Atomistry » Xenon, Xe » PDB 4zzc-6qii » 5m69
Atomistry »
  Xenon, Xe »
    PDB 4zzc-6qii »
      5m69 »

Xenon in PDB 5m69: Thermolysin in Complex with Inhibitor and Xenon

Enzymatic activity of Thermolysin in Complex with Inhibitor and Xenon

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

Protein crystallography data

The structure of Thermolysin in Complex with Inhibitor and Xenon, PDB code: 5m69 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) 46.24 / 1.44
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.476, 92.476, 129.938, 90.00, 90.00, 120.00
R / Rfree (%) 10.8 / 14.1

Other elements in 5m69:

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

Zinc (Zn) 1 atom
Calcium (Ca) 4 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Thermolysin in Complex with Inhibitor and Xenon (pdb code 5m69). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 2 binding sites of Xenon where determined in the Thermolysin in Complex with Inhibitor and Xenon, PDB code: 5m69:
Jump to Xenon binding site number: 1; 2;

Xenon binding site 1 out of 2 in 5m69

Go back to Xenon Binding Sites List in 5m69
Xenon binding site 1 out of 2 in the Thermolysin in Complex with Inhibitor and Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Thermolysin in Complex with Inhibitor and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe409

b:14.7
occ:0.68
HG E:LEU144 3.0 21.4 1.0
HA E:SER92 3.2 11.3 1.0
HD2 E:TYR84 3.2 12.0 1.0
HD21 E:LEU144 3.3 23.9 1.0
HA E:TYR81 3.5 10.6 1.0
HB2 E:TYR84 3.6 12.0 1.0
HA E:TYR93 3.6 12.8 1.0
CD2 E:TYR84 3.6 10.0 1.0
HB3 E:TYR93 3.7 12.9 1.0
C E:SER92 3.7 10.0 1.0
HG22 E:THR80 3.7 12.8 1.0
N E:TYR93 3.8 10.3 1.0
HD23 E:LEU144 3.8 23.9 1.0
CG E:LEU144 3.8 17.8 1.0
CD2 E:LEU144 3.8 19.9 1.0
HD11 E:LEU144 3.9 22.4 1.0
CA E:SER92 3.9 9.5 1.0
HD11 E:ILE100 4.0 15.4 1.0
HG22 E:VAL148 4.0 12.6 1.0
H E:TYR93 4.0 12.4 1.0
HG23 E:VAL148 4.0 12.6 1.0
O E:HOH570 4.0 10.8 1.0
HG21 E:VAL148 4.1 12.6 1.0
CG E:TYR84 4.1 9.6 1.0
O E:SER92 4.1 11.1 1.0
CA E:TYR93 4.1 10.7 1.0
CB E:TYR84 4.2 10.0 1.0
CG2 E:VAL148 4.2 10.5 1.0
CE2 E:TYR84 4.3 10.1 1.0
HB3 E:TYR84 4.3 12.0 1.0
CD1 E:LEU144 4.4 18.7 1.0
CB E:TYR93 4.4 10.8 1.0
HE2 E:TYR84 4.4 12.1 1.0
CA E:TYR81 4.4 8.8 1.0
HD13 E:ILE100 4.5 15.4 1.0
O E:THR80 4.5 9.5 1.0
HD2 E:TYR93 4.6 15.6 1.0
H E:SER92 4.6 11.7 1.0
CG2 E:THR80 4.6 10.6 1.0
HD2 E:TYR81 4.6 12.2 1.0
CD1 E:ILE100 4.7 12.8 1.0
HD12 E:LEU144 4.7 22.4 1.0
N E:SER92 4.7 9.8 1.0
N E:TYR81 4.7 9.0 1.0
HD22 E:LEU144 4.7 23.9 1.0
HG21 E:THR80 4.8 12.8 1.0
HD3 E:ARG90 4.8 13.9 1.0
C E:THR80 4.8 9.6 1.0
HB2 E:TYR81 4.8 10.8 1.0
OG E:SER92 4.8 10.6 1.0
HB3 E:LEU144 4.8 15.8 1.0
CB E:LEU144 5.0 13.2 1.0
HB2 E:TYR93 5.0 12.9 1.0

Xenon binding site 2 out of 2 in 5m69

Go back to Xenon Binding Sites List in 5m69
Xenon binding site 2 out of 2 in the Thermolysin in Complex with Inhibitor and Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Thermolysin in Complex with Inhibitor and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe410

b:12.6
occ:0.17
HG22 E:VAL139 2.9 14.2 1.0
HH12 E:ARG203 3.2 12.7 1.0
HA E:VAL139 3.2 11.6 1.0
HG13 E:VAL139 3.3 13.7 1.0
HG22 E:ILE188 3.3 16.6 1.0
HG21 E:ILE188 3.4 16.6 1.0
C2 E:7GR408 3.6 12.7 1.0
CG2 E:ILE188 3.6 13.9 1.0
HD23 E:LEU202 3.7 21.2 0.6
HG23 E:ILE188 3.7 16.6 1.0
HB3 E:HIS142 3.7 11.3 1.0
HD13 E:LEU202 3.7 19.2 0.4
HH11 E:ARG203 3.7 12.7 1.0
NH1 E:ARG203 3.7 10.5 1.0
CG E:HIS142 3.7 9.7 1.0
O6 E:7GR408 3.8 14.9 1.0
CG2 E:VAL139 3.8 11.9 1.0
ND1 E:HIS142 3.8 9.2 1.0
HD1 E:HIS142 4.0 11.0 1.0
CA E:VAL139 4.0 9.6 1.0
HB2 E:HIS142 4.0 11.3 1.0
CB E:HIS142 4.1 9.4 1.0
C5 E:7GR408 4.1 14.0 1.0
CD2 E:HIS142 4.1 9.8 1.0
CG1 E:VAL139 4.1 11.4 1.0
CB E:VAL139 4.2 10.0 1.0
CE1 E:HIS142 4.2 9.1 1.0
HG23 E:VAL139 4.3 14.2 1.0
HG21 E:VAL139 4.4 14.2 1.0
CD2 E:LEU202 4.4 17.7 0.6
NE2 E:HIS142 4.4 9.1 1.0
CD1 E:LEU202 4.4 16.0 0.4
OE2 E:GLU143 4.4 16.1 1.0
HD22 E:LEU202 4.4 21.2 0.6
HD21 E:LEU202 4.5 21.2 0.6
HD2 E:HIS142 4.5 11.7 1.0
HD12 E:LEU202 4.5 19.2 0.4
HD11 E:LEU202 4.5 19.2 0.4
HG11 E:VAL139 4.6 13.7 1.0
HE1 E:HIS142 4.7 10.9 1.0
OD1 E:ASP170 4.7 10.8 1.0
CZ E:ARG203 4.8 11.0 1.0
HG12 E:VAL139 4.8 13.7 1.0
HH22 E:ARG203 4.8 13.9 1.0
N E:VAL139 4.8 9.9 1.0
N1 E:7GR408 4.9 12.1 1.0
O E:VAL139 4.9 9.0 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 02:40:22 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy