Atomistry » Zinc » PDB 2xjy-2xxg » 2xs4
Atomistry »
  Zinc »
    PDB 2xjy-2xxg »
      2xs4 »

Zinc in PDB 2xs4: Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium

Protein crystallography data

The structure of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium, PDB code: 2xs4 was solved by N.Cerda-Costa, T.Guevara, A.Y.Karim, M.Ksiazek, K.-A.Nguyen, J.L.Arolas, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.70
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 85.790, 85.790, 53.480, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.6

Other elements in 2xs4:

The structure of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium (pdb code 2xs4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium, PDB code: 2xs4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2xs4

Go back to Zinc Binding Sites List in 2xs4
Zinc binding site 1 out of 2 in the Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn998

b:14.5
occ:1.00
NE2 A:HIS117 2.0 14.9 1.0
NE2 A:HIS102 2.0 14.3 1.0
OD1 A:ASP104 2.0 16.1 1.0
ND1 A:HIS133 2.1 13.8 1.0
CG A:ASP104 2.9 19.4 1.0
CD2 A:HIS102 2.9 15.2 1.0
CE1 A:HIS117 3.0 16.3 1.0
CE1 A:HIS133 3.0 15.3 1.0
CD2 A:HIS117 3.0 14.6 1.0
CE1 A:HIS102 3.0 14.7 1.0
CG A:HIS133 3.1 14.1 1.0
OD2 A:ASP104 3.2 18.7 1.0
CB A:HIS133 3.5 13.5 1.0
O A:TYR106 4.0 23.3 1.0
ND1 A:HIS117 4.1 15.8 1.0
CG A:HIS102 4.1 16.8 1.0
ND1 A:HIS102 4.1 14.2 1.0
CG A:HIS117 4.1 15.1 1.0
NE2 A:HIS133 4.1 14.6 1.0
CD2 A:HIS133 4.2 14.5 1.0
CB A:ASP104 4.3 20.3 1.0
CE2 A:PHE119 4.5 16.0 1.0
CB A:TYR106 4.6 24.3 1.0
CZ A:PHE119 4.8 17.7 1.0
C A:TYR106 4.9 24.0 1.0
CE1 A:PHE108 4.9 19.4 1.0
O A:HOH2108 4.9 8.4 1.0
CZ A:PHE108 5.0 19.1 1.0
CA A:HIS133 5.0 13.3 1.0

Zinc binding site 2 out of 2 in 2xs4

Go back to Zinc Binding Sites List in 2xs4
Zinc binding site 2 out of 2 in the Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn999

b:13.3
occ:1.00
NE2 A:HIS155 2.0 12.3 1.0
NE2 A:HIS165 2.1 13.8 1.0
N B:ALA301 2.1 14.5 1.0
NE2 A:HIS159 2.2 12.7 1.0
O B:ALA301 2.2 15.2 1.0
C B:ALA301 2.9 16.4 1.0
CD2 A:HIS165 3.0 13.9 1.0
CE1 A:HIS155 3.0 13.4 1.0
CA B:ALA301 3.0 15.7 1.0
CD2 A:HIS155 3.0 12.7 1.0
CE1 A:HIS165 3.1 14.5 1.0
CD2 A:HIS159 3.1 12.8 1.0
CE1 A:HIS159 3.1 13.9 1.0
CB B:ALA301 3.8 16.0 1.0
OE2 A:GLU156 4.1 14.6 1.0
ND1 A:HIS155 4.1 12.4 1.0
CG A:HIS165 4.1 13.3 1.0
CG A:HIS155 4.2 12.6 1.0
ND1 A:HIS165 4.2 14.2 1.0
N B:PHE302 4.2 17.8 1.0
ND1 A:HIS159 4.3 13.8 1.0
O A:HOH2191 4.3 12.0 1.0
CG A:HIS159 4.3 13.1 1.0
OE1 A:GLU156 4.7 15.8 1.0
CD A:GLU156 4.7 13.3 1.0
O A:HOH2115 4.8 30.1 1.0
CB A:PRO175 4.9 15.7 1.0
CE A:MET173 4.9 12.6 1.0
CA B:PHE302 5.0 19.1 1.0

Reference:

N.Cerda-Costa, T.Guevara, A.Y.Karim, M.Ksiazek, K.A.Nguyen, J.L.Arolas, J.Potempa, F.X.Gomis-Ruth. The Structure of the Catalytic Domain of Tannerella Forsythia Karilysin Reveals It Is A Bacterial Xenologue of Animal Matrix Metalloproteinases. Mol.Microbiol. V. 79 119 2011.
ISSN: ISSN 0950-382X
PubMed: 21166898
DOI: 10.1111/J.1365-2958.2010.07434.X
Page generated: Wed Dec 16 04:00:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy