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Calcium in PDB 6d5t: 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: 6d5t 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) 13.74 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.790, 92.790, 128.872, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 19.6

Other elements in 6d5t:

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 6d5t). 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: 6d5t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6d5t

Go back to Calcium Binding Sites List in 6d5t
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:11.3
occ:1.00
 O A:GLU187 2.3 10.7 1.0
OD2 A:ASP138 2.4 11.1 1.0
O A:HOH620 2.5 10.1 1.0
OD1 A:ASP185 2.5 7.6 1.0
OE2 A:GLU190 2.5 12.7 1.0
OE1 A:GLU177 2.5 9.4 1.0
OE1 A:GLU190 2.6 9.6 1.0
OE2 A:GLU177 2.7 14.4 1.0
CD A:GLU190 2.9 16.3 1.0
CD A:GLU177 3.0 14.7 1.0
C A:GLU187 3.3 11.9 1.0
CG A:ASP185 3.4 12.4 1.0
CG A:ASP138 3.5 11.8 1.0
HB3 A:ASP138 3.6 9.3 1.0
HA A:ILE188 3.6 11.2 1.0
H A:GLU187 3.7 17.9 1.0
OD2 A:ASP185 3.7 18.8 1.0
H A:GLY189 3.8 8.3 1.0
HB2 A:GLU187 3.9 21.2 1.0
CA A:CA407 3.9 24.7 1.0
CB A:ASP138 4.0 9.3 1.0
O A:ASP185 4.1 15.2 1.0
H A:ASP185 4.1 15.3 1.0
H A:GLU190 4.2 11.4 1.0
N A:ILE188 4.2 14.2 1.0
N A:GLU187 4.2 17.9 1.0
CA A:GLU187 4.2 19.2 1.0
HB2 A:ASP138 4.3 9.3 1.0
CA A:ILE188 4.3 11.2 1.0
O A:HOH618 4.3 15.6 1.0
HD13 A:ILE188 4.3 13.9 1.0
CG A:GLU190 4.4 9.9 1.0
OD1 A:ASP138 4.4 10.6 1.0
N A:GLY189 4.4 8.3 1.0
CG A:GLU177 4.4 7.6 1.0
CB A:GLU187 4.5 21.2 1.0
C A:ASP185 4.6 22.0 1.0
HG3 A:GLU190 4.6 9.9 1.0
HB2 A:GLU177 4.7 6.5 1.0
CB A:ASP185 4.7 15.8 1.0
N A:ASP185 4.8 15.3 1.0
C A:ILE188 4.8 15.1 1.0
O A:HOH516 4.8 18.1 1.0
HB3 A:GLU177 4.8 6.5 1.0
HG2 A:GLU190 4.8 9.9 1.0
HG2 A:GLU177 4.9 7.6 1.0
HA A:THR174 4.9 9.1 1.0
H A:ILE188 4.9 14.2 1.0
HG3 A:GLU177 4.9 7.6 1.0
CB A:GLU177 4.9 6.5 1.0
N A:GLU190 5.0 11.4 1.0
CA A:ASP185 5.0 11.3 1.0

Calcium binding site 2 out of 4 in 6d5t

Go back to Calcium Binding Sites List in 6d5t
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:10.7
occ:1.00
 O A:GLN61 2.3 8.6 1.0
OD1 A:ASP57 2.4 13.3 1.0
OD1 A:ASP59 2.4 12.1 1.0
O A:HOH574 2.4 7.5 1.0
O A:HOH701 2.5 14.7 1.0
O A:HOH538 2.5 5.0 1.0
OD2 A:ASP57 2.6 7.1 1.0
CG A:ASP57 2.8 13.9 1.0
H A:GLN61 3.3 10.5 1.0
CG A:ASP59 3.4 13.8 1.0
C A:GLN61 3.4 7.0 1.0
H A:ASP59 3.5 16.2 1.0
HB2 A:GLN61 3.8 12.8 1.0
OD2 A:ASP59 3.8 13.4 1.0
N A:GLN61 3.9 10.5 1.0
O A:HOH635 4.0 11.7 1.0
HA A:PHE62 4.0 12.4 1.0
CA A:GLN61 4.2 14.0 1.0
H A:ALA58 4.2 10.0 1.0
H A:ASN60 4.3 11.8 1.0
CB A:ASP57 4.3 8.6 1.0
N A:ASP59 4.3 16.2 1.0
CB A:GLN61 4.5 12.8 1.0
O A:HOH656 4.5 16.7 1.0
O A:HOH728 4.5 15.7 1.0
N A:PHE62 4.5 9.1 1.0
N A:ASN60 4.6 11.8 1.0
O A:HOH537 4.6 4.7 1.0
CB A:ASP59 4.7 10.3 1.0
OD2 A:ASP67 4.7 11.1 1.0
HB2 A:ASP57 4.7 8.6 1.0
N A:ALA58 4.7 10.0 1.0
CA A:PHE62 4.7 12.4 1.0
O A:HOH724 4.8 24.9 1.0
HB3 A:ASP57 4.8 8.6 1.0
H A:PHE63 4.8 9.0 1.0
CA A:ASP59 4.8 7.3 1.0
C A:ASP59 4.8 13.9 1.0
HA A:ASP57 4.9 7.2 1.0
HB3 A:GLN61 5.0 12.8 1.0

