Atomistry » Zinc » PDB 4ih3-4iuu » 4in9
Atomistry »
  Zinc »
    PDB 4ih3-4iuu »
      4in9 »

Zinc in PDB 4in9: Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp

Protein crystallography data

The structure of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp, PDB code: 4in9 was solved by T.Guevara, M.Ksiazek, P.D.Skottrup, N.Cerda-Costa, S.Trillo-Muyo, I.Dediego, E.Riise, 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) 42.87 / 1.55
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 86.050, 86.050, 49.440, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.1

Other elements in 4in9:

The structure of Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp (pdb code 4in9). 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 Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp, PDB code: 4in9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4in9

Go back to Zinc Binding Sites List in 4in9
Zinc binding site 1 out of 2 in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp


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 Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.1
occ:1.00
NE2 A:HIS155 2.0 8.8 1.0
NE2 A:HIS165 2.1 11.1 1.0
NE2 A:HIS159 2.1 9.1 1.0
N B:SER1 2.2 10.4 1.0
O B:SER1 2.2 12.4 1.0
C B:SER1 3.0 13.4 1.0
CE1 A:HIS155 3.0 9.7 1.0
CA B:SER1 3.0 10.2 1.0
CD2 A:HIS165 3.1 10.5 1.0
CE1 A:HIS165 3.1 11.9 1.0
CD2 A:HIS155 3.1 9.0 1.0
CD2 A:HIS159 3.1 9.5 1.0
CE1 A:HIS159 3.1 10.1 1.0
OG B:SER1 3.5 14.9 1.0
CB B:SER1 3.8 12.9 1.0
OE2 A:GLU156 4.1 10.9 1.0
ND1 A:HIS155 4.2 9.9 1.0
CG A:HIS155 4.2 8.8 1.0
CG A:HIS165 4.2 11.1 1.0
ND1 A:HIS165 4.2 13.6 1.0
N B:TRP2 4.3 11.9 1.0
CG A:HIS159 4.3 9.8 1.0
ND1 A:HIS159 4.3 11.2 1.0
O A:HOH605 4.3 19.4 1.0
OE1 A:GLU156 4.6 10.4 1.0
CD A:GLU156 4.7 9.9 1.0
NE1 B:TRP2 4.8 11.4 1.0
O A:HOH594 4.8 43.5 1.0
CB A:PRO175 4.9 12.2 1.0
O3 A:GOL306 4.9 44.2 1.0
CD1 B:TRP2 4.9 13.0 1.0
CE2 B:TRP2 5.0 12.3 1.0
CE A:MET173 5.0 9.1 1.0
CA B:TRP2 5.0 12.8 1.0

Zinc binding site 2 out of 2 in 4in9

Go back to Zinc Binding Sites List in 4in9
Zinc binding site 2 out of 2 in the Structure of Karilysin Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp


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 Mmp-Like Catalytic Domain in Complex with Inhibitory Tetrapeptide Swfp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.4
occ:1.00
OD2 A:ASP104 2.0 10.3 1.0
NE2 A:HIS102 2.0 11.0 1.0
NE2 A:HIS117 2.0 10.8 1.0
ND1 A:HIS133 2.0 11.6 1.0
CG A:ASP104 2.8 12.9 1.0
CD2 A:HIS102 2.9 11.2 1.0
CE1 A:HIS133 2.9 12.2 1.0
CE1 A:HIS117 3.0 10.0 1.0
CD2 A:HIS117 3.0 10.9 1.0
CE1 A:HIS102 3.0 10.9 1.0
OD1 A:ASP104 3.1 12.0 1.0
CG A:HIS133 3.1 11.4 1.0
CB A:HIS133 3.5 9.6 1.0
CG A:HIS102 4.1 11.3 1.0
CG A:HIS117 4.1 9.3 1.0
ND1 A:HIS117 4.1 9.8 1.0
NE2 A:HIS133 4.1 12.4 1.0
ND1 A:HIS102 4.1 11.5 1.0
CD2 A:HIS133 4.2 12.8 1.0
CB A:ASP104 4.2 13.3 1.0
O A:TYR106 4.2 10.5 1.0
CE1 A:PHE119 4.4 13.1 1.0
CZ A:PHE119 4.7 13.5 1.0
CB A:TYR106 4.8 10.6 1.0
C A:TYR106 4.9 12.1 1.0
CE2 A:PHE108 4.9 12.8 1.0
O A:HOH429 5.0 13.4 1.0
CA A:HIS133 5.0 8.3 1.0

Reference:

T.Guevara, M.Ksiazek, P.D.Skottrup, N.Cerda-Costa, S.Trillo-Muyo, I.De Diego, E.Riise, J.Potempa, F.X.Gomis-Ruth. Structure of the Catalytic Domain of the Tannerella Forsythia Matrix Metallopeptidase Karilysin in Complex with A Tetrapeptidic Inhibitor. Acta Crystallogr.,Sect.F V. 69 472 2013.
ISSN: ESSN 1744-3091
PubMed: 23695557
DOI: 10.1107/S1744309113007392
Page generated: Wed Dec 16 05:24:22 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