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Zinc in PDB 5uu9: Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant

Enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant:
3.4.24.27;

Protein crystallography data

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant, PDB code: 5uu9 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) 20.99 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.819, 96.819, 106.900, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.8

Other elements in 5uu9:

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant (pdb code 5uu9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant, PDB code: 5uu9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5uu9

Go back to Zinc Binding Sites List in 5uu9
Zinc binding site 1 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:10.3
occ:0.85
 OD2 A:ASP185 2.0 15.7 1.0
O A:HOH538 2.0 14.3 1.0
OE2 A:GLU190 2.0 13.9 1.0
OE2 A:GLU177 2.1 13.7 1.0
O A:ASN183 2.3 15.0 1.0
CG A:ASP185 3.0 16.4 1.0
CD A:GLU177 3.0 14.6 1.0
CD A:GLU190 3.1 12.6 1.0
OD1 A:ASP185 3.4 14.2 1.0
HA A:PRO184 3.4 17.6 1.0
HG3 A:GLU190 3.4 16.7 1.0
C A:ASN183 3.5 14.5 1.0
OE1 A:GLU177 3.5 14.0 1.0
CA A:CA401 3.6 6.8 0.9
CG A:GLU190 3.7 13.9 1.0
HG2 A:GLU190 3.7 16.7 1.0
HG2 A:GLU177 4.0 15.2 1.0
OD2 A:ASP191 4.0 17.3 1.0
CA A:PRO184 4.0 14.7 1.0
CG A:GLU177 4.0 12.7 1.0
OD1 A:ASN183 4.0 23.6 1.0
OE1 A:GLU190 4.0 13.7 1.0
C A:PRO184 4.1 17.3 1.0
OD1 A:ASP191 4.1 16.2 1.0
HB2 A:ASN183 4.1 23.9 1.0
N A:ASP185 4.1 14.6 1.0
H A:ASP185 4.2 17.5 1.0
HG3 A:GLU177 4.2 15.2 1.0
CG A:ASN183 4.2 26.2 1.0
N A:PRO184 4.2 14.2 1.0
CB A:ASP185 4.2 13.8 1.0
HB3 A:ASP185 4.3 16.5 1.0
CG A:ASP191 4.4 16.7 1.0
CB A:ASN183 4.5 19.9 1.0
O A:PRO184 4.6 18.4 1.0
CA A:ASN183 4.6 15.6 1.0
ND2 A:ASN183 4.7 29.4 1.0
CA A:ASP185 4.8 13.3 1.0
HD21 A:ASN183 4.9 35.3 1.0
HB2 A:ASP185 5.0 16.5 1.0

Zinc binding site 2 out of 4 in 5uu9

Go back to Zinc Binding Sites List in 5uu9
Zinc binding site 2 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:7.8
occ:0.82
 O A:HOH731 1.8 15.2 1.0
OE1 A:GLU166 1.9 12.6 0.4
OE2 A:GLU166 2.0 13.5 0.6
NE2 A:HIS142 2.0 10.8 1.0
NE2 A:HIS146 2.0 12.6 1.0
CD A:GLU166 2.8 15.5 0.6
CD A:GLU166 2.8 11.8 0.4
CE1 A:HIS146 3.0 13.1 1.0
CE1 A:HIS142 3.0 12.5 1.0
CD2 A:HIS142 3.0 11.7 1.0
HH A:TYR157 3.1 21.2 0.5
OE2 A:GLU166 3.1 14.9 0.4
OE1 A:GLU166 3.1 15.2 0.6
CD2 A:HIS146 3.1 13.4 1.0
HE1 A:HIS146 3.1 15.7 1.0
HD2 A:HIS142 3.2 14.1 1.0
HE1 A:HIS142 3.2 15.0 1.0
HD2 A:HIS146 3.3 16.1 1.0
ZN A:ZN406 3.3 19.4 0.5
O A:HOH710 3.4 30.1 0.7
ZN A:ZN407 3.5 22.0 0.3
OE2 A:GLU143 3.7 18.0 1.0
HA A:GLU166 3.8 14.5 0.6
OH A:TYR157 3.8 17.7 0.5
HA A:GLU166 3.8 14.0 0.4
HE1 A:TYR157 4.0 18.7 0.5
HB2 A:SER169 4.1 15.4 1.0
ND1 A:HIS142 4.1 12.9 1.0
ND1 A:HIS146 4.1 11.6 1.0
O A:HOH783 4.1 29.5 1.0
CG A:HIS142 4.1 11.8 1.0
NE2 A:HIS231 4.2 23.9 1.0
CG A:HIS146 4.2 12.5 1.0
CG A:GLU166 4.2 14.3 0.6
CG A:GLU166 4.3 12.1 0.4
HB3 A:SER169 4.3 15.4 1.0
HG2 A:GLU166 4.3 17.1 0.6
CD A:GLU143 4.5 15.6 1.0
HB3 A:GLU166 4.5 14.5 0.4
CB A:SER169 4.5 12.9 1.0
HD2 A:HIS231 4.6 27.4 1.0
HG3 A:GLU166 4.7 14.5 0.4
CE1 A:TYR157 4.7 15.6 0.5
CA A:GLU166 4.7 11.7 0.4
O A:HOH684 4.7 45.7 1.0
OG A:SER169 4.7 13.3 1.0
CA A:GLU166 4.7 12.1 0.6
CD2 A:HIS231 4.7 22.9 1.0
CB A:GLU166 4.7 12.1 0.4
CZ A:TYR157 4.7 14.2 0.5
HG3 A:GLU166 4.8 17.1 0.6
OE1 A:GLU143 4.8 15.5 1.0
HH22 A:ARG203 4.8 18.1 1.0
HG2 A:GLU166 4.9 14.5 0.4
HD1 A:HIS142 4.9 15.4 1.0
HD1 A:HIS146 4.9 13.9 1.0
O A:HOH821 4.9 37.9 1.0
CB A:GLU166 5.0 13.0 0.6
HA A:GLU143 5.0 15.4 1.0

