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Calcium in PDB 6d5r: Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant

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

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

Protein crystallography data

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant, PDB code: 6d5r 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 (°) 92.920, 92.920, 130.122, 90.00, 90.00, 120.00
R / Rfree (%) 15.4 / 20.5

Other elements in 6d5r:

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

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant (pdb code 6d5r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant, PDB code: 6d5r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6d5r

Go back to Calcium Binding Sites List in 6d5r
Calcium binding site 1 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:10.9
occ:1.00
 O A:GLU187 2.3 12.2 0.7
O A:GLU187 2.3 12.3 0.3
OE1 A:GLU177 2.4 10.4 1.0
O A:HOH578 2.4 7.5 1.0
OE2 A:GLU190 2.4 12.4 1.0
OD1 A:ASP185 2.5 10.5 1.0
OD2 A:ASP138 2.6 13.5 1.0
OE1 A:GLU190 2.6 9.3 1.0
OE2 A:GLU177 2.8 13.0 1.0
CD A:GLU190 2.8 13.3 1.0
CD A:GLU177 2.9 16.6 1.0
C A:GLU187 3.3 8.1 0.7
C A:GLU187 3.3 8.3 0.3
CG A:ASP185 3.5 15.4 1.0
CG A:ASP138 3.5 20.3 1.0
HB3 A:ASP138 3.6 13.9 1.0
H A:GLU187 3.6 17.1 0.7
HA A:ILE188 3.7 16.1 1.0
H A:GLU187 3.7 17.2 0.3
CA A:CA407 3.8 12.7 0.9
OD2 A:ASP185 3.8 13.1 1.0
HB2 A:GLU187 3.9 21.6 0.7
H A:GLY189 3.9 11.4 1.0
HB2 A:GLU187 3.9 21.6 0.3
CB A:ASP138 4.0 11.6 1.0
O A:ASP185 4.1 15.7 1.0
H A:GLU190 4.1 13.2 1.0
N A:GLU187 4.1 14.3 0.7
N A:GLU187 4.1 14.3 0.3
N A:ILE188 4.2 6.9 1.0
H A:ASP185 4.2 11.5 1.0
CA A:GLU187 4.2 14.6 0.7
CA A:GLU187 4.2 14.6 0.3
HB2 A:ASP138 4.2 13.9 1.0
CA A:ILE188 4.3 13.4 1.0
HD13 A:ILE188 4.3 20.7 1.0
CG A:GLU190 4.3 16.2 1.0
CG A:GLU177 4.4 8.7 1.0
OD1 A:ASP138 4.4 11.6 1.0
N A:GLY189 4.5 9.5 1.0
O A:HOH564 4.5 14.6 1.0
CB A:GLU187 4.5 18.0 0.7
CB A:GLU187 4.6 18.0 0.3
C A:ASP185 4.6 13.6 1.0
HG3 A:GLU190 4.6 19.4 1.0
HB2 A:GLU177 4.7 11.4 1.0
CB A:ASP185 4.8 14.3 1.0
HB3 A:GLU177 4.8 11.4 1.0
N A:ASP185 4.8 9.6 1.0
HG2 A:GLU190 4.8 19.4 1.0
C A:ILE188 4.8 10.5 1.0
HA A:THR174 4.8 14.2 1.0
HG2 A:GLU177 4.8 10.4 1.0
O A:HOH524 4.8 13.5 1.0
HG3 A:GLU177 4.9 10.4 1.0
CB A:GLU177 4.9 9.5 1.0
HB3 A:GLU190 4.9 14.9 1.0
H A:ILE188 4.9 8.3 0.3
H A:ILE188 4.9 8.3 0.7
N A:GLU190 4.9 11.0 1.0
CA A:ASP185 5.0 12.2 1.0
HB3 A:GLU187 5.0 21.6 0.3

