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Krypton 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:

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

Krypton Binding Sites:

The binding sites of Krypton atom in the Thermolysin in Complex with Inhibitor and Krypton (pdb code 5m5f). This binding sites where shown within 5.0 Angstroms radius around Krypton atom.
In total 2 binding sites of Krypton where determined in the Thermolysin in Complex with Inhibitor and Krypton, PDB code: 5m5f:
Jump to Krypton binding site number: 1; 2;

Krypton binding site 1 out of 2 in 5m5f

Go back to Krypton Binding Sites List in 5m5f
Krypton binding site 1 out of 2 in the Thermolysin in Complex with Inhibitor and Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 1 of Thermolysin in Complex with Inhibitor and Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Kr413

b:13.7
occ:0.20
HD21 E:LEU144 3.1 16.4 1.0
HG E:LEU144 3.1 14.0 1.0
HA E:SER92 3.1 9.4 1.0
HD2 E:TYR84 3.2 9.6 1.0
HA E:TYR93 3.5 9.8 1.0
CD2 E:TYR84 3.5 8.0 1.0
HB2 E:TYR84 3.5 9.6 1.0
C E:SER92 3.6 7.7 1.0
N E:TYR93 3.6 7.9 1.0
HA E:TYR81 3.6 8.7 1.0
HD23 E:LEU144 3.6 16.4 1.0
CD2 E:LEU144 3.7 13.7 1.0
HB3 E:TYR93 3.7 11.0 1.0
CG E:LEU144 3.8 11.7 1.0
CA E:SER92 3.8 7.9 1.0
HG22 E:VAL148 3.8 9.9 1.0
HD11 E:LEU144 3.9 16.2 1.0
H E:TYR93 3.9 9.5 1.0
HG22 E:THR80 3.9 9.5 1.0
O E:SER92 3.9 8.3 1.0
HG21 E:VAL148 3.9 9.9 1.0
CG E:TYR84 4.0 7.4 1.0
CA E:TYR93 4.0 8.2 1.0
HG23 E:VAL148 4.0 9.9 1.0
O E:HOH578 4.0 8.9 1.0
HD11 E:ILE100 4.1 12.2 1.0
CB E:TYR84 4.1 8.0 1.0
CG2 E:VAL148 4.1 8.2 1.0
CE2 E:TYR84 4.2 8.0 1.0
HB3 E:TYR84 4.2 9.6 1.0
HE2 E:TYR84 4.3 9.6 1.0
CD1 E:LEU144 4.4 13.5 1.0
CB E:TYR93 4.4 9.1 1.0
H E:SER92 4.4 9.5 1.0
HD3 E:ARG90 4.5 11.4 1.0
CA E:TYR81 4.6 7.2 1.0
HD22 E:LEU144 4.6 16.4 1.0
N E:SER92 4.6 7.9 1.0
HD2 E:TYR93 4.6 13.0 1.0
HD13 E:ILE100 4.6 12.2 1.0
O E:THR80 4.6 7.6 1.0
HD2 E:TYR81 4.7 9.6 1.0
OG E:SER92 4.8 8.1 1.0
HD12 E:LEU144 4.8 16.2 1.0
CD1 E:ILE100 4.8 10.2 1.0
CG2 E:THR80 4.8 7.9 1.0
N E:TYR81 4.9 7.1 1.0
C E:THR80 4.9 6.9 1.0
HG21 E:THR80 4.9 9.5 1.0
CD1 E:TYR84 4.9 8.2 1.0
CB E:SER92 5.0 8.4 1.0
HB2 E:TYR81 5.0 8.2 1.0
HB2 E:TYR93 5.0 11.0 1.0

Krypton binding site 2 out of 2 in 5m5f

Go back to Krypton Binding Sites List in 5m5f
Krypton binding site 2 out of 2 in the Thermolysin in Complex with Inhibitor and Krypton


Mono view


Stereo pair view

A full contact list of Krypton with other atoms in the Kr binding site number 2 of Thermolysin in Complex with Inhibitor and Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Kr414

b:12.5
occ:0.08
HG22 E:VAL139 2.9 11.0 1.0
HH22 E:ARG203 3.0 9.7 1.0
HA E:VAL139 3.2 8.8 1.0
HG13 E:VAL139 3.3 10.9 1.0
HG21 E:ILE188 3.3 12.1 1.0
HG22 E:ILE188 3.4 12.1 1.0
C2 E:7GR408 3.5 9.3 1.0
HD23 E:LEU202 3.6 15.4 0.6
NH2 E:ARG203 3.6 8.1 1.0
HH21 E:ARG203 3.6 9.7 1.0
CG2 E:ILE188 3.6 10.1 1.0
HD12 E:LEU202 3.7 16.1 0.5
HG23 E:ILE188 3.7 12.1 1.0
HB3 E:HIS142 3.7 8.5 1.0
CG E:HIS142 3.7 7.0 1.0
O6 E:7GR408 3.7 10.7 1.0
ND1 E:HIS142 3.7 7.1 1.0
CG2 E:VAL139 3.8 9.1 1.0
HD1 E:HIS142 3.9 8.5 1.0
C5 E:7GR408 4.0 9.9 1.0
HB2 E:HIS142 4.0 8.5 1.0
CB E:HIS142 4.0 7.1 1.0
CD2 E:HIS142 4.0 7.1 1.0
CA E:VAL139 4.1 7.3 1.0
CE1 E:HIS142 4.1 6.9 1.0
CG1 E:VAL139 4.1 9.1 1.0
CB E:VAL139 4.2 8.3 1.0
CD2 E:LEU202 4.3 12.9 0.6
HD21 E:LEU202 4.3 15.4 0.6
NE2 E:HIS142 4.3 7.3 1.0
HG23 E:VAL139 4.3 11.0 1.0
HD13 E:LEU202 4.3 16.1 0.5
CD1 E:LEU202 4.3 13.4 0.5
HG21 E:VAL139 4.4 11.0 1.0
OE2 E:GLU143 4.4 12.1 1.0
HD22 E:LEU202 4.5 15.4 0.6
HD2 E:HIS142 4.5 8.6 1.0
HD11 E:LEU202 4.5 16.1 0.5
HE1 E:HIS142 4.5 8.2 1.0
HG11 E:VAL139 4.6 10.9 1.0
CZ E:ARG203 4.7 8.2 1.0
OD1 E:ASP170 4.7 8.1 1.0
HH12 E:ARG203 4.8 10.4 1.0
HG12 E:VAL139 4.8 10.9 1.0
N1 E:7GR408 4.8 9.2 1.0
N E:VAL139 4.9 7.4 1.0
O E:VAL139 4.9 6.9 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: Mon Dec 14 02:54:48 2020

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