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

Enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B 2-(3-Aminomethyl-Phenyl)-3-{[1-((S)-2- Benzyloxycarbonylamino-3-Phenyl-Propane-1-Sulfonylamino)-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-{[1-((S)-2- Benzyloxycarbonylamino-3-Phenyl-Propane-1-Sulfonylamino)-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-{[1-((S)-2- Benzyloxycarbonylamino-3-Phenyl-Propane-1-Sulfonylamino)-2- Methyl-Propyl]-Hydroxy-Phosphinoyl}-Propionic Acid Complex, PDB code: 2pjb 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) 22.66 / 1.70
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 (%) 18.2 / 20.7

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 2pjb

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

b:12.5
occ:1.00
 OE1 A:GLU72 2.1 9.3 1.0
ND1 A:HIS69 2.1 10.1 1.0
ND1 A:HIS196 2.1 11.5 1.0
O25 A:983401 2.1 12.0 1.0
OE2 A:GLU72 2.6 10.5 1.0
CD A:GLU72 2.6 9.5 1.0
O26 A:983401 2.8 13.3 1.0
P24 A:983401 2.8 11.9 1.0
CE1 A:HIS69 3.0 9.3 1.0
CE1 A:HIS196 3.1 10.6 1.0
CG A:HIS196 3.2 9.9 1.0
CG A:HIS69 3.2 9.6 1.0
CB A:HIS196 3.5 8.9 1.0
CB A:HIS69 3.6 7.5 1.0
O A:HOH437 4.1 10.8 1.0
C27 A:983401 4.1 11.8 1.0
CG A:GLU72 4.1 10.1 1.0
O A:SER197 4.1 9.1 1.0
NE2 A:HIS69 4.2 9.1 1.0
NE2 A:HIS196 4.3 11.0 1.0
C15 A:983401 4.3 11.3 1.0
CD2 A:HIS69 4.3 8.4 1.0
O A:HOH416 4.3 9.8 1.0
CD2 A:HIS196 4.3 8.2 1.0
C1 A:983401 4.4 11.0 1.0
NH1 A:ARG127 4.4 7.3 1.0
OE2 A:GLU270 4.4 12.7 1.0
CA A:HIS196 4.5 9.5 1.0
C2 A:983401 4.7 10.0 1.0
O14 A:983401 4.7 13.5 1.0
N A:SER197 4.7 9.8 1.0
CA A:HIS69 4.9 8.6 1.0
C28 A:983401 4.9 11.9 1.0
OE1 A:GLU270 5.0 12.1 1.0
N A:HIS69 5.0 8.9 1.0

Zinc binding site 2 out of 3 in 2pjb

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

b:12.4
occ:1.00
 OE1 B:GLU72 2.1 12.5 1.0
ND1 B:HIS69 2.1 10.0 1.0
ND1 B:HIS196 2.1 8.8 1.0
O25 B:983501 2.3 12.4 1.0
OE2 B:GLU72 2.5 11.3 1.0
CD B:GLU72 2.6 11.4 1.0
O26 B:983501 2.7 13.3 1.0
P24 B:983501 2.9 11.2 1.0
CE1 B:HIS69 3.0 10.3 1.0
CE1 B:HIS196 3.1 9.1 1.0
CG B:HIS69 3.2 8.4 1.0
CG B:HIS196 3.2 8.4 1.0
CB B:HIS196 3.5 8.3 1.0
CB B:HIS69 3.6 9.1 1.0
CG B:GLU72 4.1 10.9 1.0
O B:HOH550 4.1 12.9 1.0
C27 B:983501 4.2 12.1 1.0
O B:SER197 4.2 8.7 1.0
NE2 B:HIS69 4.2 9.4 1.0
O B:HOH545 4.2 11.7 1.0
NE2 B:HIS196 4.3 8.0 1.0
CD2 B:HIS69 4.3 10.0 1.0
C15 B:983501 4.3 10.0 1.0
CD2 B:HIS196 4.3 8.5 1.0
NH1 B:ARG127 4.4 10.9 1.0
C1 B:983501 4.4 10.2 1.0
CA B:HIS196 4.5 8.1 1.0
O14 B:983501 4.6 9.2 1.0
C2 B:983501 4.6 10.1 1.0
OE2 B:GLU270 4.6 15.1 1.0
N B:SER197 4.7 8.4 1.0
OE1 B:GLU270 4.9 11.9 1.0
CA B:HIS69 4.9 8.4 1.0

Zinc binding site 3 out of 3 in 2pjb

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

b:11.4
occ:1.00
 ND1 C:HIS196 2.1 8.3 1.0
ND1 C:HIS69 2.1 9.6 1.0
OE1 C:GLU72 2.1 9.7 1.0
O25 C:983601 2.3 10.6 1.0
OE2 C:GLU72 2.5 9.5 1.0
CD C:GLU72 2.6 8.7 1.0
O26 C:983601 2.7 12.2 1.0
P24 C:983601 2.9 10.6 1.0
CE1 C:HIS69 3.0 9.0 1.0
CE1 C:HIS196 3.0 9.1 1.0
CG C:HIS196 3.1 8.2 1.0
CG C:HIS69 3.2 9.5 1.0
CB C:HIS196 3.4 7.7 1.0
CB C:HIS69 3.6 9.0 1.0
O C:HOH640 4.1 13.6 1.0
C27 C:983601 4.1 9.5 1.0
CG C:GLU72 4.1 7.4 1.0
O C:SER197 4.2 9.7 1.0
NE2 C:HIS69 4.2 10.4 1.0
NE2 C:HIS196 4.2 8.8 1.0
CD2 C:HIS196 4.3 8.9 1.0
C15 C:983601 4.3 10.1 1.0
CD2 C:HIS69 4.3 10.2 1.0
O C:HOH642 4.3 8.6 1.0
C1 C:983601 4.3 8.8 1.0
NH1 C:ARG127 4.4 11.8 1.0
CA C:HIS196 4.5 7.3 1.0
O14 C:983601 4.5 9.2 1.0
C2 C:983601 4.6 9.4 1.0
OE2 C:GLU270 4.7 15.8 1.0
N C:SER197 4.7 9.9 1.0
OE1 C:GLU270 4.9 14.3 1.0
CA C:HIS69 4.9 8.4 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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