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Zinc in PDB 5ma7: Structure of Thermolysin in Complex with Inhibitor (JC306).

Enzymatic activity of Structure of Thermolysin in Complex with Inhibitor (JC306).

All present enzymatic activity of Structure of Thermolysin in Complex with Inhibitor (JC306).:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin in Complex with Inhibitor (JC306)., PDB code: 5ma7 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) 43.67 / 1.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.754, 92.754, 129.766, 90.00, 90.00, 120.00
R / Rfree (%) 11.2 / 13.9

Other elements in 5ma7:

The structure of Structure of Thermolysin in Complex with Inhibitor (JC306). also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Thermolysin in Complex with Inhibitor (JC306). (pdb code 5ma7). 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 Structure of Thermolysin in Complex with Inhibitor (JC306)., PDB code: 5ma7:

Zinc binding site 1 out of 1 in 5ma7

Go back to Zinc Binding Sites List in 5ma7
Zinc binding site 1 out of 1 in the Structure of Thermolysin in Complex with Inhibitor (JC306).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Thermolysin in Complex with Inhibitor (JC306). within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:8.7
occ:1.00
O15 E:7K0412 2.0 10.9 1.0
OE2 E:GLU166 2.0 10.7 1.0
NE2 E:HIS142 2.0 8.6 1.0
NE2 E:HIS146 2.0 8.3 1.0
CD E:GLU166 2.8 9.5 1.0
CE1 E:HIS146 2.9 8.3 1.0
OE1 E:GLU166 3.0 10.3 1.0
CE1 E:HIS142 3.0 8.3 1.0
CD2 E:HIS142 3.0 8.1 1.0
P13 E:7K0412 3.0 12.9 1.0
O14 E:7K0412 3.0 13.3 1.0
HE1 E:HIS146 3.0 10.0 1.0
CD2 E:HIS146 3.1 8.4 1.0
HH E:TYR157 3.2 15.9 1.0
HE1 E:HIS142 3.2 10.0 1.0
HD2 E:HIS142 3.2 9.7 1.0
HD2 E:HIS146 3.4 10.0 1.0
OH E:TYR157 3.9 13.3 1.0
HA E:GLU166 4.0 9.3 1.0
NE2 E:HIS231 4.0 10.3 1.0
ND1 E:HIS146 4.1 8.8 1.0
HB2 E:SER169 4.1 9.2 1.0
ND1 E:HIS142 4.1 8.2 1.0
CG E:HIS142 4.1 7.7 1.0
C17 E:7K0412 4.2 11.5 1.0
N16 E:7K0412 4.2 11.4 1.0
CG E:HIS146 4.2 8.6 1.0
CG E:GLU166 4.2 9.6 1.0
HB3 E:SER169 4.3 9.2 1.0
HE1 E:TYR157 4.3 14.2 1.0
HG2 E:GLU166 4.4 11.5 1.0
HD2 E:HIS231 4.4 11.7 1.0
C6 E:7K0412 4.5 17.0 1.0
C1 E:GOL406 4.5 19.7 1.0
CB E:SER169 4.5 7.7 1.0
N5 E:7K0412 4.5 19.7 0.3
CD2 E:HIS231 4.6 9.8 1.0
N5 E:7K0412 4.6 20.9 0.7
O1 E:GOL406 4.6 13.7 1.0
C18 E:7K0412 4.7 12.1 1.0
OE1 E:GLU143 4.7 17.5 1.0
OG E:SER169 4.7 8.2 1.0
HG3 E:GLU166 4.8 11.5 1.0
CZ E:TYR157 4.8 12.1 1.0
HD1 E:HIS146 4.8 10.5 1.0
O27 E:7K0412 4.9 13.7 1.0
CA E:GLU166 4.9 7.7 1.0
HD1 E:HIS142 4.9 9.9 1.0
CE1 E:TYR157 4.9 11.8 1.0
HH22 E:ARG203 4.9 11.4 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 06:32:40 2020

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