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Calcium 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:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant, PDB code: 6d5s:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6d5s

Go back to Calcium Binding Sites List in 6d5s
Calcium binding site 1 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd 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% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:10.6
occ:1.00
O A:GLU187 2.2 8.0 0.5
O A:GLU187 2.4 7.4 0.5
OE1 A:GLU177 2.5 6.2 1.0
OD1 A:ASP185 2.5 6.3 1.0
OD2 A:ASP138 2.5 6.8 1.0
OE2 A:GLU190 2.5 9.5 1.0
O A:HOH614 2.5 9.2 1.0
OE1 A:GLU190 2.6 9.5 1.0
OE2 A:GLU177 2.8 8.1 1.0
CD A:GLU190 2.9 11.6 1.0
CD A:GLU177 3.0 9.9 1.0
C A:GLU187 3.3 7.2 0.5
C A:GLU187 3.4 7.3 0.5
CG A:ASP185 3.4 10.9 1.0
CG A:ASP138 3.5 12.9 1.0
HB3 A:ASP138 3.6 8.3 1.0
HA A:ILE188 3.6 9.8 1.0
H A:GLU187 3.7 21.4 0.5
OD2 A:ASP185 3.7 10.0 1.0
H A:GLU187 3.8 21.5 0.5
H A:GLY189 3.8 7.2 1.0
CA A:CA407 3.8 10.1 1.0
HB2 A:GLU187 3.9 16.0 0.5
CB A:ASP138 4.0 7.0 1.0
H A:GLU190 4.1 9.3 1.0
HB2 A:GLU187 4.1 16.6 0.5
O A:ASP185 4.2 11.5 1.0
N A:GLU187 4.2 17.9 0.5
N A:ILE188 4.2 7.2 1.0
N A:GLU187 4.2 17.9 0.5
H A:ASP185 4.3 10.6 1.0
CA A:GLU187 4.3 15.5 0.5
O A:HOH583 4.3 36.9 1.0
HB2 A:ASP138 4.3 8.3 1.0
CA A:GLU187 4.3 15.4 0.5
HD13 A:ILE188 4.3 16.4 1.0
CA A:ILE188 4.3 8.2 1.0
CG A:GLU190 4.4 11.4 1.0
CG A:GLU177 4.4 8.7 1.0
N A:GLY189 4.4 6.0 1.0
OD1 A:ASP138 4.5 10.1 1.0
O A:HOH643 4.6 12.6 1.0
CB A:GLU187 4.6 13.3 0.5
C A:ASP185 4.6 10.9 1.0
HG3 A:GLU190 4.6 13.7 1.0
HB2 A:GLU177 4.7 9.9 1.0
CB A:ASP185 4.7 9.7 1.0
CB A:GLU187 4.7 13.8 0.5
HB3 A:GLU177 4.8 9.9 1.0
C A:ILE188 4.8 11.2 1.0
N A:ASP185 4.8 8.8 1.0
HA A:THR174 4.8 6.7 1.0
HG2 A:GLU190 4.8 13.7 1.0
HG2 A:GLU177 4.9 10.5 1.0
HG3 A:GLU177 4.9 10.5 1.0
N A:GLU190 4.9 7.7 1.0
CB A:GLU177 4.9 8.3 1.0
H A:ILE188 5.0 8.6 0.5
HB3 A:GLU190 5.0 10.7 1.0
H A:ILE188 5.0 8.6 0.5
CA A:ASP185 5.0 6.5 1.0
O A:HOH531 5.0 10.8 1.0

Calcium binding site 2 out of 4 in 6d5s

Go back to Calcium Binding Sites List in 6d5s
Calcium binding site 2 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd 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% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:8.9
occ:1.00
O A:GLN61 2.3 6.5 1.0
O A:HOH742 2.3 9.5 1.0
OD1 A:ASP57 2.3 9.2 1.0
OD1 A:ASP59 2.4 7.2 1.0
O A:HOH524 2.4 7.8 1.0
OD2 A:ASP57 2.5 5.7 1.0
O A:HOH521 2.6 5.9 1.0
CG A:ASP57 2.8 9.4 1.0
H A:GLN61 3.3 11.7 1.0
CG A:ASP59 3.3 15.4 1.0
C A:GLN61 3.4 5.5 1.0
H A:ASP59 3.5 14.2 1.0
HB2 A:GLN61 3.7 9.6 1.0
OD2 A:ASP59 3.7 11.2 1.0
N A:GLN61 3.9 9.8 1.0
O A:HOH681 4.0 11.1 1.0
HA A:PHE62 4.1 15.0 1.0
CA A:GLN61 4.1 9.0 1.0
H A:ALA58 4.2 9.5 1.0
CB A:ASP57 4.3 5.3 1.0
N A:ASP59 4.3 11.8 1.0
H A:ASN60 4.4 8.3 1.0
CB A:GLN61 4.4 8.0 1.0
O A:HOH780 4.5 18.5 1.0
N A:PHE62 4.5 5.0 1.0
O A:HOH707 4.5 17.1 1.0
O A:HOH528 4.6 5.5 1.0
CB A:ASP59 4.6 8.4 1.0
N A:ASN60 4.6 6.9 1.0
HB2 A:ASP57 4.6 6.3 1.0
O A:HOH783 4.6 20.7 1.0
OD2 A:ASP67 4.7 12.4 1.0
N A:ALA58 4.7 7.9 1.0
HB3 A:ASP57 4.7 6.3 1.0
O A:HOH792 4.8 31.9 1.0
CA A:PHE62 4.8 12.5 1.0
CA A:ASP59 4.8 6.9 1.0
HA A:ASP57 4.8 6.7 1.0
C A:ASP59 4.8 8.9 1.0
H A:PHE63 4.8 7.0 1.0
HB3 A:GLN61 4.9 9.6 1.0
HB3 A:ASP59 4.9 10.1 1.0

