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Zinc in PDB 1ks7: Thermolysin Complexed with Z-D-Aspartic Acid (Benzyloxycarbonyl-D- Aspartic Acid)

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

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

Protein crystallography data

The structure of Thermolysin Complexed with Z-D-Aspartic Acid (Benzyloxycarbonyl-D- Aspartic Acid), PDB code: 1ks7 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) 23.42 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.668, 93.668, 131.505, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 18.6

Other elements in 1ks7:

The structure of Thermolysin Complexed with Z-D-Aspartic Acid (Benzyloxycarbonyl-D- Aspartic Acid) 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-Aspartic Acid (Benzyloxycarbonyl-D- Aspartic Acid) (pdb code 1ks7). 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-Aspartic Acid (Benzyloxycarbonyl-D- Aspartic Acid), PDB code: 1ks7:

Zinc binding site 1 out of 1 in 1ks7

Go back to Zinc Binding Sites List in 1ks7
Zinc binding site 1 out of 1 in the Thermolysin Complexed with Z-D-Aspartic Acid (Benzyloxycarbonyl-D- Aspartic Acid)


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-Aspartic Acid (Benzyloxycarbonyl-D- Aspartic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:10.8
occ:1.00
 OE2 A:GLU166 1.9 13.8 1.0
NE2 A:HIS146 2.0 9.7 1.0
NE2 A:HIS142 2.1 11.3 1.0
OD2 A:DAS1317 2.3 20.1 1.0
OD1 A:DAS1317 2.5 21.5 1.0
CG A:DAS1317 2.7 20.0 1.0
CD A:GLU166 2.8 12.6 1.0
CE1 A:HIS146 2.9 11.8 1.0
OE1 A:GLU166 3.0 15.2 1.0
CD2 A:HIS142 3.0 10.5 1.0
CE1 A:HIS142 3.1 12.4 1.0
CD2 A:HIS146 3.1 12.6 1.0
OH A:TYR157 3.8 21.6 1.0
ND1 A:HIS146 4.1 10.6 1.0
CB A:DAS1317 4.1 19.9 1.0
ND1 A:HIS142 4.2 9.1 1.0
CG A:HIS142 4.2 9.6 1.0
CG A:GLU166 4.2 10.3 1.0
CG A:HIS146 4.2 10.2 1.0
O A:HOH1425 4.3 22.2 1.0
NE2 A:HIS231 4.4 15.1 1.0
OE2 A:GLU143 4.5 18.8 1.0
CB A:SER169 4.5 9.3 1.0
OG A:SER169 4.6 9.4 1.0
O A:HOH1424 4.7 14.7 1.0
CZ A:TYR157 4.8 21.4 1.0
CA A:GLU166 4.8 9.1 1.0
CD2 A:HIS231 4.9 15.9 1.0
OE1 A:GLU143 4.9 16.6 1.0
CE1 A:TYR157 4.9 20.7 1.0

Reference:

M.Senda, T.Senda, S.Kidokoro. Crystal Structure Analyses of Thermolysin in Complex with Its Inhibitors. To Be Published.
Page generated: Wed Dec 16 02:55:37 2020

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