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Zinc in PDB 2pjc: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex

Enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex

All present enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- 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)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex, PDB code: 2pjc 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) 21.59 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.487, 95.350, 135.279, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex (pdb code 2pjc). 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 ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex, PDB code: 2pjc:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2pjc

Go back to Zinc Binding Sites List in 2pjc
Zinc binding site 1 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- 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)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:19.1
occ:1.00
ND1 A:HIS69 2.0 17.3 1.0
O25 A:343401 2.1 17.1 1.0
ND1 A:HIS196 2.1 18.3 1.0
OE1 A:GLU72 2.1 16.9 1.0
OE2 A:GLU72 2.3 15.6 1.0
CD A:GLU72 2.5 17.1 1.0
O26 A:343401 2.9 19.6 1.0
P24 A:343401 2.9 18.5 1.0
CE1 A:HIS69 3.0 17.4 1.0
CG A:HIS196 3.1 15.8 1.0
CG A:HIS69 3.1 18.7 1.0
CE1 A:HIS196 3.2 18.4 1.0
CB A:HIS196 3.4 14.6 1.0
CB A:HIS69 3.5 17.6 1.0
O A:HOH410 4.0 15.7 1.0
CG A:GLU72 4.0 17.0 1.0
O23 A:343401 4.1 16.1 1.0
O A:SER197 4.1 16.1 1.0
NE2 A:HIS69 4.1 16.1 1.0
C27 A:343401 4.2 19.2 1.0
C1 A:343401 4.2 16.8 1.0
CD2 A:HIS69 4.2 17.2 1.0
O A:HOH502 4.3 20.4 1.0
CD2 A:HIS196 4.3 16.6 1.0
NE2 A:HIS196 4.3 17.0 1.0
CA A:HIS196 4.3 15.3 1.0
OE2 A:GLU270 4.4 18.4 1.0
NH1 A:ARG127 4.5 18.8 1.0
N A:SER197 4.5 16.2 1.0
CA A:HIS69 4.8 16.9 1.0
C2 A:343401 4.9 18.2 1.0
N A:HIS69 4.9 17.4 1.0
O14 A:343401 4.9 17.8 1.0
CB A:GLU72 4.9 15.2 1.0
C A:HIS196 5.0 14.7 1.0

Zinc binding site 2 out of 3 in 2pjc

Go back to Zinc Binding Sites List in 2pjc
Zinc binding site 2 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- 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)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:19.1
occ:1.00
O25 B:343501 2.1 19.3 1.0
ND1 B:HIS69 2.1 16.9 1.0
ND1 B:HIS196 2.1 14.8 1.0
OE1 B:GLU72 2.2 17.9 1.0
OE2 B:GLU72 2.3 18.0 1.0
CD B:GLU72 2.5 17.1 1.0
O26 B:343501 2.9 17.8 1.0
P24 B:343501 2.9 18.7 1.0
CE1 B:HIS69 3.0 18.8 1.0
CE1 B:HIS196 3.1 16.1 1.0
CG B:HIS196 3.2 15.3 1.0
CG B:HIS69 3.2 16.1 1.0
CB B:HIS196 3.4 13.9 1.0
CB B:HIS69 3.5 16.2 1.0
O B:HOH506 4.0 18.2 1.0
CG B:GLU72 4.0 17.1 1.0
O23 B:343501 4.0 19.2 1.0
O B:SER197 4.1 18.3 1.0
C27 B:343501 4.2 17.8 1.0
C1 B:343501 4.2 18.3 1.0
NE2 B:HIS69 4.2 17.3 1.0
O B:HOH526 4.3 21.6 1.0
NE2 B:HIS196 4.3 16.2 1.0
CD2 B:HIS69 4.3 16.7 1.0
CD2 B:HIS196 4.3 16.1 1.0
CA B:HIS196 4.4 16.4 1.0
OE2 B:GLU270 4.5 18.5 1.0
NH1 B:ARG127 4.6 20.2 1.0
N B:SER197 4.6 16.1 1.0
C2 B:343501 4.8 18.4 1.0
O14 B:343501 4.8 15.9 1.0
CA B:HIS69 4.8 16.3 1.0
N B:HIS69 4.9 16.3 1.0
CB B:GLU72 4.9 15.9 1.0
OE1 B:GLU270 5.0 15.5 1.0

Zinc binding site 3 out of 3 in 2pjc

Go back to Zinc Binding Sites List in 2pjc
Zinc binding site 3 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- 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 3 of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B ({(R)-1-[(S)-2-Benzyloxycarbonylamino-3- (4-Hydroxy-Phenyl)-Propionylamino]-2-Methyl-Propyl}- Hydroxy-Phosphinoyloxy)-(3-Guanidino-Phenyl)-Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:18.5
occ:1.00
O25 C:343601 2.1 17.9 1.0
ND1 C:HIS69 2.1 16.7 1.0
ND1 C:HIS196 2.1 18.2 1.0
OE1 C:GLU72 2.2 15.8 1.0
OE2 C:GLU72 2.3 17.7 1.0
CD C:GLU72 2.6 16.1 1.0
P24 C:343601 2.9 18.4 1.0
O26 C:343601 2.9 18.2 1.0
CE1 C:HIS69 3.0 18.1 1.0
CG C:HIS196 3.1 17.4 1.0
CE1 C:HIS196 3.1 19.1 1.0
CG C:HIS69 3.2 17.2 1.0
CB C:HIS196 3.4 16.2 1.0
CB C:HIS69 3.5 15.4 1.0
CG C:GLU72 4.1 15.4 1.0
O23 C:343601 4.1 17.1 1.0
O C:HOH604 4.1 17.0 1.0
O C:SER197 4.1 17.8 1.0
C27 C:343601 4.2 17.7 1.0
NE2 C:HIS69 4.2 18.1 1.0
C1 C:343601 4.2 17.5 1.0
CD2 C:HIS196 4.3 17.6 1.0
NE2 C:HIS196 4.3 16.0 1.0
CD2 C:HIS69 4.3 17.6 1.0
CA C:HIS196 4.4 16.4 1.0
O C:HOH605 4.4 18.2 1.0
OE2 C:GLU270 4.4 19.0 1.0
NH1 C:ARG127 4.5 16.0 1.0
N C:SER197 4.6 18.2 1.0
C2 C:343601 4.8 18.5 1.0
CA C:HIS69 4.8 15.5 1.0
N C:HIS69 4.9 15.6 1.0
O14 C:343601 4.9 15.6 1.0
CB C:GLU72 4.9 16.1 1.0
OE1 C:GLU270 5.0 17.4 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: Sat Sep 26 03:31:04 2020
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