Zinc in PDB 6d5s: Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant

Enzymatic activity of Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant

All present enzymatic activity of Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant:
3.4.24.27;

Protein crystallography data

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant, PDB code: 6d5s was solved by D.H.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.81 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.960, 92.960, 128.832, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 19.1

Other elements in 6d5s:

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant (pdb code 6d5s). 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 Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant, PDB code: 6d5s:

Zinc binding site 1 out of 1 in 6d5s

Go back to Zinc Binding Sites List in 6d5s
Zinc binding site 1 out of 1 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:12.4
occ:1.00
 O A:HOH546 1.8 16.6 1.0
OE2 A:GLU166 1.9 5.8 0.5
NE2 A:HIS146 2.1 7.3 1.0
NE2 A:HIS142 2.1 8.3 1.0
OE1 A:GLU166 2.1 5.9 0.5
CD A:GLU166 2.7 6.2 0.5
CD A:GLU166 2.9 7.0 0.5
OE1 A:GLU166 2.9 7.0 0.5
OE2 A:GLU166 3.0 10.3 0.5
CE1 A:HIS146 3.0 6.7 1.0
CE1 A:HIS142 3.1 7.2 1.0
CD2 A:HIS142 3.1 8.2 1.0
CD2 A:HIS146 3.1 6.3 1.0
HE1 A:HIS146 3.1 8.1 1.0
O A:HOH504 3.2 17.8 1.0
HE1 A:HIS142 3.3 8.7 1.0
HD2 A:HIS142 3.3 9.8 1.0
HD2 A:HIS146 3.3 7.5 1.0
HA A:VAL401 3.5 27.9 1.0
OH A:TYR157 3.8 7.8 0.5
HA A:GLU166 3.9 10.9 0.5
HA A:GLU166 3.9 10.9 0.5
HB2 A:SER169 4.1 8.6 1.0
CG A:GLU166 4.1 6.9 0.5
ND1 A:HIS146 4.1 11.4 1.0
ND1 A:HIS142 4.2 7.7 1.0
NE2 A:HIS231 4.2 18.5 1.0
CG A:HIS146 4.2 12.4 1.0
CG A:HIS142 4.2 6.7 1.0
HG2 A:GLU166 4.2 8.3 0.5
HH A:TYR157 4.3 9.4 0.5
OE1 A:GLU143 4.3 12.9 1.0
HB3 A:SER169 4.3 8.6 1.0
HE2 A:TYR157 4.3 17.5 0.5
CG A:GLU166 4.3 7.1 0.5
CA A:VAL401 4.4 23.3 1.0
HD2 A:HIS231 4.5 23.4 1.0
O A:HOH743 4.5 24.3 1.0
CB A:SER169 4.5 7.1 1.0
OE2 A:GLU143 4.7 27.5 1.0
OG A:SER169 4.7 7.6 1.0
O A:VAL401 4.7 22.2 1.0
HB3 A:GLU166 4.7 8.4 0.5
HG3 A:GLU166 4.7 8.3 0.5
CD2 A:HIS231 4.7 19.5 1.0
C A:VAL401 4.7 24.3 1.0
N A:VAL401 4.7 25.1 1.0
CD A:GLU143 4.8 10.9 1.0
CA A:GLU166 4.8 9.1 0.5
CA A:GLU166 4.8 9.1 0.5
HG3 A:GLU166 4.8 8.5 0.5
HG2 A:GLU166 4.8 8.5 0.5
CZ A:TYR157 4.8 3.6 0.5
CB A:GLU166 4.8 7.0 0.5
HE1 A:TYR157 4.9 11.8 0.5
HD1 A:HIS146 4.9 13.7 1.0
CE2 A:TYR157 4.9 14.6 0.5
CB A:GLU166 4.9 7.0 0.5
HA A:GLU143 4.9 12.2 1.0
HH22 A:ARG203 4.9 10.7 1.0
HD1 A:HIS142 5.0 9.2 1.0
HG23 A:VAL401 5.0 21.5 1.0

Reference:

D.H.Juers, C.A.Farley, C.P.Saxby, R.A.Cotter, J.K.B.Cahn, R.C.Holton-Burke, K.Harrison, Z.Wu. The Impact of Cryosolution Thermal Contraction on Proteins and Protein Crystals: Volumes, Conformation and Order. Acta Crystallogr D Struct V. 74 922 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198901
DOI: 10.1107/S2059798318008793
Page generated: Wed Dec 16 11:39:09 2020

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