Calcium binding site 2 out of 4 in 6d5r

Go back to Calcium Binding Sites List in 6d5r
Calcium binding site 2 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:14.3
occ:1.00
 O A:GLN61 2.2 12.5 0.6
O A:GLN61 2.2 12.7 0.4
O A:HOH717 2.3 10.8 1.0
OD1 A:ASP57 2.4 13.7 1.0
OD1 A:ASP59 2.4 14.9 1.0
O A:HOH547 2.5 12.2 1.0
O A:HOH533 2.5 14.4 1.0
OD2 A:ASP57 2.6 14.4 1.0
CG A:ASP57 2.8 11.6 1.0
H A:GLN61 3.2 18.8 0.4
H A:GLN61 3.3 18.7 0.6
CG A:ASP59 3.4 16.0 1.0
C A:GLN61 3.4 15.5 0.6
C A:GLN61 3.4 15.5 0.4
H A:ASP59 3.5 21.5 1.0
HB2 A:GLN61 3.6 21.4 0.6
HB2 A:GLN61 3.6 21.5 0.4
OD2 A:ASP59 3.7 14.5 1.0
N A:GLN61 3.9 15.6 0.4
N A:GLN61 3.9 15.6 0.6
O A:HOH670 4.0 15.3 1.0
HA A:PHE62 4.0 20.5 1.0
CA A:GLN61 4.1 14.2 0.6
CA A:GLN61 4.1 14.3 0.4
H A:ALA58 4.1 18.3 1.0
CB A:GLN61 4.3 17.9 0.6
N A:ASP59 4.3 17.9 1.0
CB A:GLN61 4.3 17.9 0.4
CB A:ASP57 4.3 13.2 1.0
H A:ASN60 4.4 14.4 1.0
O A:HOH773 4.4 21.6 1.0
O A:HOH703 4.4 18.2 1.0
N A:PHE62 4.5 11.8 1.0
CB A:ASP59 4.6 12.4 1.0
OD2 A:ASP67 4.6 17.9 1.0
O A:HOH540 4.6 10.8 1.0
N A:ALA58 4.6 15.3 1.0
O A:HOH776 4.6 32.8 1.0
N A:ASN60 4.7 12.0 1.0
HB2 A:ASP57 4.7 15.8 1.0
CA A:PHE62 4.7 17.1 1.0
HB3 A:GLN61 4.8 21.4 0.6
O A:HOH769 4.8 36.8 1.0
HB3 A:ASP57 4.8 15.8 1.0
HB3 A:GLN61 4.8 21.5 0.4
H A:PHE63 4.8 11.7 1.0
CA A:ASP59 4.8 12.8 1.0
HA A:ASP57 4.9 16.9 1.0
C A:ASP59 4.9 14.5 1.0
HB3 A:ALA58 4.9 20.8 1.0
HB3 A:ASP59 5.0 14.9 1.0
HA A:GLN61 5.0 17.1 0.6
HA A:GLN61 5.0 17.2 0.4

