Zinc in PDB 6qf3: X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip

Enzymatic activity of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip

All present enzymatic activity of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip:
3.4.24.27;

Protein crystallography data

The structure of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip, PDB code: 6qf3 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) 46.58 / 1.52
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.154, 93.154, 129.294, 90.00, 90.00, 120.00
R / Rfree (%) 12.3 / 15

Other elements in 6qf3:

The structure of X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip (pdb code 6qf3). 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 X-Ray Structure of Thermolysin Soaked with Sodium Aspartate on A Silicon Chip, PDB code: 6qf3:

Zinc binding site 1 out of 1 in 6qf3

Go back to Zinc Binding Sites List in 6qf3
Zinc binding site 1 out of 1 in the X-Ray Structure of Thermolysin Soaked with Sodium Aspartate 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 Soaked with Sodium Aspartate on A Silicon Chip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:11.1
occ:1.00
 OE2 A:GLU166 2.0 12.8 1.0
NE2 A:HIS142 2.0 8.8 1.0
NE2 A:HIS146 2.0 8.5 1.0
O A:ASP427 2.2 17.1 0.9
N A:ASP427 2.5 22.6 0.9
CD A:GLU166 2.8 10.3 1.0
HB3 A:ASP427 2.8 44.1 0.9
CE1 A:HIS146 2.9 10.8 1.0
OE1 A:GLU166 3.0 13.3 1.0
CD2 A:HIS142 3.0 8.2 1.0
CE1 A:HIS142 3.0 10.5 1.0
HE1 A:HIS146 3.1 13.0 1.0
CD2 A:HIS146 3.1 9.5 1.0
CA A:ASP427 3.1 34.2 0.9
C A:ASP427 3.1 28.9 0.9
HD2 A:HIS142 3.2 9.8 1.0
HE1 A:HIS142 3.2 12.6 1.0
CB A:ASP427 3.2 36.7 0.9
HH A:TYR157 3.2 17.8 1.0
HB2 A:ASP427 3.3 44.1 0.9
HD2 A:HIS146 3.4 11.4 1.0
HB2 A:ASP428 3.5 20.0 0.8
HE2 A:HIS231 3.5 16.4 1.0
OH A:TYR157 3.9 14.8 1.0
HA A:GLU166 4.0 10.9 1.0
HB2 A:SER169 4.0 9.7 1.0
HA A:ASP427 4.1 41.1 0.9
ND1 A:HIS146 4.1 10.7 1.0
ND1 A:HIS142 4.1 8.1 1.0
CG A:HIS142 4.1 8.0 1.0
CG A:HIS146 4.2 10.2 1.0
NE2 A:HIS231 4.2 13.6 1.0
CG A:GLU166 4.2 9.7 1.0
HB3 A:SER169 4.3 9.7 1.0
OXT A:ASP427 4.3 30.2 0.9
CB A:ASP428 4.3 16.7 0.8
HE1 A:TYR157 4.4 14.9 1.0
HG2 A:GLU166 4.4 11.6 1.0
CB A:SER169 4.5 8.0 1.0
OE1 A:GLU143 4.5 11.0 0.6
CG A:ASP428 4.5 25.3 0.8
OE1 A:GLU143 4.5 13.6 0.4
HD2 A:HIS231 4.6 16.2 1.0
NA A:NA408 4.6 23.0 1.0
HA A:ASP428 4.6 41.5 0.8
CG A:ASP427 4.7 35.7 0.9
OE2 A:GLU143 4.7 14.2 0.4
OG A:SER169 4.7 9.8 1.0
HG3 A:GLU166 4.8 11.6 1.0
CD2 A:HIS231 4.8 13.5 1.0
OD2 A:ASP428 4.8 44.9 0.8
CA A:GLU166 4.9 9.1 1.0
HD1 A:HIS146 4.9 12.8 1.0
HD1 A:HIS142 4.9 9.7 1.0
CZ A:TYR157 4.9 14.5 1.0
HH22 A:ARG203 4.9 13.0 1.0
H11 A:EDO421 4.9 43.6 1.0
CD A:GLU143 5.0 12.9 0.4
CE1 A:TYR157 5.0 12.4 1.0
HB3 A:ASP428 5.0 20.0 0.8
OD1 A:ASP428 5.0 21.0 0.8

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 12:34:06 2020

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