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Calcium in PDB 6d5p: Hexagonal Thermolysin Cryocooled to 100 K with 20% Xylose As Cryoprotectant

Enzymatic activity of Hexagonal Thermolysin Cryocooled to 100 K with 20% Xylose As Cryoprotectant

All present enzymatic activity of Hexagonal Thermolysin Cryocooled to 100 K with 20% Xylose As Cryoprotectant:
3.4.24.27;

Protein crystallography data

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 20% Xylose As Cryoprotectant, PDB code: 6d5p 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) 13.75 / 3.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.307, 93.307, 129.125, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 30.8

Other elements in 6d5p:

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 20% 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 20% Xylose As Cryoprotectant (pdb code 6d5p). 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 20% Xylose As Cryoprotectant, PDB code: 6d5p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6d5p

Go back to Calcium Binding Sites List in 6d5p
Calcium binding site 1 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 20% 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 20% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:19.6
occ:1.00
 OE2 A:GLU190 2.3 64.5 1.0
O A:GLU187 2.3 12.5 1.0
OE1 A:GLU177 2.4 30.4 1.0
OE2 A:GLU177 2.5 48.0 1.0
O A:HOH525 2.6 13.7 1.0
OE1 A:GLU190 2.6 36.5 1.0
OD2 A:ASP138 2.6 50.0 1.0
OD1 A:ASP185 2.7 30.0 1.0
CD A:GLU190 2.8 40.8 1.0
CD A:GLU177 2.8 44.5 1.0
C A:GLU187 3.4 22.6 1.0
H A:GLU187 3.6 32.7 1.0
CG A:ASP185 3.6 24.0 1.0
HB3 A:ASP138 3.6 47.5 1.0
CG A:ASP138 3.7 44.0 1.0
HA A:ILE188 3.8 31.5 1.0
H A:GLY189 3.8 30.4 1.0
CA A:CA407 3.8 39.7 0.9
H A:ASP185 3.9 41.7 1.0
OD2 A:ASP185 3.9 37.4 1.0
HB2 A:GLU187 4.0 49.0 1.0
H A:GLU190 4.1 23.2 1.0
CB A:ASP138 4.1 39.6 1.0
N A:GLU187 4.2 27.2 1.0
O A:ASP185 4.2 19.8 1.0
CG A:GLU190 4.2 27.3 1.0
CG A:GLU177 4.2 53.4 1.0
N A:ILE188 4.2 36.5 1.0
CA A:GLU187 4.3 32.6 1.0
HB2 A:ASP138 4.3 47.5 1.0
CA A:ILE188 4.4 26.3 1.0
HD13 A:ILE188 4.4 44.3 1.0
N A:GLY189 4.4 25.4 1.0
HG3 A:GLU190 4.5 32.8 1.0
HB2 A:GLU177 4.6 50.0 1.0
C A:ASP185 4.6 21.5 1.0
N A:ASP185 4.6 34.8 1.0
HG2 A:GLU177 4.6 64.1 1.0
CB A:GLU187 4.7 40.9 1.0
HB3 A:GLU177 4.7 50.0 1.0
HG2 A:GLU190 4.7 32.8 1.0
HA A:THR174 4.7 25.9 1.0
OD1 A:ASP138 4.8 39.5 1.0
HG3 A:GLU177 4.8 64.1 1.0
CB A:GLU177 4.8 41.7 1.0
CB A:ASP185 4.8 39.2 1.0
C A:ILE188 4.9 21.8 1.0
HB3 A:GLU190 4.9 60.4 1.0
N A:GLU190 4.9 19.4 1.0
CA A:ASP185 4.9 45.8 1.0
H A:ILE188 5.0 43.8 1.0

Calcium binding site 2 out of 4 in 6d5p

Go back to Calcium Binding Sites List in 6d5p
Calcium binding site 2 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 20% 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 20% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:18.5
occ:1.00
 OD1 A:ASP59 2.3 30.2 1.0
O A:GLN61 2.4 26.7 1.0
OD2 A:ASP57 2.4 14.0 1.0
O A:HOH511 2.4 29.0 1.0
OD1 A:ASP57 2.8 21.8 1.0
O A:HOH569 2.8 21.3 1.0
CG A:ASP57 2.9 28.1 1.0
CG A:ASP59 3.2 30.6 1.0
H A:GLN61 3.5 37.3 1.0
OD2 A:ASP59 3.5 20.7 1.0
C A:GLN61 3.5 14.1 1.0
O A:HOH554 3.6 4.3 1.0
H A:ASP59 3.6 34.1 1.0
HB2 A:GLN61 3.9 27.7 1.0
H A:ALA58 4.0 30.2 1.0
HA A:PHE62 4.0 22.8 1.0
N A:GLN61 4.1 31.1 1.0
O A:HOH587 4.1 30.9 1.0
CA A:GLN61 4.3 22.2 1.0
N A:ASP59 4.4 28.4 1.0
CB A:ASP57 4.4 16.9 1.0
H A:ASN60 4.4 27.5 1.0
OD2 A:ASP67 4.5 40.5 1.0
CB A:ASP59 4.5 25.1 1.0
O A:HOH509 4.6 12.5 1.0
CB A:GLN61 4.6 23.1 1.0
N A:PHE62 4.6 10.2 1.0
N A:ALA58 4.6 25.1 1.0
O A:HOH505 4.7 16.8 1.0
CA A:PHE62 4.8 19.0 1.0
HB3 A:ASP57 4.8 20.3 1.0
N A:ASN60 4.8 22.9 1.0
HA A:ASP57 4.8 25.4 1.0
HB3 A:ALA58 4.8 28.9 1.0
CA A:ASP59 4.9 35.7 1.0
HB3 A:ASP59 4.9 30.1 1.0
HB2 A:ASP57 4.9 20.3 1.0
H A:PHE63 4.9 34.1 1.0

