Atomistry » Zinc » PDB 5lyi-5m8o » 5m5f
Atomistry »
  Zinc »
    PDB 5lyi-5m8o »
      5m5f »

Zinc in PDB 5m5f: Thermolysin in Complex with Inhibitor and Krypton

Enzymatic activity of Thermolysin in Complex with Inhibitor and Krypton

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

Protein crystallography data

The structure of Thermolysin in Complex with Inhibitor and Krypton, PDB code: 5m5f was solved by S.G.Krimmer, J.Cramer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 1.33
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.428, 92.428, 130.192, 90.00, 90.00, 120.00
R / Rfree (%) 11.1 / 13.9

Other elements in 5m5f:

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

Krypton (Kr) 2 atoms
Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermolysin in Complex with Inhibitor and Krypton (pdb code 5m5f). 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 and Krypton, PDB code: 5m5f:

Zinc binding site 1 out of 1 in 5m5f

Go back to Zinc Binding Sites List in 5m5f
Zinc binding site 1 out of 1 in the Thermolysin in Complex with Inhibitor and Krypton


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 and Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:7.2
occ:1.00
O30 E:7GR408 2.0 7.8 1.0
OE2 E:GLU166 2.0 8.0 1.0
NE2 E:HIS142 2.0 7.3 1.0
NE2 E:HIS146 2.0 7.2 1.0
CD E:GLU166 2.8 7.2 1.0
CE1 E:HIS146 2.9 7.6 1.0
OE1 E:GLU166 3.0 7.7 1.0
CE1 E:HIS142 3.0 6.9 1.0
CD2 E:HIS142 3.0 7.1 1.0
HE1 E:HIS146 3.0 9.1 1.0
P28 E:7GR408 3.0 8.9 1.0
O29 E:7GR408 3.1 9.6 1.0
HH E:TYR157 3.1 10.8 1.0
CD2 E:HIS146 3.1 7.1 1.0
HD2 E:HIS142 3.2 8.6 1.0
HE1 E:HIS142 3.2 8.2 1.0
HE2 E:HIS231 3.3 10.0 1.0
HD2 E:HIS146 3.4 8.5 1.0
OH E:TYR157 3.8 9.0 1.0
HA E:GLU166 4.0 8.7 1.0
NE2 E:HIS231 4.0 8.3 1.0
N1 E:7GR408 4.0 9.2 1.0
ND1 E:HIS146 4.1 7.7 1.0
HB2 E:SER169 4.1 8.7 1.0
C2 E:7GR408 4.1 9.3 1.0
ND1 E:HIS142 4.1 7.1 1.0
CG E:HIS142 4.1 7.0 1.0
CG E:HIS146 4.2 7.1 1.0
CG E:GLU166 4.2 7.5 1.0
HB3 E:SER169 4.3 8.7 1.0
HE1 E:TYR157 4.3 10.3 1.0
HG2 E:GLU166 4.4 9.1 1.0
HD2 E:HIS231 4.4 9.3 1.0
C31 E:7GR408 4.5 10.8 1.0
CB E:SER169 4.5 7.3 1.0
CD2 E:HIS231 4.6 7.8 1.0
N34 E:7GR408 4.6 12.4 0.7
C5 E:7GR408 4.6 9.9 1.0
C3 E:GOL407 4.6 14.0 1.0
OG E:SER169 4.7 7.2 1.0
OE1 E:GLU143 4.7 10.8 1.0
O3 E:GOL407 4.8 9.7 1.0
HG3 E:GLU166 4.8 9.1 1.0
N34 E:7GR408 4.8 12.6 0.3
CZ E:TYR157 4.8 8.2 1.0
HD1 E:HIS146 4.8 9.2 1.0
O6 E:7GR408 4.9 10.7 1.0
CA E:GLU166 4.9 7.2 1.0
CE1 E:TYR157 4.9 8.6 1.0
HD1 E:HIS142 4.9 8.5 1.0
HH22 E:ARG203 4.9 9.7 1.0
CE1 E:HIS231 5.0 8.4 1.0

Reference:

S.G.Krimmer, J.Cramer, J.Schiebel, A.Heine, G.Klebe. How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin. J. Am. Chem. Soc. V. 139 10419 2017.
ISSN: ESSN 1520-5126
PubMed: 28696673
DOI: 10.1021/JACS.7B05028
Page generated: Wed Dec 16 06:31:49 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