Zinc in PDB 6qf2: X-Ray Structure of Thermolysin Crystallized on A Silicon Chip

Enzymatic activity of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip

All present enzymatic activity of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip:
3.4.24.27;

Protein crystallography data

The structure of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip, PDB code: 6qf2 was solved by J.Lieske, M.Cerv, S.Kreida, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.33 / 1.73
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.667, 92.667, 128.311, 90.00, 90.00, 120.00
R / Rfree (%) 12.8 / 16.1

Other elements in 6qf2:

The structure of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip (pdb code 6qf2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip, PDB code: 6qf2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6qf2

Go back to Zinc Binding Sites List in 6qf2
Zinc binding site 1 out of 2 in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:11.4
occ:1.00
OE2 A:GLU166 1.9 10.8 0.6
NE2 A:HIS142 2.0 9.3 1.0
OE1 A:GLU166 2.1 11.6 0.4
NE2 A:HIS146 2.1 9.6 1.0
O A:HOH531 2.1 18.7 1.0
CD A:GLU166 2.7 10.0 0.6
CD A:GLU166 2.9 12.3 0.4
OE1 A:GLU166 2.9 11.8 0.6
CE1 A:HIS142 3.0 12.5 1.0
OE2 A:GLU166 3.0 10.9 0.4
CE1 A:HIS146 3.0 11.9 1.0
CD2 A:HIS142 3.0 9.1 1.0
CD2 A:HIS146 3.1 12.0 1.0
HE1 A:HIS142 3.1 15.0 1.0
HE1 A:HIS146 3.2 14.3 1.0
ZN A:ZN408 3.2 18.1 0.5
HD2 A:HIS142 3.2 10.9 1.0
HD2 A:HIS146 3.3 14.4 1.0
HA A:LEU406 3.5 30.9 1.0
OH A:TYR157 3.9 14.3 0.5
HA A:GLU166 3.9 9.9 0.6
HA A:GLU166 3.9 11.2 0.4
HB2 A:SER169 4.0 11.1 1.0
ND1 A:HIS142 4.1 9.0 1.0
CG A:GLU166 4.1 12.0 0.6
CG A:HIS142 4.1 8.9 1.0
ND1 A:HIS146 4.1 10.8 1.0
NE2 A:HIS231 4.2 15.2 1.0
CG A:HIS146 4.2 9.4 1.0
CA A:LEU406 4.2 25.7 1.0
N A:LEU406 4.2 26.3 1.0
HB3 A:SER169 4.3 11.1 1.0
HG2 A:GLU166 4.3 14.4 0.6
CG A:GLU166 4.3 9.6 0.4
HD2 A:HIS231 4.4 22.0 1.0
O A:HOH796 4.4 22.3 1.0
HE1 A:TYR157 4.4 14.3 0.5
OE1 A:GLU143 4.4 17.0 1.0
O A:HOH635 4.5 38.8 1.0
O A:LEU406 4.5 26.3 1.0
CB A:SER169 4.5 9.2 1.0
HB3 A:GLU166 4.6 12.6 0.4
C A:LEU406 4.6 26.1 1.0
CD2 A:HIS231 4.6 18.3 1.0
OG A:SER169 4.6 11.2 1.0
HG3 A:GLU166 4.7 14.4 0.6
O A:HOH842 4.7 44.6 1.0
CA A:GLU166 4.7 9.3 0.4
HG2 A:GLU166 4.8 11.5 0.4
CB A:GLU166 4.8 10.5 0.4
CA A:GLU166 4.8 8.2 0.6
OE2 A:GLU143 4.8 19.6 1.0
HG3 A:GLU166 4.8 11.5 0.4
HH22 A:ARG203 4.8 11.7 1.0
HD1 A:HIS142 4.9 10.8 1.0
CZ A:TYR157 4.9 16.6 0.5
HE2 A:TYR157 4.9 25.1 0.5
HD12 A:LEU406 4.9 29.4 1.0
HD1 A:HIS146 4.9 12.9 1.0
CD A:GLU143 4.9 14.7 1.0
CE1 A:TYR157 5.0 11.9 0.5
CB A:GLU166 5.0 10.4 0.6

