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Zinc in PDB 2pj3: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- Acetic Acid Complex

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

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

Protein crystallography data

The structure of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- Acetic Acid Complex, PDB code: 2pj3 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) 20.19 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.570, 95.950, 135.649, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- Acetic Acid Complex (pdb code 2pj3). 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-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- Acetic Acid Complex, PDB code: 2pj3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2pj3

Go back to Zinc Binding Sites List in 2pj3
Zinc binding site 1 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- 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 (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:9.5
occ:1.00
ND1 A:HIS196 2.1 7.2 1.0
ND1 A:HIS69 2.1 8.4 1.0
OE1 A:GLU72 2.1 8.7 1.0
O34 A:86A401 2.2 12.9 1.0
OE2 A:GLU72 2.4 10.1 1.0
CD A:GLU72 2.5 10.3 1.0
O35 A:86A401 2.7 12.0 1.0
P24 A:86A401 2.9 11.9 1.0
CE1 A:HIS196 3.0 9.3 1.0
CE1 A:HIS69 3.0 8.2 1.0
CG A:HIS69 3.1 8.2 1.0
CG A:HIS196 3.1 8.6 1.0
CB A:HIS69 3.5 7.4 1.0
CB A:HIS196 3.5 9.0 1.0
CG A:GLU72 4.1 8.8 1.0
O23 A:86A401 4.1 9.8 1.0
O A:HOH431 4.1 8.5 1.0
O A:HOH517 4.2 9.3 1.0
O A:SER197 4.2 8.1 1.0
C1 A:86A401 4.2 10.4 1.0
NE2 A:HIS196 4.2 7.9 1.0
NE2 A:HIS69 4.2 8.7 1.0
C25 A:86A401 4.2 10.6 1.0
CD2 A:HIS69 4.3 8.6 1.0
CD2 A:HIS196 4.3 6.8 1.0
NH1 A:ARG127 4.4 8.8 1.0
CA A:HIS196 4.4 7.9 1.0
OE2 A:GLU270 4.6 11.9 1.0
N A:SER197 4.6 7.8 1.0
C2 A:86A401 4.7 10.1 1.0
O14 A:86A401 4.8 10.0 1.0
CA A:HIS69 4.8 7.1 1.0
N A:HIS69 4.9 8.2 1.0
CB A:GLU72 5.0 8.0 1.0

Zinc binding site 2 out of 3 in 2pj3

Go back to Zinc Binding Sites List in 2pj3
Zinc binding site 2 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- 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 (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:8.8
occ:1.00
ND1 B:HIS196 2.1 6.5 1.0
ND1 B:HIS69 2.1 10.1 1.0
OE1 B:GLU72 2.1 9.2 1.0
O34 B:86A501 2.2 10.4 1.0
OE2 B:GLU72 2.4 8.3 1.0
CD B:GLU72 2.6 7.7 1.0
O35 B:86A501 2.7 11.5 1.0
P24 B:86A501 2.9 8.1 1.0
CE1 B:HIS69 3.0 9.1 1.0
CE1 B:HIS196 3.0 7.8 1.0
CG B:HIS196 3.1 5.0 1.0
CG B:HIS69 3.2 8.7 1.0
CB B:HIS196 3.5 5.4 1.0
CB B:HIS69 3.5 9.0 1.0
O23 B:86A501 4.0 7.6 1.0
O B:HOH503 4.1 8.2 1.0
CG B:GLU72 4.1 8.5 1.0
C1 B:86A501 4.1 7.3 1.0
O B:SER197 4.1 8.1 1.0
C25 B:86A501 4.2 8.3 1.0
O B:HOH509 4.2 9.5 1.0
NE2 B:HIS196 4.2 7.7 1.0
NE2 B:HIS69 4.2 9.5 1.0
CD2 B:HIS196 4.3 7.3 1.0
CD2 B:HIS69 4.3 9.6 1.0
CA B:HIS196 4.4 7.2 1.0
NH1 B:ARG127 4.5 10.1 1.0
OE2 B:GLU270 4.5 9.6 1.0
N B:SER197 4.6 7.2 1.0
C2 B:86A501 4.7 8.8 1.0
O14 B:86A501 4.8 9.9 1.0
CA B:HIS69 4.8 7.8 1.0
N B:HIS69 4.9 8.2 1.0
CB B:GLU72 5.0 7.5 1.0

Zinc binding site 3 out of 3 in 2pj3

Go back to Zinc Binding Sites List in 2pj3
Zinc binding site 3 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- 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 (3-Guanidino-Phenyl)-{Hydroxy-[(R)-2- Methyl-1-(3-Phenyl-Propionylamino)-Propyl]-Phosphinoyloxy}- Acetic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:10.4
occ:1.00
OE2 C:GLU72 2.1 7.8 1.0
ND1 C:HIS196 2.1 10.0 1.0
ND1 C:HIS69 2.1 8.1 1.0
O34 C:86A601 2.3 9.8 1.0
OE1 C:GLU72 2.4 8.8 1.0
CD C:GLU72 2.5 8.7 1.0
O35 C:86A601 2.6 12.4 1.0
P24 C:86A601 2.9 9.6 1.0
CE1 C:HIS69 3.0 8.2 1.0
CE1 C:HIS196 3.1 8.8 1.0
CG C:HIS196 3.1 6.6 1.0
CG C:HIS69 3.2 8.4 1.0
CB C:HIS196 3.5 7.5 1.0
CB C:HIS69 3.5 7.7 1.0
O23 C:86A601 4.0 9.4 1.0
CG C:GLU72 4.0 6.9 1.0
O C:HOH628 4.1 9.4 1.0
C1 C:86A601 4.1 9.6 1.0
O C:SER197 4.2 8.5 1.0
O C:HOH627 4.2 10.4 1.0
C25 C:86A601 4.2 9.8 1.0
NE2 C:HIS69 4.2 8.0 1.0
NE2 C:HIS196 4.2 9.0 1.0
CD2 C:HIS69 4.3 9.6 1.0
CD2 C:HIS196 4.3 8.7 1.0
NH1 C:ARG127 4.3 9.6 1.0
CA C:HIS196 4.4 6.5 1.0
OE2 C:GLU270 4.6 12.1 1.0
O14 C:86A601 4.7 8.7 1.0
C2 C:86A601 4.7 8.3 1.0
N C:SER197 4.7 7.4 1.0
CA C:HIS69 4.8 7.4 1.0
N C:HIS69 4.9 7.8 1.0
CB C:GLU72 5.0 8.1 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 03:30:19 2020
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