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Zinc in PDB 6yms: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

Enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

All present enzymatic activity of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6yms was solved by M.Kljajic, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.31 / 1.32
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.619, 92.619, 129.982, 90, 90, 120
R / Rfree (%) 11.6 / 14.8

Other elements in 6yms:

The structure of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin (pdb code 6yms). 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 Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin, PDB code: 6yms:

Zinc binding site 1 out of 1 in 6yms

Go back to Zinc Binding Sites List in 6yms
Zinc binding site 1 out of 1 in the Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn405

b:7.4
occ:1.00
 O1 E:OZH409 2.0 15.7 0.5
OE2 E:GLU166 2.0 7.8 1.0
O1 E:OZH409 2.0 3.8 0.6
NE2 E:HIS146 2.0 7.0 1.0
NE2 E:HIS142 2.0 7.8 1.0
CD E:GLU166 2.8 7.1 1.0
P E:OZH409 2.9 4.2 0.6
O2 E:OZH409 2.9 4.6 0.6
P E:OZH409 2.9 15.7 0.5
CE1 E:HIS146 2.9 7.6 1.0
OE1 E:GLU166 3.0 7.3 1.0
CE1 E:HIS142 3.0 7.3 1.0
HE1 E:HIS146 3.0 9.1 1.0
CD2 E:HIS142 3.0 7.2 1.0
CD2 E:HIS146 3.1 7.4 1.0
O2 E:OZH409 3.1 16.2 0.5
HH E:TYR157 3.2 10.9 1.0
HD2 E:HIS142 3.2 8.7 1.0
HE1 E:HIS142 3.2 8.7 1.0
HE2 E:HIS231 3.4 10.6 1.0
HD2 E:HIS146 3.4 8.8 1.0
C7 E:OZH409 3.7 15.8 0.5
C7 E:OZH409 3.8 5.4 0.6
OH E:TYR157 3.9 9.1 1.0
HA E:GLU166 3.9 8.4 1.0
NE2 E:HIS231 4.1 8.8 1.0
ND1 E:HIS146 4.1 7.6 1.0
ND1 E:HIS142 4.1 7.7 1.0
HB2 E:SER169 4.2 8.8 1.0
CG E:HIS142 4.2 7.5 1.0
CG E:HIS146 4.2 7.4 1.0
CG E:GLU166 4.2 7.3 1.0
N1 E:OZH409 4.3 5.2 0.6
HB3 E:SER169 4.3 8.8 1.0
N1 E:OZH409 4.4 16.4 0.5
HG2 E:GLU166 4.4 8.8 1.0
HD2 E:HIS231 4.4 10.8 1.0
HE1 E:TYR157 4.4 10.3 1.0
O E:HOH553 4.5 9.4 1.0
CB E:SER169 4.6 7.4 1.0
CD2 E:HIS231 4.6 9.0 1.0
C8 E:OZH409 4.7 15.7 0.5
HG3 E:GLU166 4.7 8.8 1.0
OG E:SER169 4.8 7.9 1.0
N2 E:OZH409 4.8 15.8 0.5
HD1 E:HIS146 4.8 9.1 1.0
N2 E:OZH409 4.8 5.6 0.6
CA E:GLU166 4.8 7.0 1.0
CZ E:TYR157 4.9 8.4 1.0
C8 E:OZH409 4.9 6.3 0.6
HH22 E:ARG203 4.9 10.0 1.0
O3 E:OZH409 4.9 7.8 0.6
HD1 E:HIS142 4.9 9.2 1.0
O3 E:OZH409 5.0 16.3 0.5
C6 E:OZH409 5.0 17.1 0.5
CE1 E:TYR157 5.0 8.6 1.0

Reference:

M.Kljajic, H.-D.Gerber, A.Heine, G.Klebe. Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin To Be Published.
Page generated: Thu Aug 21 21:31:42 2025

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