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Zinc in PDB 2pja: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 3-{[(R)-1-((S)-2-Benzyloxycarbonylamino- 3-Phenyl-Propionylamino)-2-Methyl-Propyl]-Hydroxy- Phosphinoyl}-2-(3-Guanidino-Phenyl)-Propionic Acid Complex

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

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

Protein crystallography data

The structure of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 3-{[(R)-1-((S)-2-Benzyloxycarbonylamino- 3-Phenyl-Propionylamino)-2-Methyl-Propyl]-Hydroxy- Phosphinoyl}-2-(3-Guanidino-Phenyl)-Propionic Acid Complex, PDB code: 2pja 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) 21.40 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.964, 96.379, 135.641, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 24.9

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 2pja

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

b:16.3
occ:1.00
 ND1 A:HIS69 2.1 15.8 1.0
ND1 A:HIS196 2.1 17.0 1.0
OE1 A:GLU72 2.1 13.7 1.0
O25 A:33Z401 2.2 16.2 1.0
OE2 A:GLU72 2.5 14.0 1.0
CD A:GLU72 2.6 13.8 1.0
O26 A:33Z401 2.7 17.7 1.0
P24 A:33Z401 2.8 15.1 1.0
CE1 A:HIS69 3.0 15.3 1.0
CE1 A:HIS196 3.0 17.2 1.0
CG A:HIS69 3.1 14.5 1.0
CG A:HIS196 3.1 14.7 1.0
CB A:HIS196 3.5 12.4 1.0
CB A:HIS69 3.5 12.5 1.0
CG A:GLU72 4.1 12.3 1.0
C27 A:33Z401 4.1 15.1 1.0
O A:SER197 4.1 12.5 1.0
NE2 A:HIS69 4.2 14.6 1.0
NE2 A:HIS196 4.2 14.1 1.0
C1 A:33Z401 4.2 19.4 1.0
C23 A:33Z401 4.2 16.5 1.0
O A:HOH436 4.2 12.0 1.0
O A:HOH443 4.2 12.8 1.0
CD2 A:HIS69 4.3 14.2 1.0
CD2 A:HIS196 4.3 13.2 1.0
NH1 A:ARG127 4.3 15.2 1.0
CA A:HIS196 4.5 13.2 1.0
OE2 A:GLU270 4.5 19.4 1.0
O13 A:33Z401 4.6 16.9 1.0
C2 A:33Z401 4.6 19.3 1.0
N A:SER197 4.7 11.5 1.0
CA A:HIS69 4.8 12.7 1.0
N A:HIS69 4.9 12.5 1.0

Zinc binding site 2 out of 3 in 2pja

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

b:15.4
occ:1.00
 ND1 B:HIS69 2.1 14.0 1.0
OE1 B:GLU72 2.1 14.3 1.0
ND1 B:HIS196 2.1 13.4 1.0
O25 B:33Z501 2.2 17.5 1.0
OE2 B:GLU72 2.4 14.3 1.0
CD B:GLU72 2.6 13.8 1.0
O26 B:33Z501 2.8 17.2 1.0
P24 B:33Z501 3.0 14.9 1.0
CE1 B:HIS69 3.0 13.2 1.0
CE1 B:HIS196 3.1 14.1 1.0
CG B:HIS196 3.1 12.3 1.0
CG B:HIS69 3.2 12.3 1.0
CB B:HIS196 3.5 12.0 1.0
CB B:HIS69 3.5 13.4 1.0
CG B:GLU72 4.1 14.0 1.0
O B:SER197 4.1 14.3 1.0
O B:HOH529 4.2 12.7 1.0
O B:HOH685 4.2 15.9 1.0
NE2 B:HIS69 4.2 13.5 1.0
C27 B:33Z501 4.2 14.1 1.0
NE2 B:HIS196 4.2 12.9 1.0
CD2 B:HIS69 4.3 12.6 1.0
CD2 B:HIS196 4.3 12.4 1.0
C1 B:33Z501 4.3 16.2 1.0
C23 B:33Z501 4.3 15.8 1.0
NH1 B:ARG127 4.4 16.9 1.0
CA B:HIS196 4.4 12.1 1.0
OE2 B:GLU270 4.5 18.8 1.0
N B:SER197 4.7 12.2 1.0
O13 B:33Z501 4.7 16.8 1.0
C2 B:33Z501 4.8 18.4 1.0
CA B:HIS69 4.9 12.3 1.0
N B:HIS69 5.0 13.3 1.0
OE1 B:GLU270 5.0 16.4 1.0
CB B:GLU72 5.0 12.3 1.0

Zinc binding site 3 out of 3 in 2pja

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

b:15.9
occ:1.00
 ND1 C:HIS196 2.0 13.5 1.0
OE1 C:GLU72 2.1 13.1 1.0
ND1 C:HIS69 2.1 12.7 1.0
O25 C:33Z601 2.4 15.7 1.0
OE2 C:GLU72 2.6 14.3 1.0
O26 C:33Z601 2.6 17.2 1.0
CD C:GLU72 2.6 13.9 1.0
P24 C:33Z601 2.9 15.6 1.0
CE1 C:HIS196 3.0 14.4 1.0
CE1 C:HIS69 3.0 12.5 1.0
CG C:HIS196 3.1 13.3 1.0
CG C:HIS69 3.2 13.1 1.0
CB C:HIS196 3.5 11.5 1.0
CB C:HIS69 3.6 11.6 1.0
O C:HOH608 4.1 13.3 1.0
CG C:GLU72 4.1 12.5 1.0
NE2 C:HIS196 4.2 13.1 1.0
NH1 C:ARG127 4.2 14.4 1.0
C27 C:33Z601 4.2 13.6 1.0
O C:SER197 4.2 13.9 1.0
NE2 C:HIS69 4.2 12.8 1.0
O C:HOH640 4.2 14.1 1.0
CD2 C:HIS196 4.2 14.2 1.0
CD2 C:HIS69 4.3 13.4 1.0
C23 C:33Z601 4.3 15.6 1.0
O13 C:33Z601 4.4 16.0 1.0
C1 C:33Z601 4.4 16.5 1.0
CA C:HIS196 4.5 11.5 1.0
C2 C:33Z601 4.5 16.7 1.0
N C:SER197 4.7 13.5 1.0
CA C:HIS69 4.9 12.9 1.0
OE1 C:GLU270 4.9 19.5 1.0
N C:HIS69 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: Thu Oct 17 03:04:32 2024

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