Calcium binding site 3 out of 4 in 6d5t

Go back to Calcium Binding Sites List in 6d5t
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:15.9
occ:1.00
 OG1 A:THR194 2.3 20.8 1.0
O A:TYR193 2.3 15.0 1.0
OD1 A:ASP200 2.3 18.6 1.0
O A:THR194 2.3 16.2 1.0
O A:ILE197 2.4 18.8 1.0
O A:HOH532 2.4 18.1 1.0
O A:HOH693 2.5 18.1 1.0
C A:THR194 3.2 15.1 1.0
C A:TYR193 3.3 10.4 1.0
CB A:THR194 3.4 17.1 1.0
CG A:ASP200 3.4 15.8 1.0
HB A:ILE197 3.5 32.7 1.0
H A:ILE197 3.5 28.1 1.0
C A:ILE197 3.5 21.5 1.0
CA A:THR194 3.6 15.9 1.0
HB A:THR194 3.6 17.1 1.0
OD2 A:ASP200 3.7 16.8 1.0
H A:ASP200 3.8 16.4 1.0
N A:THR194 3.8 16.3 1.0
HB3 A:TYR193 4.0 11.8 1.0
HD2 A:TYR193 4.1 18.6 1.0
N A:ILE197 4.2 28.1 1.0
CA A:ILE197 4.2 22.0 1.0
N A:PRO195 4.2 16.7 1.0
HA A:PRO195 4.3 25.3 1.0
CB A:ILE197 4.3 32.7 1.0
HA A:SER198 4.3 32.6 1.0
O A:ASP200 4.3 14.7 1.0
CA A:TYR193 4.5 15.4 1.0
HG22 A:ILE197 4.5 25.8 1.0
HA A:THR194 4.6 15.9 1.0
N A:ASP200 4.6 16.4 1.0
N A:SER198 4.6 19.3 1.0
O A:GLU190 4.6 13.3 1.0
CB A:TYR193 4.6 11.8 1.0
CG2 A:THR194 4.6 19.0 1.0
CA A:PRO195 4.6 25.3 1.0
H A:GLY199 4.6 26.7 1.0
H A:THR194 4.7 16.3 1.0
CD2 A:TYR193 4.7 18.6 1.0
CB A:ASP200 4.7 14.1 1.0
HG23 A:THR194 4.7 19.0 1.0
H A:TYR193 4.7 12.0 1.0
O A:HOH705 4.8 24.9 1.0
CA A:SER198 4.8 32.6 1.0
C A:ASP200 4.8 17.3 1.0
HG21 A:THR194 4.8 19.0 1.0
C A:PRO195 4.9 27.2 1.0
C A:SER198 4.9 21.5 1.0
N A:GLY199 4.9 26.7 1.0
CA A:ASP200 4.9 17.4 1.0
N A:TYR193 5.0 12.0 1.0
CG A:TYR193 5.0 18.1 1.0
CG2 A:ILE197 5.0 25.8 1.0

Calcium binding site 4 out of 4 in 6d5t

Go back to Calcium Binding Sites List in 6d5t
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:24.7
occ:1.00
 O A:ASN183 2.4 16.9 1.0
OD2 A:ASP185 2.4 18.8 1.0
O A:HOH557 2.4 23.8 1.0
OE2 A:GLU190 2.5 12.7 1.0
O A:HOH516 2.6 18.1 1.0
OE2 A:GLU177 2.7 14.4 1.0
CG A:ASP185 3.3 12.4 1.0
CD A:GLU190 3.4 16.3 1.0
CD A:GLU177 3.4 14.7 1.0
HG3 A:GLU190 3.6 9.9 1.0
C A:ASN183 3.6 14.6 1.0
HA A:PRO184 3.6 15.7 1.0
HG2 A:GLU190 3.8 9.9 1.0
OD1 A:ASP185 3.8 7.6 1.0
CG A:GLU190 3.8 9.9 1.0
OE1 A:GLU177 3.8 9.4 1.0
HB3 A:ASN183 3.9 24.6 1.0
HB2 A:ASN183 3.9 24.6 1.0
CA A:CA404 3.9 11.3 1.0
H A:ASP185 4.0 15.3 1.0
N A:ASP185 4.2 15.3 1.0
OD1 A:ASP191 4.2 14.7 1.0
CA A:PRO184 4.2 15.7 1.0
HB3 A:ASP185 4.2 15.8 1.0
CB A:ASN183 4.3 24.6 1.0
OD2 A:ASP191 4.3 13.8 1.0
C A:PRO184 4.3 19.5 1.0
CB A:ASP185 4.3 15.8 1.0
N A:PRO184 4.4 20.4 1.0
HG2 A:GLU177 4.4 7.6 1.0
O A:LYS182 4.4 33.8 1.0
CG A:GLU177 4.4 7.6 1.0
OE1 A:GLU190 4.4 9.6 1.0
HG3 A:GLU177 4.5 7.6 1.0
CG A:ASP191 4.5 15.2 1.0
CA A:ASN183 4.6 22.5 1.0
CA A:ASP185 4.9 11.3 1.0
O A:HOH618 5.0 15.6 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 Jul 9 13:16:03 2025

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