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Zinc in PDB 2piy: Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex

Enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex

All present enzymatic activity of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex:
3.4.17.2;

Protein crystallography data

The structure of Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex, PDB code: 2piy 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) 21.45 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.877, 96.570, 136.025, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex (pdb code 2piy). 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 (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex, PDB code: 2piy:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2piy

Go back to Zinc Binding Sites List in 2piy
Zinc binding site 1 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} 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 (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:13.0
occ:1.00
ND1 A:HIS196 2.1 10.3 1.0
ND1 A:HIS69 2.1 12.1 1.0
OE1 A:GLU72 2.1 12.2 1.0
O25 A:528401 2.2 16.9 1.0
OE2 A:GLU72 2.5 12.0 1.0
CD A:GLU72 2.6 11.4 1.0
O26 A:528401 2.8 19.5 1.0
P24 A:528401 2.9 16.2 1.0
CE1 A:HIS196 3.0 11.9 1.0
CE1 A:HIS69 3.0 12.2 1.0
CG A:HIS196 3.1 10.7 1.0
CG A:HIS69 3.2 11.5 1.0
CB A:HIS196 3.5 10.2 1.0
CB A:HIS69 3.6 10.2 1.0
O A:SER197 4.1 10.8 1.0
CG A:GLU72 4.1 11.1 1.0
O A:HOH428 4.2 15.1 1.0
O A:HOH411 4.2 11.4 1.0
C27 A:528401 4.2 16.0 1.0
NE2 A:HIS196 4.2 12.1 1.0
NE2 A:HIS69 4.2 11.4 1.0
CD2 A:HIS196 4.3 11.6 1.0
CD2 A:HIS69 4.3 10.7 1.0
C15 A:528401 4.3 17.6 1.0
C1 A:528401 4.4 16.6 1.0
OE2 A:GLU270 4.4 17.1 1.0
CA A:HIS196 4.5 10.6 1.0
NH1 A:ARG127 4.5 12.1 1.0
N A:SER197 4.7 9.5 1.0
O14 A:528401 4.7 16.9 1.0
C2 A:528401 4.7 17.9 1.0
OE1 A:GLU270 4.9 16.7 1.0
CA A:HIS69 4.9 10.1 1.0
C28 A:528401 5.0 15.7 1.0

Zinc binding site 2 out of 3 in 2piy

Go back to Zinc Binding Sites List in 2piy
Zinc binding site 2 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} 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 (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:9.7
occ:1.00
ND1 B:HIS196 2.1 8.2 1.0
OE1 B:GLU72 2.1 9.8 1.0
ND1 B:HIS69 2.1 10.3 1.0
O25 B:528501 2.2 12.1 1.0
OE2 B:GLU72 2.5 9.9 1.0
CD B:GLU72 2.6 9.6 1.0
O26 B:528501 2.9 14.1 1.0
P24 B:528501 3.0 10.9 1.0
CE1 B:HIS196 3.0 8.5 1.0
CE1 B:HIS69 3.0 10.5 1.0
CG B:HIS196 3.1 6.9 1.0
CG B:HIS69 3.2 8.1 1.0
CB B:HIS196 3.5 7.8 1.0
CB B:HIS69 3.6 8.9 1.0
O B:SER197 4.1 10.1 1.0
CG B:GLU72 4.1 9.3 1.0
O B:HOH532 4.2 10.7 1.0
NE2 B:HIS196 4.2 8.2 1.0
C27 B:528501 4.2 10.5 1.0
NE2 B:HIS69 4.2 9.5 1.0
O B:HOH503 4.3 9.3 1.0
CD2 B:HIS196 4.3 9.1 1.0
CD2 B:HIS69 4.3 8.7 1.0
C15 B:528501 4.3 11.5 1.0
OE2 B:GLU270 4.4 14.1 1.0
C1 B:528501 4.4 12.0 1.0
NH1 B:ARG127 4.4 9.9 1.0
CA B:HIS196 4.5 7.9 1.0
N B:SER197 4.7 8.1 1.0
O14 B:528501 4.7 10.2 1.0
C2 B:528501 4.8 12.4 1.0
OE1 B:GLU270 4.9 11.8 1.0
CA B:HIS69 4.9 9.2 1.0

Zinc binding site 3 out of 3 in 2piy

Go back to Zinc Binding Sites List in 2piy
Zinc binding site 3 out of 3 in the Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} 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 (S)-2-(3-Aminomethyl-Phenyl)-3-{Hydroxy- [(R)-2-Methyl-1-(3-Phenyl-Propane-1-Sulfonylamino)-Propyl]- Phosphinoyl}-Propionic Acid {Zk 528} Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:10.1
occ:1.00
ND1 C:HIS196 2.1 10.6 1.0
OE1 C:GLU72 2.1 10.8 1.0
ND1 C:HIS69 2.1 11.5 1.0
O25 C:528601 2.3 11.2 1.0
OE2 C:GLU72 2.5 10.1 1.0
CD C:GLU72 2.6 8.7 1.0
O26 C:528601 2.7 15.6 1.0
P24 C:528601 2.9 11.2 1.0
CE1 C:HIS196 3.0 11.4 1.0
CE1 C:HIS69 3.0 10.0 1.0
CG C:HIS196 3.1 9.9 1.0
CG C:HIS69 3.2 9.3 1.0
CB C:HIS196 3.5 11.4 1.0
CB C:HIS69 3.6 10.2 1.0
CG C:GLU72 4.1 9.2 1.0
O C:SER197 4.1 10.4 1.0
C27 C:528601 4.2 10.3 1.0
O C:HOH607 4.2 11.9 1.0
NE2 C:HIS196 4.2 11.5 1.0
NE2 C:HIS69 4.2 10.8 1.0
O C:HOH611 4.2 11.7 1.0
CD2 C:HIS196 4.3 10.6 1.0
C15 C:528601 4.3 11.3 1.0
CD2 C:HIS69 4.3 10.0 1.0
NH1 C:ARG127 4.3 9.3 1.0
C1 C:528601 4.4 10.0 1.0
CA C:HIS196 4.5 10.0 1.0
O14 C:528601 4.6 11.4 1.0
C2 C:528601 4.6 11.9 1.0
N C:SER197 4.7 9.9 1.0
OE2 C:GLU270 4.8 17.5 1.0
OE1 C:GLU270 4.9 13.9 1.0
CA C:HIS69 4.9 9.3 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: Wed Dec 16 03:48:10 2020

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