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Zinc in PDB 1zg8: Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B

Enzymatic activity of Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B

All present enzymatic activity of Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B:
3.4.17.2;

Protein crystallography data

The structure of Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B, PDB code: 1zg8 was solved by M.Adler, J.Bryant, B.Buckman, I.Islam, B.Larsen, S.Finster, L.Kent, K.May, R.Mohan, S.Yuan, M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.896, 99.511, 136.379, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 29.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B (pdb code 1zg8). 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 (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B, PDB code: 1zg8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1zg8

Go back to Zinc Binding Sites List in 1zg8
Zinc binding site 1 out of 3 in the Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B


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 (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:28.3
occ:1.00
 ND1 A:HIS69 2.0 21.4 1.0
OE1 A:GLU72 2.2 29.1 1.0
S A:L98401 2.3 38.3 1.0
ND1 A:HIS196 2.3 28.9 1.0
OE2 A:GLU72 2.4 28.9 1.0
CD A:GLU72 2.6 22.6 1.0
CE1 A:HIS69 2.9 23.2 1.0
C1 A:L98401 3.0 37.9 1.0
CG A:HIS69 3.0 22.1 1.0
CE1 A:HIS196 3.1 20.1 1.0
CG A:HIS196 3.2 20.4 1.0
CB A:HIS69 3.5 25.2 1.0
CB A:HIS196 3.5 21.8 1.0
O A:HOH1002 3.8 19.3 1.0
NE2 A:HIS69 4.1 21.8 1.0
CD2 A:HIS69 4.1 22.2 1.0
CG A:GLU72 4.1 21.4 1.0
NE2 A:HIS196 4.2 24.2 1.0
CD2 A:HIS196 4.2 24.6 1.0
C2 A:L98401 4.3 38.3 1.0
O A:SER197 4.4 19.3 1.0
O A:HOH1067 4.4 28.9 1.0
CA A:HIS196 4.4 23.4 1.0
O14 A:L98401 4.4 44.1 1.0
NH1 A:ARG127 4.4 46.1 1.0
C13 A:L98401 4.4 41.9 1.0
O A:HOH1014 4.5 25.8 1.0
N A:HIS69 4.6 23.9 1.0
CA A:HIS69 4.7 22.5 1.0
N A:SER197 4.8 22.8 1.0
CB A:GLU72 4.9 20.7 1.0
OE2 A:GLU270 5.0 34.5 1.0
CB A:PHE68 5.0 22.4 1.0

Zinc binding site 2 out of 3 in 1zg8

Go back to Zinc Binding Sites List in 1zg8
Zinc binding site 2 out of 3 in the Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B


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 (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:28.2
occ:1.00
 ND1 B:HIS69 2.0 15.7 1.0
ND1 B:HIS196 2.0 20.3 1.0
OE1 B:GLU72 2.3 25.4 1.0
S B:L98501 2.3 39.9 1.0
OE2 B:GLU72 2.4 30.3 1.0
CD B:GLU72 2.6 28.6 1.0
CE1 B:HIS196 2.9 23.8 1.0
CE1 B:HIS69 2.9 16.9 1.0
CG B:HIS69 3.0 17.8 1.0
CG B:HIS196 3.1 23.1 1.0
C1 B:L98501 3.3 41.4 1.0
CB B:HIS69 3.4 17.3 1.0
CB B:HIS196 3.6 22.9 1.0
O B:HOH1006 3.8 22.4 1.0
NE2 B:HIS196 4.1 28.1 1.0
O B:HOH1341 4.1 24.9 1.0
NE2 B:HIS69 4.1 16.4 1.0
CG B:GLU72 4.1 23.8 1.0
CD2 B:HIS69 4.2 14.1 1.0
CD2 B:HIS196 4.2 22.2 1.0
O B:HOH1410 4.3 35.5 1.0
CA B:HIS196 4.4 23.6 1.0
O B:SER197 4.4 28.0 1.0
O14 B:L98501 4.5 51.7 1.0
N B:HIS69 4.6 21.4 1.0
CA B:HIS69 4.7 19.8 1.0
N B:SER197 4.7 21.1 1.0
C2 B:L98501 4.7 42.5 1.0
NH1 B:ARG127 4.9 41.9 1.0
CB B:GLU72 4.9 19.1 1.0
C13 B:L98501 5.0 47.5 1.0

Zinc binding site 3 out of 3 in 1zg8

Go back to Zinc Binding Sites List in 1zg8
Zinc binding site 3 out of 3 in the Crystal Structure of (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B


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 (R)-2-(3-{[Amino(Imino) Methyl]Amino}Phenyl)-3-Sulfanylpropanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:32.5
occ:1.00
 ND1 C:HIS196 2.0 19.4 1.0
S C:L98601 2.1 43.6 1.0
OE2 C:GLU72 2.2 32.4 1.0
ND1 C:HIS69 2.2 28.1 1.0
OE1 C:GLU72 2.3 26.6 1.0
CD C:GLU72 2.5 30.8 1.0
CE1 C:HIS196 3.0 23.6 1.0
CG C:HIS196 3.1 26.4 1.0
CE1 C:HIS69 3.1 25.0 1.0
C1 C:L98601 3.1 48.9 1.0
CG C:HIS69 3.3 26.3 1.0
CB C:HIS196 3.4 32.0 1.0
CB C:HIS69 3.7 30.5 1.0
O C:HOH1018 4.0 19.9 1.0
CG C:GLU72 4.1 28.3 1.0
O C:SER197 4.1 32.6 1.0
NE2 C:HIS196 4.1 27.1 1.0
NH2 C:ARG127 4.2 37.3 1.0
CD2 C:HIS196 4.2 23.8 1.0
CA C:HIS196 4.2 32.0 1.0
N C:SER197 4.3 29.8 1.0
NE2 C:HIS69 4.3 22.6 1.0
CD2 C:HIS69 4.4 20.3 1.0
C2 C:L98601 4.5 54.1 1.0
O C:HOH1211 4.5 36.5 1.0
O14 C:L98601 4.6 52.8 1.0
C13 C:L98601 4.7 54.7 1.0
O C:HOH1344 4.7 33.8 1.0
N C:HIS69 4.8 32.7 1.0
OE1 C:GLU270 4.8 42.6 1.0
C C:HIS196 4.8 28.9 1.0
CB C:GLU72 4.9 26.3 1.0
CA C:HIS69 4.9 30.3 1.0
CZ C:ARG127 5.0 39.5 1.0

Reference:

M.Adler, J.Bryant, B.Buckman, I.Islam, B.Larsen, S.Finster, L.Kent, K.May, R.Mohan, S.Yuan, M.Whitlow. Crystal Structures of Potent Thiol-Based Inhibitors Bound to Carboxypeptidase B. Biochemistry V. 44 9339 2005.
ISSN: ISSN 0006-2960
PubMed: 15982000
DOI: 10.1021/BI0501941
Page generated: Wed Oct 16 21:14:41 2024

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