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Zinc in PDB 1zg9: Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B

Enzymatic activity of Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B

All present enzymatic activity of Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B:
3.4.17.2;

Protein crystallography data

The structure of Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B, PDB code: 1zg9 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 (°) 66.839, 102.484, 136.157, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 27.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B (pdb code 1zg9). 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 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B, PDB code: 1zg9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1zg9

Go back to Zinc Binding Sites List in 1zg9
Zinc binding site 1 out of 3 in the Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic 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 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:23.2
occ:1.00
 ND1 A:HIS69 2.1 14.7 1.0
ND1 A:HIS196 2.1 18.6 1.0
S A:L06401 2.2 30.3 1.0
OE1 A:GLU72 2.3 20.9 1.0
OE2 A:GLU72 2.5 18.9 1.0
CD A:GLU72 2.7 19.6 1.0
CE1 A:HIS69 3.0 16.7 1.0
CG A:HIS196 3.1 16.6 1.0
CE1 A:HIS196 3.1 16.6 1.0
CG A:HIS69 3.1 13.2 1.0
C1 A:L06401 3.2 31.0 1.0
CB A:HIS196 3.4 14.7 1.0
CB A:HIS69 3.5 12.2 1.0
O A:HOH1013 4.0 13.1 1.0
NE2 A:HIS69 4.2 17.0 1.0
O A:SER197 4.2 14.2 1.0
NE2 A:HIS196 4.2 18.6 1.0
CD2 A:HIS69 4.2 15.3 1.0
CD2 A:HIS196 4.2 16.1 1.0
CG A:GLU72 4.3 16.1 1.0
CA A:HIS196 4.4 17.6 1.0
C2 A:L06401 4.5 36.0 1.0
O A:HOH1029 4.6 23.2 1.0
O11 A:L06401 4.6 29.8 1.0
NH1 A:ARG127 4.6 30.8 1.0
C10 A:L06401 4.6 34.5 1.0
N A:SER197 4.6 17.4 1.0
CA A:HIS69 4.8 12.0 1.0
N A:HIS69 4.8 10.9 1.0
OE1 A:GLU270 4.9 33.7 1.0

Zinc binding site 2 out of 3 in 1zg9

Go back to Zinc Binding Sites List in 1zg9
Zinc binding site 2 out of 3 in the Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic 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 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:24.1
occ:1.00
 ND1 B:HIS69 2.1 18.8 1.0
OE2 B:GLU72 2.1 16.0 1.0
ND1 B:HIS196 2.1 17.4 1.0
OE1 B:GLU72 2.4 19.8 1.0
S B:L06501 2.5 33.4 1.0
CD B:GLU72 2.6 16.4 1.0
CE1 B:HIS69 3.0 18.5 1.0
CG B:HIS196 3.1 16.2 1.0
CG B:HIS69 3.1 19.2 1.0
CE1 B:HIS196 3.2 13.2 1.0
CB B:HIS196 3.3 14.1 1.0
CB B:HIS69 3.5 16.9 1.0
C1 B:L06501 3.6 35.5 1.0
O B:HOH1412 3.8 32.5 1.0
O B:HOH1097 4.1 10.2 1.0
NE2 B:HIS69 4.1 19.4 1.0
CG B:GLU72 4.1 18.5 1.0
O B:SER197 4.2 19.9 1.0
CA B:HIS196 4.2 15.1 1.0
CD2 B:HIS69 4.2 20.0 1.0
CD2 B:HIS196 4.3 16.7 1.0
NE2 B:HIS196 4.3 16.9 1.0
NH1 B:ARG127 4.4 28.3 1.0
N B:SER197 4.4 14.8 1.0
O B:HOH1115 4.5 26.4 1.0
O11 B:L06501 4.7 42.5 1.0
C10 B:L06501 4.7 38.2 1.0
C2 B:L06501 4.8 38.5 1.0
CA B:HIS69 4.8 16.9 1.0
N B:HIS69 4.9 18.2 1.0
C B:HIS196 4.9 13.8 1.0
OE1 B:GLU270 4.9 30.5 1.0
CB B:GLU72 5.0 14.9 1.0

Zinc binding site 3 out of 3 in 1zg9

Go back to Zinc Binding Sites List in 1zg9
Zinc binding site 3 out of 3 in the Crystal Structure of 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic 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 5-{[Amino(Imino)Methyl]Amino}-2- (Sulfanylmethyl)Pentanoic Acid Bound to Activated Porcine Pancreatic Carboxypeptidase B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:22.0
occ:1.00
 ND1 C:HIS69 2.0 17.6 1.0
OE1 C:GLU72 2.1 14.6 1.0
ND1 C:HIS196 2.1 12.3 1.0
S C:L06601 2.4 23.8 1.0
OE2 C:GLU72 2.4 19.7 1.0
CD C:GLU72 2.6 16.3 1.0
CE1 C:HIS69 2.9 14.2 1.0
CE1 C:HIS196 3.0 13.1 1.0
C1 C:L06601 3.0 31.1 1.0
CG C:HIS196 3.2 16.4 1.0
CG C:HIS69 3.2 13.5 1.0
CB C:HIS196 3.6 15.4 1.0
CB C:HIS69 3.6 11.8 1.0
O C:HOH1185 4.1 11.8 1.0
NE2 C:HIS69 4.1 18.2 1.0
CG C:GLU72 4.1 16.0 1.0
NE2 C:HIS196 4.2 15.7 1.0
O C:SER197 4.2 23.5 1.0
NH1 C:ARG127 4.2 22.1 1.0
CD2 C:HIS69 4.2 13.4 1.0
CD2 C:HIS196 4.3 15.5 1.0
O C:HOH1195 4.3 25.2 1.0
C2 C:L06601 4.4 31.5 1.0
O11 C:L06601 4.4 30.6 1.0
CA C:HIS196 4.4 16.8 1.0
C10 C:L06601 4.6 33.9 1.0
N C:SER197 4.6 18.4 1.0
OE1 C:GLU270 4.7 33.7 1.0
CA C:HIS69 4.9 10.5 1.0
N C:HIS69 5.0 15.7 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 Dec 16 03:15:39 2020

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