Calcium binding site 3 out of 4 in 6d5s

Go back to Calcium Binding Sites List in 6d5s
Calcium binding site 3 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd 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% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:13.9
occ:1.00
OG1 A:THR194 2.3 16.9 1.0
O A:TYR193 2.3 12.2 1.0
O A:ILE197 2.3 19.6 1.0
OD1 A:ASP200 2.3 15.3 1.0
O A:HOH737 2.4 14.3 1.0
O A:THR194 2.4 12.7 1.0
O A:HOH532 2.4 12.4 1.0
C A:THR194 3.2 9.7 1.0
C A:TYR193 3.3 10.8 1.0
CB A:THR194 3.4 13.3 1.0
CG A:ASP200 3.4 9.8 1.0
C A:ILE197 3.5 22.8 1.0
HB A:ILE197 3.5 30.4 1.0
H A:ILE197 3.5 32.2 1.0
HB A:THR194 3.6 16.0 1.0
CA A:THR194 3.6 10.8 1.0
OD2 A:ASP200 3.7 14.0 1.0
H A:ASP200 3.8 18.9 1.0
N A:THR194 3.9 12.1 1.0
HB3 A:TYR193 4.0 15.4 1.0
HD2 A:TYR193 4.1 12.7 1.0
CA A:ILE197 4.2 18.3 1.0
N A:ILE197 4.2 26.9 1.0
O A:HOH506 4.2 38.6 1.0
HA A:PRO195 4.3 23.0 1.0
CB A:ILE197 4.3 25.3 1.0
N A:PRO195 4.3 13.4 1.0
HA A:SER198 4.3 19.6 1.0
O A:ASP200 4.4 13.8 1.0
HG22 A:ILE197 4.5 22.3 1.0
CA A:TYR193 4.5 13.3 1.0
N A:SER198 4.6 17.0 1.0
N A:ASP200 4.6 15.8 1.0
HA A:THR194 4.6 12.9 1.0
O A:GLU190 4.6 8.4 1.0
CB A:TYR193 4.6 12.8 1.0
H A:GLY199 4.6 22.8 1.0
CA A:PRO195 4.6 19.1 1.0
CG2 A:THR194 4.7 17.4 1.0
CD2 A:TYR193 4.7 10.6 1.0
H A:THR194 4.7 14.5 1.0
O A:HOH749 4.7 27.0 1.0
CB A:ASP200 4.7 11.3 1.0
H A:TYR193 4.8 10.5 1.0
CA A:SER198 4.8 16.3 1.0
HG23 A:THR194 4.8 20.9 1.0
C A:ASP200 4.8 9.7 1.0
HG21 A:THR194 4.9 20.9 1.0
C A:PRO195 4.9 18.4 1.0
N A:GLY199 4.9 19.0 1.0
CG2 A:ILE197 4.9 18.6 1.0
C A:SER198 4.9 18.1 1.0
CA A:ASP200 4.9 19.4 1.0
N A:TYR193 5.0 8.8 1.0

Calcium binding site 4 out of 4 in 6d5s

Go back to Calcium Binding Sites List in 6d5s
Calcium binding site 4 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Mpd 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% Mpd As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:10.1
occ:1.00
O A:ASN183 2.3 11.2 1.0
OD2 A:ASP185 2.3 10.0 1.0
OE2 A:GLU190 2.3 9.5 1.0
O A:HOH556 2.3 12.2 1.0
OE2 A:GLU177 2.4 8.1 1.0
O A:HOH531 2.4 10.8 1.0
CG A:ASP185 3.2 10.9 1.0
CD A:GLU177 3.3 9.9 1.0
CD A:GLU190 3.3 11.6 1.0
C A:ASN183 3.5 12.5 1.0
HG3 A:GLU190 3.6 13.7 1.0
HA A:PRO184 3.6 16.5 1.0
OD1 A:ASP185 3.7 6.3 1.0
HG2 A:GLU190 3.8 13.7 1.0
HB3 A:ASN183 3.8 20.4 1.0
OE1 A:GLU177 3.8 6.2 1.0
CG A:GLU190 3.8 11.4 1.0
HB2 A:ASN183 3.8 20.4 1.0
CA A:CA404 3.8 10.6 1.0
O A:HOH670 4.0 37.4 1.0
H A:ASP185 4.1 10.6 1.0
CA A:PRO184 4.1 13.7 1.0
OD2 A:ASP191 4.2 9.0 1.0
CB A:ASN183 4.2 17.0 1.0
N A:ASP185 4.2 8.8 1.0
OD1 A:ASP191 4.2 8.9 1.0
HG2 A:GLU177 4.2 10.5 1.0
C A:PRO184 4.2 15.4 1.0
HB3 A:ASP185 4.2 11.6 1.0
CG A:GLU177 4.3 8.7 1.0
N A:PRO184 4.3 15.7 1.0
O A:LYS182 4.3 21.8 1.0
CB A:ASP185 4.3 9.7 1.0
OE1 A:GLU190 4.3 9.5 1.0
HG3 A:GLU177 4.4 10.5 1.0
CA A:ASN183 4.5 14.8 1.0
O A:HOH784 4.5 33.4 1.0
CG A:ASP191 4.5 15.7 1.0
O A:HOH583 4.5 36.9 1.0
O A:PRO184 4.8 16.0 1.0
CA A:ASP185 4.9 6.5 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: Sat Dec 12 06:02:28 2020

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