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Zinc in PDB 3zuk: Crystal Structure of Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor, PDB code: 3zuk was solved by D.M.Ferraris, D.Sbardella, A.Petrera, S.Marini, B.Amstutz, M.Coletta, P.Sander, M.Rizzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.290, 198.770, 63.270, 90.00, 90.00, 90.00
R / Rfree (%) 17.509 / 24.964

Other elements in 3zuk:

The structure of Crystal Structure of Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor (pdb code 3zuk). 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 Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor, PDB code: 3zuk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3zuk

Go back to Zinc Binding Sites List in 3zuk
Zinc binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor


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 Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1664

b:18.6
occ:1.00
O1P A:RDF1665 1.9 15.6 1.0
NE2 A:HIS497 2.0 16.0 1.0
OE1 A:GLU560 2.0 17.8 1.0
NE2 A:HIS493 2.2 13.2 1.0
CD A:GLU560 2.9 14.5 1.0
P A:RDF1665 2.9 15.5 1.0
CD2 A:HIS497 2.9 15.2 1.0
CE1 A:HIS497 3.0 16.1 1.0
OE2 A:GLU560 3.0 15.0 1.0
O2P A:RDF1665 3.1 17.9 1.0
CE1 A:HIS493 3.1 13.9 1.0
CD2 A:HIS493 3.2 13.6 1.0
NE2 A:HIS622 3.8 14.6 1.0
O1 A:RDF1665 3.9 16.9 1.0
ND1 A:HIS497 4.0 15.5 1.0
CG A:HIS497 4.1 16.8 1.0
CD2 A:HIS622 4.1 14.9 1.0
N A:RDF1665 4.1 17.4 1.0
CA A:RDF1665 4.1 18.8 1.0
ND1 A:HIS493 4.3 14.0 1.0
CG A:GLU560 4.3 12.8 1.0
CG A:HIS493 4.3 14.7 1.0
O A:RDF1665 4.5 19.2 1.0
C A:RDF1665 4.5 20.0 1.0
O1 A:PGE1684 4.7 32.6 1.0
O5 A:RDF1665 4.7 19.3 1.0
C1 A:RDF1665 4.7 18.4 1.0
CA A:GLU560 4.8 12.9 1.0
NH2 A:ARG628 4.8 9.9 1.0
CB A:GLU560 4.9 11.6 1.0
OE1 A:GLU494 4.9 15.9 1.0
C1 A:PGE1684 4.9 36.5 1.0
CE1 A:HIS622 5.0 14.7 1.0

Zinc binding site 2 out of 2 in 3zuk

Go back to Zinc Binding Sites List in 3zuk
Zinc binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor


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 Mycobacterium Tuberculosis Zinc Metalloprotease ZMP1 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1664

b:16.7
occ:1.00
OE1 B:GLU560 1.9 19.6 1.0
O1P B:RDF1665 2.0 17.0 1.0
NE2 B:HIS493 2.1 11.7 1.0
NE2 B:HIS497 2.1 17.1 1.0
CD B:GLU560 2.9 18.2 1.0
P B:RDF1665 3.0 16.7 1.0
CE1 B:HIS497 3.0 18.1 1.0
CE1 B:HIS493 3.0 14.0 1.0
OE2 B:GLU560 3.1 20.8 1.0
CD2 B:HIS493 3.1 13.2 1.0
O2P B:RDF1665 3.2 19.0 1.0
CD2 B:HIS497 3.2 14.7 1.0
NE2 B:HIS622 3.7 9.1 1.0
CA B:RDF1665 4.0 19.8 1.0
N B:RDF1665 4.0 19.2 1.0
O1 B:RDF1665 4.1 19.0 1.0
CD2 B:HIS622 4.1 9.2 1.0
ND1 B:HIS497 4.1 16.4 1.0
ND1 B:HIS493 4.2 14.4 1.0
CG B:HIS493 4.3 13.4 1.0
CG B:GLU560 4.3 15.7 1.0
CG B:HIS497 4.3 15.9 1.0
O B:RDF1665 4.3 20.6 1.0
C B:RDF1665 4.4 20.8 1.0
O5 B:RDF1665 4.7 17.3 1.0
CB B:GLU560 4.7 13.2 1.0
CA B:GLU560 4.7 13.6 1.0
C1 B:RDF1665 4.9 18.1 1.0
CH3 B:ACT1691 4.9 53.5 1.0
CE1 B:HIS622 4.9 11.8 1.0
OE2 B:GLU494 5.0 16.5 1.0

Reference:

D.M.Ferraris, D.Sbardella, A.Petrera, S.Marini, B.Amstutz, M.Coletta, P.Sander, M.Rizzi. Crystal Structure of Mycobacterium Tuberculosis Zinc-Dependent Metalloprotease-1 (ZMP1), A Metalloprotease Involved in Pathogenicity. J.Biol.Chem. V. 286 32475 2011.
ISSN: ISSN 0021-9258
PubMed: 21813647
DOI: 10.1074/JBC.M111.271809
Page generated: Wed Dec 16 05:00:02 2020

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