Atomistry » Zinc » PDB 5dor-5e6a » 5dpe
Atomistry »
  Zinc »
    PDB 5dor-5e6a »
      5dpe »

Zinc in PDB 5dpe: Thermolysin in Complex with Inhibitor.

Enzymatic activity of Thermolysin in Complex with Inhibitor.

All present enzymatic activity of Thermolysin in Complex with Inhibitor.:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Inhibitor., PDB code: 5dpe was solved by S.G.Krimmer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.17 / 1.34
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.690, 92.690, 130.261, 90.00, 90.00, 120.00
R / Rfree (%) 12.7 / 15.6

Other elements in 5dpe:

The structure of Thermolysin in Complex with Inhibitor. also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermolysin in Complex with Inhibitor. (pdb code 5dpe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Thermolysin in Complex with Inhibitor., PDB code: 5dpe:

Zinc binding site 1 out of 1 in 5dpe

Go back to Zinc Binding Sites List in 5dpe
Zinc binding site 1 out of 1 in the Thermolysin 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 Thermolysin in Complex with Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:8.6
occ:1.00
O19 E:5H8401 2.0 8.7 1.0
OE2 E:GLU166 2.0 9.6 1.0
NE2 E:HIS142 2.0 8.3 1.0
NE2 E:HIS146 2.0 8.2 1.0
CD E:GLU166 2.8 9.2 1.0
CE1 E:HIS146 2.9 8.4 1.0
OE1 E:GLU166 3.0 9.6 1.0
CE1 E:HIS142 3.0 8.2 1.0
HE1 E:HIS146 3.0 10.1 1.0
P12 E:5H8401 3.0 8.9 1.0
CD2 E:HIS142 3.0 8.0 1.0
O18 E:5H8401 3.1 10.2 1.0
HH E:TYR157 3.1 12.6 1.0
CD2 E:HIS146 3.1 8.3 1.0
HE1 E:HIS142 3.2 9.8 1.0
HD2 E:HIS142 3.2 9.6 1.0
HE2 E:HIS231 3.3 11.6 1.0
HD2 E:HIS146 3.4 10.0 1.0
OH E:TYR157 3.8 10.5 1.0
NE2 E:HIS231 4.0 9.7 1.0
HA E:GLU166 4.0 10.2 1.0
N13 E:5H8401 4.1 9.3 1.0
ND1 E:HIS146 4.1 8.4 1.0
ND1 E:HIS142 4.1 9.1 1.0
C14 E:5H8401 4.1 9.0 1.0
HB2 E:SER169 4.1 10.6 1.0
CG E:HIS142 4.2 8.7 1.0
CG E:HIS146 4.2 8.3 1.0
CG E:GLU166 4.2 9.0 1.0
HB3 E:SER169 4.3 10.6 1.0
HE1 E:TYR157 4.3 11.0 1.0
HG2 E:GLU166 4.4 10.8 1.0
HD2 E:HIS231 4.4 11.8 1.0
C11 E:5H8401 4.5 13.6 1.0
C1 E:GOL411 4.5 16.1 1.0
CB E:SER169 4.6 8.8 1.0
CD2 E:HIS231 4.6 9.8 1.0
N10 E:5H8401 4.6 15.6 0.3
C15 E:5H8401 4.6 8.8 1.0
O24 E:5H8401 4.7 10.0 1.0
OG E:SER169 4.7 8.9 1.0
O1 E:GOL411 4.8 10.9 1.0
HG3 E:GLU166 4.8 10.8 1.0
N10 E:5H8401 4.8 17.0 0.7
CZ E:TYR157 4.8 9.9 1.0
HD1 E:HIS146 4.8 10.1 1.0
OE1 E:GLU143 4.9 15.9 1.0
HH22 E:ARG203 4.9 11.5 1.0
HD1 E:HIS142 4.9 10.9 1.0
CA E:GLU166 4.9 8.5 1.0
CE1 E:TYR157 4.9 9.1 1.0
OE2 E:GLU143 5.0 16.0 1.0

Reference:

S.G.Krimmer, G.Klebe. Thermodynamics of Protein-Ligand Interactions As A Reference For Computational Analysis: How to Assess Accuracy, Reliability and Relevance of Experimental Data. J. Comput. Aided Mol. Des. V. 29 867 2015.
ISSN: ISSN 1573-4951
PubMed: 26376645
DOI: 10.1007/S10822-015-9867-Y
Page generated: Wed Dec 16 06:08:39 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