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Zinc in PDB 3b7i: Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid

Enzymatic activity of Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid

All present enzymatic activity of Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid:
3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid, PDB code: 3b7i was solved by N.J.Ataie, Q.Q.Hoang, M.P.D.Zahniser, A.Milne, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.37 / 1.75
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.907, 109.907, 91.095, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 20.9

Other elements in 3b7i:

The structure of Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid also contains other interesting chemical elements:

Potassium (K) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid (pdb code 3b7i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid, PDB code: 3b7i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3b7i

Go back to Zinc Binding Sites List in 3b7i
Zinc binding site 1 out of 2 in the Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid


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 the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn292

b:11.8
occ:1.00
 NE2 A:HIS256 2.0 15.2 1.0
OE2 A:GLU152 2.0 11.9 1.0
O1 A:PLU500 2.0 4.5 0.4
OD2 A:ASP117 2.0 11.6 1.0
O A:LEU604 2.1 23.4 0.6
OE1 A:GLU152 2.4 9.0 1.0
CD A:GLU152 2.5 8.6 1.0
OXT A:LEU604 2.6 23.1 0.6
O2 A:PLU500 2.6 6.6 0.4
C A:LEU604 2.7 23.3 0.6
P A:PLU500 2.8 6.3 0.4
CD2 A:HIS256 3.0 13.8 1.0
CE1 A:HIS256 3.0 15.8 1.0
CG A:ASP117 3.0 10.5 1.0
OD1 A:ASP117 3.3 10.4 1.0
ZN A:ZN293 3.9 10.4 1.0
O A:HOH613 3.9 9.1 1.0
N A:PLU500 3.9 6.1 0.4
O3 A:PLU500 3.9 6.8 0.4
O A:HOH824 3.9 25.2 1.0
CG A:GLU152 4.0 10.2 1.0
CA A:LEU604 4.1 23.2 0.6
ND1 A:HIS256 4.1 17.2 1.0
CA A:PLU500 4.1 6.1 0.4
CG A:HIS256 4.1 12.9 1.0
CB A:ASP117 4.3 7.8 1.0
OE1 A:GLU151 4.4 8.9 1.0
CB A:LEU604 4.4 23.2 0.6
CE1 A:HIS97 4.5 8.5 1.0
CG2 A:THR101 4.6 11.3 1.0
O A:HOH683 4.6 25.9 1.0
NE2 A:HIS97 4.7 9.2 1.0
N A:LEU604 4.7 23.3 0.6
CD1 A:ILE255 4.8 6.0 1.0
CB A:GLU152 5.0 8.9 1.0
CB A:PLU500 5.0 6.4 0.4

Zinc binding site 2 out of 2 in 3b7i

Go back to Zinc Binding Sites List in 3b7i
Zinc binding site 2 out of 2 in the Crystal Structure of the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid


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 the S228A Mutant of the Aminopeptidase From Vibrio Proteolyticus in Complex with Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn293

b:10.4
occ:1.00
 OD1 A:ASP117 2.1 10.4 1.0
NE2 A:HIS97 2.1 9.2 1.0
OD1 A:ASP179 2.1 9.2 1.0
O2 A:PLU500 2.2 6.6 0.4
O A:LEU604 2.4 23.4 0.6
N A:LEU604 2.5 23.3 0.6
N A:PLU500 2.5 6.1 0.4
OD2 A:ASP179 2.6 15.1 1.0
CG A:ASP179 2.7 10.8 1.0
CA A:PLU500 3.0 6.1 0.4
CD2 A:HIS97 3.1 8.0 1.0
CE1 A:HIS97 3.1 8.5 1.0
C A:LEU604 3.1 23.3 0.6
CG A:ASP117 3.2 10.5 1.0
CA A:LEU604 3.2 23.2 0.6
P A:PLU500 3.2 6.3 0.4
OD2 A:ASP117 3.7 11.6 1.0
CB A:LEU604 3.7 23.2 0.6
OE1 A:GLU151 3.8 8.9 1.0
ZN A:ZN292 3.9 11.8 1.0
O1 A:PLU500 4.0 4.5 0.4
CB A:ASP118 4.2 6.8 1.0
CB A:ASP179 4.2 9.3 1.0
ND1 A:HIS97 4.2 9.6 1.0
CD A:GLU151 4.2 12.6 1.0
CG A:HIS97 4.2 8.0 1.0
OE2 A:GLU151 4.3 12.8 1.0
OE2 A:GLU152 4.3 11.9 1.0
OXT A:LEU604 4.3 23.1 0.6
CB A:ASP117 4.3 7.8 1.0
O3 A:PLU500 4.5 6.8 0.4
CB A:PLU500 4.5 6.4 0.4
CA A:ASP117 4.6 8.4 1.0
CG A:ASP118 4.7 7.2 1.0
CG A:MET180 4.8 7.1 1.0
C A:ASP117 4.8 7.9 1.0
SD A:MET180 4.8 8.3 1.0
CD A:GLU152 4.9 8.6 1.0
CA A:ASP179 4.9 8.7 1.0
OD2 A:ASP118 5.0 7.7 1.0
CG A:LEU604 5.0 23.4 0.6
N A:ASP118 5.0 6.7 1.0

Reference:

N.J.Ataie, Q.Q.Hoang, M.P.Zahniser, Y.Tu, A.Milne, G.A.Petsko, D.Ringe. Zinc Coordination Geometry and Ligand Binding Affinity: the Structural and Kinetic Analysis of the Second-Shell Serine 228 Residue and the Methionine 180 Residue of the Aminopeptidase From Vibrio Proteolyticus. Biochemistry V. 47 7673 2008.
ISSN: ISSN 0006-2960
PubMed: 18576673
DOI: 10.1021/BI702188E
Page generated: Thu Oct 24 11:27:08 2024

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