Calcium binding site 3 out of 4 in 6d5r

Go back to Calcium Binding Sites List in 6d5r
Calcium binding site 3 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:15.2
occ:1.00
 O A:TYR193 2.3 15.9 1.0
O A:HOH683 2.3 18.6 1.0
O A:ILE197 2.3 22.8 1.0
OD1 A:ASP200 2.3 21.6 1.0
OG1 A:THR194 2.3 16.2 1.0
O A:THR194 2.4 17.4 1.0
O A:HOH537 2.4 12.2 1.0
C A:THR194 3.2 22.6 1.0
C A:TYR193 3.3 13.6 1.0
CG A:ASP200 3.3 10.9 1.0
CB A:THR194 3.4 17.5 1.0
HB A:ILE197 3.5 36.0 1.0
C A:ILE197 3.5 27.7 1.0
H A:ILE197 3.6 29.2 1.0
CA A:THR194 3.6 13.7 1.0
HB A:THR194 3.7 21.0 1.0
OD2 A:ASP200 3.7 17.1 1.0
N A:THR194 3.8 12.4 1.0
H A:ASP200 3.9 21.6 1.0
HB3 A:TYR193 4.0 23.2 1.0
HD2 A:TYR193 4.1 18.7 1.0
O A:HOH637 4.2 41.7 1.0
HA A:SER198 4.2 26.4 1.0
CA A:ILE197 4.2 23.6 1.0
N A:ILE197 4.2 24.3 1.0
CB A:ILE197 4.3 30.0 1.0
N A:PRO195 4.3 15.1 1.0
HA A:PRO195 4.3 22.5 1.0
O A:ASP200 4.4 15.0 1.0
CA A:TYR193 4.4 15.1 1.0
HG22 A:ILE197 4.5 23.5 1.0
N A:SER198 4.5 25.9 1.0
O A:GLU190 4.6 14.0 1.0
HA A:THR194 4.6 16.5 1.0
CB A:TYR193 4.6 19.3 1.0
CD2 A:TYR193 4.6 15.6 1.0
N A:ASP200 4.6 18.0 1.0
H A:THR194 4.7 14.8 1.0
CB A:ASP200 4.7 16.8 1.0
CG2 A:THR194 4.7 17.4 1.0
CA A:PRO195 4.7 18.7 1.0
O A:HOH733 4.7 23.6 1.0
H A:TYR193 4.8 16.5 1.0
C A:ASP200 4.8 20.6 1.0
CA A:SER198 4.8 22.0 1.0
HG23 A:THR194 4.8 20.8 1.0
H A:GLY199 4.8 28.1 1.0
CG2 A:ILE197 4.9 19.6 1.0
HG21 A:THR194 4.9 20.8 1.0
CG A:TYR193 4.9 15.9 1.0
N A:TYR193 4.9 13.8 1.0
C A:PRO195 4.9 18.8 1.0
CA A:ASP200 4.9 16.4 1.0

Calcium binding site 4 out of 4 in 6d5r

Go back to Calcium Binding Sites List in 6d5r
Calcium binding site 4 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hexagonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:12.7
occ:0.91
 OE2 A:GLU190 2.3 12.4 1.0
O A:ASN183 2.3 15.8 1.0
O A:HOH566 2.3 14.7 1.0
O A:HOH524 2.4 13.5 1.0
OE2 A:GLU177 2.4 13.0 1.0
OD2 A:ASP185 2.4 13.1 1.0
CG A:ASP185 3.2 15.4 1.0
CD A:GLU177 3.2 16.6 1.0
CD A:GLU190 3.3 13.3 1.0
HG3 A:GLU190 3.5 19.4 1.0
C A:ASN183 3.5 13.5 1.0
HA A:PRO184 3.6 18.5 1.0
OD1 A:ASP185 3.6 10.5 1.0
CG A:GLU190 3.7 16.2 1.0
HG2 A:GLU190 3.8 19.4 1.0
OE1 A:GLU177 3.8 10.4 1.0
CA A:CA404 3.8 10.9 1.0
HB3 A:ASN183 3.8 24.7 1.0
HB2 A:ASN183 3.8 24.7 1.0
H A:ASP185 4.0 11.5 1.0
N A:ASP185 4.1 9.6 1.0
CA A:PRO184 4.2 15.4 1.0
OD2 A:ASP191 4.2 13.3 1.0
OD1 A:ASP191 4.2 16.4 1.0
CB A:ASN183 4.2 20.6 1.0
O A:HOH671 4.2 31.1 1.0
C A:PRO184 4.3 21.4 1.0
HB3 A:ASP185 4.3 17.2 1.0
OE1 A:GLU190 4.3 9.3 1.0
HG2 A:GLU177 4.3 10.4 1.0
CG A:GLU177 4.3 8.7 1.0
N A:PRO184 4.3 15.3 1.0
CB A:ASP185 4.3 14.3 1.0
HG3 A:GLU177 4.4 10.4 1.0
O A:LYS182 4.4 26.0 1.0
CA A:ASN183 4.5 16.8 1.0
CG A:ASP191 4.5 17.6 1.0
O A:HOH768 4.5 39.1 1.0
CA A:ASP185 4.9 12.2 1.0
O A:PRO184 4.9 14.2 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 Jul 15 17:38:41 2024

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