Zinc binding site 2 out of 2 in 6qf2

Go back to Zinc Binding Sites List in 6qf2
Zinc binding site 2 out of 2 in the X-Ray Structure of Thermolysin Crystallized on A Silicon Chip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Thermolysin Crystallized on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:18.1
occ:0.47
OH A:TYR157 1.8 14.3 0.5
O A:HOH531 2.1 18.7 1.0
OE2 A:GLU166 2.2 10.9 0.4
NE2 A:HIS231 2.3 15.2 1.0
O A:HOH635 2.3 38.8 1.0
HE1 A:HIS231 2.6 17.8 1.0
OE2 A:GLU166 2.7 10.8 0.6
CE1 A:HIS231 2.7 14.8 1.0
CZ A:TYR157 3.0 16.6 0.5
CD A:GLU166 3.1 12.3 0.4
O A:HOH842 3.1 44.6 1.0
ZN A:ZN401 3.2 11.4 1.0
OE1 A:GLU166 3.4 11.6 0.4
CD2 A:HIS231 3.5 18.3 1.0
CD A:GLU166 3.5 10.0 0.6
HE2 A:TYR157 3.6 13.6 0.5
CE2 A:TYR157 3.7 11.3 0.5
HD2 A:HIS231 3.9 22.0 1.0
CE1 A:TYR157 4.0 11.9 0.5
ND1 A:HIS231 4.0 13.9 1.0
HE1 A:TYR157 4.0 14.3 0.5
N A:LEU406 4.1 26.3 1.0
OE1 A:GLU166 4.2 11.8 0.6
HG2 A:GLU166 4.2 14.4 0.6
CG A:GLU166 4.3 12.0 0.6
HG3 A:GLU166 4.3 11.5 0.4
HG3 A:GLU166 4.3 14.4 0.6
CG A:GLU166 4.3 9.6 0.4
NE2 A:HIS146 4.4 9.6 1.0
CG A:HIS231 4.4 12.6 1.0
O A:HOH796 4.4 22.3 1.0
C A:LEU406 4.5 26.1 1.0
OXT A:LYS407 4.5 27.6 1.0
HG23 A:VAL230 4.6 12.9 1.0
HD1 A:HIS231 4.7 16.6 1.0
N A:LYS407 4.7 26.4 1.0
HA A:LEU406 4.7 30.9 1.0
HG2 A:GLU166 4.7 11.5 0.4
HG21 A:VAL230 4.7 12.9 1.0
CA A:LEU406 4.7 25.7 1.0
HA A:LYS407 4.8 33.6 1.0
O A:LEU406 4.8 26.3 1.0
HE1 A:HIS146 4.9 14.3 1.0
C A:LYS407 4.9 27.5 1.0
H A:LYS407 4.9 31.7 1.0
HE2 A:TYR157 4.9 25.1 0.5
CE1 A:HIS146 4.9 11.9 1.0
HD2 A:TYR157 4.9 15.7 0.5
NE2 A:HIS142 5.0 9.3 1.0

Reference:

J.Lieske, M.Cerv, S.Kreida, D.Komadina, J.Fischer, M.Barthelmess, P.Fischer, T.Pakendorf, O.Yefanov, V.Mariani, T.Seine, B.H.Ross, E.Crosas, O.Lorbeer, A.Burkhardt, T.J.Lane, S.Guenther, J.Bergtholdt, S.Schoen, S.Tornroth-Horsefield, H.N.Chapman, A.Meents. On-Chip Crystallization For Serial Crystallography Experiments and on-Chip Ligand-Binding Studies. Iucrj V. 6 714 2019.
ISSN: ESSN 2052-2525
PubMed: 31316815
DOI: 10.1107/S2052252519007395
Page generated: Wed Dec 16 12:34:04 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy