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Zinc in PDB 2pj0: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-1-Benzyloxycarbonylamino-2-Methyl- Propyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex

Enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-1-Benzyloxycarbonylamino-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-Benzyloxycarbonylamino-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-Benzyloxycarbonylamino-2-Methyl- Propyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex, PDB code: 2pj0 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) 20.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.579, 101.804, 136.092, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-1-Benzyloxycarbonylamino-2-Methyl- Propyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex (pdb code 2pj0). 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-Benzyloxycarbonylamino-2-Methyl- Propyl)-Hydroxy-Phosphinoyloxy]-(3-Guanidino-Phenyl)- Acetic Acid Complex, PDB code: 2pj0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2pj0

Go back to Zinc Binding Sites List in 2pj0
Zinc binding site 1 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-1-Benzyloxycarbonylamino-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-Benzyloxycarbonylamino-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:17.2
occ:1.00
O34 A:922401 2.1 16.9 1.0
ND1 A:HIS196 2.1 13.8 1.0
ND1 A:HIS69 2.1 12.9 1.0
OE1 A:GLU72 2.1 17.1 1.0
OE2 A:GLU72 2.3 13.4 1.0
CD A:GLU72 2.5 14.9 1.0
O35 A:922401 2.9 17.0 1.0
P24 A:922401 2.9 17.8 1.0
CE1 A:HIS69 3.0 15.8 1.0
CE1 A:HIS196 3.0 12.7 1.0
CG A:HIS196 3.1 11.5 1.0
CG A:HIS69 3.2 14.4 1.0
CB A:HIS196 3.5 12.1 1.0
CB A:HIS69 3.6 11.9 1.0
CG A:GLU72 4.0 12.6 1.0
O23 A:922401 4.0 18.2 1.0
O A:HOH466 4.1 16.1 1.0
O A:SER197 4.2 15.9 1.0
NE2 A:HIS69 4.2 14.9 1.0
NE2 A:HIS196 4.2 14.0 1.0
C1 A:922401 4.2 16.1 1.0
C25 A:922401 4.2 18.8 1.0
CD2 A:HIS196 4.3 13.2 1.0
CD2 A:HIS69 4.3 14.6 1.0
O A:HOH475 4.3 19.0 1.0
OE2 A:GLU270 4.4 16.8 1.0
CA A:HIS196 4.4 14.1 1.0
NH1 A:ARG127 4.5 17.9 1.0
N A:SER197 4.6 14.4 1.0
O14 A:922401 4.8 17.2 1.0
C2 A:922401 4.8 16.7 1.0
CA A:HIS69 4.8 12.2 1.0
N A:HIS69 4.9 12.1 1.0
CB A:GLU72 4.9 13.6 1.0

Zinc binding site 2 out of 3 in 2pj0

Go back to Zinc Binding Sites List in 2pj0
Zinc binding site 2 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-1-Benzyloxycarbonylamino-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-Benzyloxycarbonylamino-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:17.0
occ:1.00
O34 B:922501 2.0 18.4 1.0
ND1 B:HIS196 2.0 14.3 1.0
OE1 B:GLU72 2.1 15.2 1.0
ND1 B:HIS69 2.1 16.1 1.0
OE2 B:GLU72 2.3 15.6 1.0
CD B:GLU72 2.5 16.0 1.0
P24 B:922501 2.9 18.2 1.0
O35 B:922501 2.9 19.1 1.0
CE1 B:HIS196 3.0 12.9 1.0
CE1 B:HIS69 3.1 16.0 1.0
CG B:HIS196 3.1 13.5 1.0
CG B:HIS69 3.1 13.4 1.0
CB B:HIS196 3.5 12.7 1.0
CB B:HIS69 3.5 14.8 1.0
O B:HOH566 4.0 14.8 1.0
CG B:GLU72 4.0 14.1 1.0
O23 B:922501 4.0 16.7 1.0
O B:SER197 4.1 15.3 1.0
NE2 B:HIS196 4.2 13.9 1.0
C25 B:922501 4.2 18.4 1.0
C1 B:922501 4.2 17.7 1.0
CD2 B:HIS196 4.2 14.6 1.0
NE2 B:HIS69 4.3 15.3 1.0
CD2 B:HIS69 4.3 15.2 1.0
O B:HOH537 4.3 19.9 1.0
CA B:HIS196 4.4 14.0 1.0
OE2 B:GLU270 4.4 16.8 1.0
N B:SER197 4.6 15.2 1.0
NH1 B:ARG127 4.7 17.7 1.0
CA B:HIS69 4.8 14.5 1.0
C2 B:922501 4.8 14.9 1.0
N B:HIS69 4.8 13.5 1.0
CB B:GLU72 4.9 14.4 1.0
OE1 B:GLU270 4.9 17.8 1.0
O14 B:922501 4.9 17.8 1.0
C26 B:922501 5.0 19.7 1.0

Zinc binding site 3 out of 3 in 2pj0

Go back to Zinc Binding Sites List in 2pj0
Zinc binding site 3 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B [((R)-1-Benzyloxycarbonylamino-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-Benzyloxycarbonylamino-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:18.1
occ:1.00
OE1 C:GLU72 2.0 18.7 1.0
ND1 C:HIS196 2.0 19.1 1.0
ND1 C:HIS69 2.1 16.8 1.0
O34 C:922601 2.2 18.9 1.0
OE2 C:GLU72 2.4 17.3 1.0
CD C:GLU72 2.5 18.3 1.0
O35 C:922601 2.7 21.9 1.0
P24 C:922601 2.9 19.1 1.0
CE1 C:HIS196 3.0 17.3 1.0
CE1 C:HIS69 3.1 18.5 1.0
CG C:HIS196 3.1 16.9 1.0
CG C:HIS69 3.2 18.8 1.0
CB C:HIS196 3.5 17.7 1.0
CB C:HIS69 3.5 17.8 1.0
CG C:GLU72 4.0 18.3 1.0
O23 C:922601 4.0 18.8 1.0
O C:HOH621 4.1 17.8 1.0
C1 C:922601 4.2 18.9 1.0
NE2 C:HIS196 4.2 18.2 1.0
C25 C:922601 4.2 21.4 1.0
O C:SER197 4.2 18.8 1.0
CD2 C:HIS196 4.2 18.1 1.0
NE2 C:HIS69 4.3 18.6 1.0
O C:HOH687 4.3 22.8 1.0
CD2 C:HIS69 4.3 18.1 1.0
NH1 C:ARG127 4.4 18.6 1.0
CA C:HIS196 4.4 17.9 1.0
OE2 C:GLU270 4.6 23.1 1.0
N C:SER197 4.6 18.1 1.0
C2 C:922601 4.7 19.3 1.0
O14 C:922601 4.7 19.9 1.0
CA C:HIS69 4.8 16.6 1.0
N C:HIS69 4.9 17.0 1.0
CB C:GLU72 4.9 17.0 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: Sat Sep 26 03:29:57 2020
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