Zinc binding site 3 out of 4 in 5uu9

Go back to Zinc Binding Sites List in 5uu9
Zinc binding site 3 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:19.4
occ:0.52
 O A:HOH731 1.9 15.2 1.0
O A:HOH821 2.0 37.9 1.0
NE2 A:HIS231 2.0 23.9 1.0
O A:HOH710 2.1 30.1 0.7
CE1 A:HIS231 2.8 24.5 1.0
ZN A:ZN407 2.8 22.0 0.3
HE1 A:HIS231 2.9 29.4 1.0
O A:HOH783 3.0 29.5 1.0
CD2 A:HIS231 3.1 22.9 1.0
HH A:TYR157 3.3 21.2 0.5
ZN A:ZN405 3.3 7.8 0.8
HD2 A:HIS231 3.4 27.4 1.0
OH A:TYR157 3.4 17.7 0.5
OE2 A:GLU166 3.5 13.5 0.6
O A:HOH854 3.8 58.2 1.0
O A:HOH598 3.8 32.4 1.0
OE1 A:GLU166 3.9 12.6 0.4
ND1 A:HIS231 4.0 22.7 1.0
CD A:GLU166 4.0 15.5 0.6
O A:HOH750 4.1 41.9 1.0
OE1 A:GLU166 4.1 15.2 0.6
CG A:HIS231 4.1 21.7 1.0
OE2 A:GLU166 4.2 14.9 0.4
CD A:GLU166 4.2 11.8 0.4
OE2 A:GLU143 4.3 18.0 1.0
O A:HOH684 4.3 45.7 1.0
NE2 A:HIS142 4.5 10.8 1.0
HD1 A:HIS231 4.7 27.2 1.0
CZ A:TYR157 4.7 14.2 0.5
HH22 A:ARG203 4.8 18.1 1.0
NE2 A:HIS146 5.0 12.6 1.0

Zinc binding site 4 out of 4 in 5uu9

Go back to Zinc Binding Sites List in 5uu9
Zinc binding site 4 out of 4 in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:22.0
occ:0.29
 OE2 A:GLU143 1.8 18.0 1.0
O A:HOH598 1.9 32.4 1.0
O A:HOH731 2.0 15.2 1.0
ZN A:ZN406 2.8 19.4 0.5
CD A:GLU143 2.8 15.6 1.0
O A:HOH821 2.8 37.9 1.0
O A:HOH684 3.1 45.7 1.0
OE1 A:GLU143 3.3 15.5 1.0
ZN A:ZN405 3.5 7.8 0.8
O A:HOH710 3.5 30.1 0.7
O A:ALA113 3.7 17.4 1.0
O A:HOH603 3.7 43.8 1.0
O A:HOH783 3.9 29.5 1.0
HD2 A:HIS142 4.0 14.1 1.0
HD2 A:HIS146 4.1 16.1 1.0
HA A:PHE114 4.1 18.0 1.0
CG A:GLU143 4.1 12.2 1.0
HG2 A:GLU143 4.2 14.7 1.0
NE2 A:HIS142 4.2 10.8 1.0
HG3 A:GLU143 4.3 14.7 1.0
CD2 A:HIS142 4.4 11.7 1.0
HB3 A:PHE114 4.4 19.6 1.0
NE2 A:HIS146 4.5 12.6 1.0
CD2 A:HIS146 4.6 13.4 1.0
OD1 A:ASN112 4.7 28.0 1.0
NE2 A:HIS231 4.7 23.9 1.0
OE2 A:GLU166 4.9 13.5 0.6
HH A:TYR157 4.9 21.2 0.5
C A:ALA113 4.9 15.8 1.0
O A:HOH790 4.9 43.0 1.0
CA A:PHE114 4.9 15.0 1.0
HB2 A:PHE114 5.0 19.6 1.0
O A:HOH854 5.0 58.2 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: Mon Oct 28 12:19:00 2024

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