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Zinc in PDB 1kto: Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)

Enzymatic activity of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)

All present enzymatic activity of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine), PDB code: 1kto was solved by M.Senda, T.Senda, S.Kidokoro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.607, 93.607, 131.332, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 18.5

Other elements in 1kto:

The structure of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) (pdb code 1kto). 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 Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine), PDB code: 1kto:

Zinc binding site 1 out of 1 in 1kto

Go back to Zinc Binding Sites List in 1kto
Zinc binding site 1 out of 1 in the Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermolysin Complexed with Z-D-Alanine (Benzyloxycarbonyl-D-Alanine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:12.4
occ:1.00
 OE2 A:GLU166 1.9 14.6 1.0
NE2 A:HIS146 2.0 11.1 1.0
O A:DAL1317 2.0 23.4 1.0
NE2 A:HIS142 2.0 11.5 1.0
C A:DAL1317 2.7 27.1 1.0
CD A:GLU166 2.8 14.6 1.0
OXT A:DAL1317 2.8 25.4 1.0
CE1 A:HIS146 2.9 10.9 1.0
OE1 A:GLU166 2.9 16.1 1.0
CD2 A:HIS142 3.0 10.7 1.0
CE1 A:HIS142 3.0 11.8 1.0
CD2 A:HIS146 3.1 12.1 1.0
OH A:TYR157 3.8 23.6 1.0
ND1 A:HIS146 4.0 11.3 1.0
ND1 A:HIS142 4.1 9.1 1.0
CG A:HIS146 4.1 11.4 1.0
NE2 A:HIS231 4.2 15.2 1.0
CG A:HIS142 4.2 9.9 1.0
CA A:DAL1317 4.2 28.4 1.0
CG A:GLU166 4.2 12.1 1.0
C1 A:PHQ317 4.3 34.7 1.0
O2 A:PHQ317 4.4 34.2 1.0
CB A:SER169 4.5 10.4 1.0
O1 A:PHQ317 4.5 31.0 1.0
O A:HOH1407 4.6 14.2 1.0
N A:DAL1317 4.7 31.6 1.0
OG A:SER169 4.7 10.9 1.0
CD2 A:HIS231 4.8 16.7 1.0
CZ A:TYR157 4.8 23.9 1.0
C2 A:PHQ317 4.8 33.6 1.0
CB A:DAL1317 4.8 30.5 1.0
CA A:GLU166 4.8 10.4 1.0
OE1 A:GLU143 4.8 16.2 1.0
CE1 A:TYR157 4.9 25.0 1.0
OE2 A:GLU143 4.9 18.8 1.0

Reference:

M.Senda, T.Senda, S.Kidokoro. Crystal Structure Analyses of Thermolysin in Complex with Its Inhibitors. To Be Published.
Page generated: Sun Oct 13 04:40:44 2024

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