9 1.0
C1 B:864501 4.3 13.0 1.0
O14 B:864501 4.4 13.0 1.0
C2 B:864501 4.4 11.0 1.0
CA B:HIS196 4.6 12.1 1.0
N B:SER197 4.8 11.6 1.0
CA B:HIS69 4.9 11.6 1.0
N29 B:864501 4.9 13.3 1.0
OE1 B:GLU270 4.9 17.7 1.0
CZ B:ARG127 5.0 14.7 1.0

Zinc binding site 3 out of 3 in 2pj2

Go back to Zinc Binding Sites List in 2pj2
Zinc binding site 3 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic 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 2-(3-Aminomethyl-Phenyl)-3-[((R)-1- Benzyloxycarbonylamino-2-Methyl-Propyl)-Hydroxy- Phosphinoyl]-Propionic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:13.1
occ:1.00
ND1 C:HIS196 2.1 12.8 1.0
OE1 C:GLU72 2.1 12.6 1.0
ND1 C:HIS69 2.2 13.5 1.0
O35 C:864601 2.3 15.3 1.0
O34 C:864601 2.6 14.3 1.0
OE2 C:GLU72 2.6 9.9 1.0
CD C:GLU72 2.7 11.7 1.0
P24 C:864601 3.0 15.9 1.0
CE1 C:HIS196 3.0 14.4 1.0
CE1 C:HIS69 3.1 11.2 1.0
CG C:HIS196 3.2 14.5 1.0
CG C:HIS69 3.2 13.3 1.0
CB C:HIS69 3.6 9.6 1.0
CB C:HIS196 3.6 14.8 1.0
NH1 C:ARG127 4.1 8.0 1.0
C25 C:864601 4.1 13.3 1.0
O C:HOH609 4.1 11.2 1.0
C15 C:864601 4.2 13.1 1.0
CG C:GLU72 4.2 10.9 1.0
NE2 C:HIS196 4.2 13.2 1.0
CD2 C:HIS196 4.3 15.8 1.0
O C:SER197 4.3 16.1 1.0
NE2 C:HIS69 4.3 13.8 1.0
C1 C:864601 4.3 12.9 1.0
O C:HOH655 4.3 13.7 1.0
CD2 C:HIS69 4.4 11.6 1.0
C2 C:864601 4.4 11.8 1.0
O14 C:864601 4.4 9.5 1.0
CA C:HIS196 4.5 11.9 1.0
N C:SER197 4.7 13.5 1.0
N29 C:864601 4.9 10.8 1.0
CA C:HIS69 4.9 11.5 1.0
CZ C:ARG127 5.0 11.6 1.0
N C:HIS69 5.0 10.9 1.0
O13 C:864601 5.0 13.6 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: Sat Sep 26 03:30:09 2020
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