Calcium binding site 3 out of 4 in 6d5p

Go back to Calcium Binding Sites List in 6d5p
Calcium binding site 3 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 20% 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 20% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:21.9
occ:1.00
 O A:ILE197 2.3 44.7 1.0
O A:THR194 2.3 29.4 1.0
O A:HOH541 2.4 14.3 1.0
OD1 A:ASP200 2.4 21.1 1.0
O A:TYR193 2.5 41.8 1.0
O A:HOH507 2.5 14.9 1.0
OG1 A:THR194 2.8 18.6 1.0
HG1 A:THR194 3.2 22.3 1.0
C A:THR194 3.4 36.3 1.0
C A:ILE197 3.5 29.7 1.0
H A:ASP200 3.5 21.3 1.0
CG A:ASP200 3.6 28.2 1.0
H A:ILE197 3.6 39.1 1.0
C A:TYR193 3.6 36.9 1.0
HB A:ILE197 3.7 37.1 1.0
H A:GLY199 3.8 40.0 1.0
CB A:THR194 3.9 27.0 1.0
HA A:SER198 4.0 65.5 1.0
O A:ASP200 4.0 32.8 1.0
CA A:THR194 4.0 28.9 1.0
OD2 A:ASP200 4.1 18.4 1.0
HB A:THR194 4.1 32.4 1.0
HA A:PRO195 4.1 38.9 1.0
N A:THR194 4.3 44.6 1.0
CA A:ILE197 4.3 24.1 1.0
N A:ILE197 4.3 32.5 1.0
N A:ASP200 4.3 17.7 1.0
HB3 A:TYR193 4.4 38.9 1.0
N A:PRO195 4.4 29.5 1.0
HD2 A:TYR193 4.4 26.8 1.0
CB A:ILE197 4.4 30.9 1.0
O A:GLU190 4.5 45.0 1.0
N A:SER198 4.5 16.9 1.0
N A:GLY199 4.5 33.3 1.0
HG22 A:ILE197 4.6 35.9 1.0
CA A:SER198 4.6 54.6 1.0
CA A:PRO195 4.6 32.4 1.0
C A:ASP200 4.7 31.9 1.0
CB A:ASP200 4.8 23.8 1.0
CA A:TYR193 4.8 31.9 1.0
C A:PRO195 4.8 40.0 1.0
CA A:ASP200 4.8 26.4 1.0
H A:TYR193 4.9 37.0 1.0
C A:SER198 4.9 39.9 1.0
HA A:THR194 5.0 34.7 1.0
CD2 A:TYR193 5.0 22.3 1.0
CB A:TYR193 5.0 32.4 1.0

Calcium binding site 4 out of 4 in 6d5p

Go back to Calcium Binding Sites List in 6d5p
Calcium binding site 4 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 20% 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 20% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:39.7
occ:0.86
 O A:ASN183 2.2 31.9 1.0
OE2 A:GLU190 2.3 64.5 1.0
OD2 A:ASP185 2.3 37.4 1.0
OE2 A:GLU177 2.4 48.0 1.0
CD A:GLU190 3.2 40.8 1.0
HG3 A:GLU190 3.2 32.8 1.0
CD A:GLU177 3.3 44.5 1.0
CG A:ASP185 3.3 24.0 1.0
C A:ASN183 3.4 38.9 1.0
HA A:PRO184 3.5 43.1 1.0
CG A:GLU190 3.6 27.3 1.0
HG2 A:GLU190 3.6 32.8 1.0
H A:ASP185 3.7 41.7 1.0
OD1 A:ASP185 3.8 30.0 1.0
HB3 A:ASN183 3.8 90.8 1.0
CA A:CA404 3.8 19.6 1.0
HB2 A:ASN183 3.8 90.8 1.0
OE1 A:GLU177 3.9 30.4 1.0
N A:ASP185 4.0 34.8 1.0
CA A:PRO184 4.1 36.0 1.0
HG2 A:GLU177 4.1 64.1 1.0
OD2 A:ASP191 4.1 57.2 1.0
CB A:ASN183 4.2 75.7 1.0
CG A:GLU177 4.2 53.4 1.0
N A:PRO184 4.2 41.8 1.0
OD1 A:ASP191 4.3 30.4 1.0
C A:PRO184 4.3 40.2 1.0
OE1 A:GLU190 4.3 36.5 1.0
HG3 A:GLU177 4.3 64.1 1.0
CA A:ASN183 4.4 49.8 1.0
CB A:ASP185 4.4 39.2 1.0
O A:LYS182 4.5 50.4 1.0
CG A:ASP191 4.5 55.3 1.0
HB3 A:ASP185 4.5 47.0 1.0
CA A:ASP185 4.9 45.8 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 13:13:37 2025

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