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Zinc in PDB 3dnz: Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline

Enzymatic activity of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline

All present enzymatic activity of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline, PDB code: 3dnz was solved by E.Pechkova, S.K.Tripathi, C.Nicolini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.04 / 1.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.535, 92.535, 128.628, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 26.7

Other elements in 3dnz:

The structure of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline (pdb code 3dnz). 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 By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline, PDB code: 3dnz:

Zinc binding site 1 out of 1 in 3dnz

Go back to Zinc Binding Sites List in 3dnz
Zinc binding site 1 out of 1 in the Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermolysin By Lb Nanotemplate Method Before High X-Ray Dose on Esrf ID14-2 Beamline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:14.4
occ:1.00
 NE2 A:HIS142 2.0 13.6 1.0
NE2 A:HIS146 2.1 14.1 1.0
OE2 A:GLU166 2.1 17.9 1.0
CD A:GLU166 2.9 15.0 1.0
OE1 A:GLU166 2.9 17.9 1.0
CE1 A:HIS146 3.0 14.3 1.0
CE1 A:HIS142 3.0 14.8 1.0
CD2 A:HIS142 3.0 13.1 1.0
CD2 A:HIS146 3.1 14.3 1.0
OH A:TYR157 4.0 11.3 0.5
ND1 A:HIS142 4.1 12.7 1.0
ND1 A:HIS146 4.1 13.1 1.0
CG A:HIS142 4.1 13.2 1.0
NE2 A:HIS231 4.2 16.5 1.0
CG A:HIS146 4.2 11.1 1.0
OE1 A:GLU143 4.2 14.8 1.0
CA A:VAL1001 4.3 22.6 1.0
CG A:GLU166 4.3 14.1 1.0
O A:HOH1137 4.3 15.9 1.0
N A:VAL1001 4.4 22.3 1.0
CB A:SER169 4.5 13.6 1.0
O A:HOH1185 4.5 28.4 1.0
O A:VAL1001 4.6 22.0 1.0
C A:VAL1001 4.6 22.7 1.0
OG A:SER169 4.7 14.0 1.0
CD2 A:HIS231 4.7 16.9 1.0
CA A:GLU166 4.9 12.4 1.0
CD A:GLU143 4.9 15.0 1.0
CZ A:TYR157 4.9 12.1 0.5
CE1 A:TYR157 5.0 10.8 0.5
OE2 A:GLU143 5.0 19.1 1.0

Reference:

E.Pechkova, S.K.Tripathi, C.Nicolini. Radiation Damage in Protein Structural Characterization By Synchrotron Radiation: State of the Art and Nanotechnology-Based Perspective To Be Published.
Page generated: Thu Oct 24 12:15:56 2024

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