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Calcium in PDB 6d5q: Hexagonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant

Enzymatic activity of Hexagonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant

All present enzymatic activity of Hexagonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant:
3.4.24.27;

Protein crystallography data

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant, PDB code: 6d5q 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) 13.83 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.386, 93.386, 129.878, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 29.8

Other elements in 6d5q:

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 30% 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 30% Xylose As Cryoprotectant (pdb code 6d5q). 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 30% Xylose As Cryoprotectant, PDB code: 6d5q:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6d5q

Go back to Calcium Binding Sites List in 6d5q
Calcium binding site 1 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 30% 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 30% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:27.2
occ:1.00
 O A:GLU187 2.2 21.8 0.5
O A:GLU187 2.3 21.9 0.5
OE2 A:GLU190 2.4 24.4 1.0
OD1 A:ASP185 2.4 25.6 1.0
OE1 A:GLU177 2.5 21.8 1.0
O A:HOH564 2.5 24.4 1.0
OD2 A:ASP138 2.7 30.8 1.0
OE1 A:GLU190 2.7 24.1 1.0
OE2 A:GLU177 2.8 30.4 1.0
CD A:GLU190 2.9 33.7 1.0
CD A:GLU177 3.0 21.7 1.0
CG A:ASP185 3.4 27.8 1.0
C A:GLU187 3.4 26.0 0.5
C A:GLU187 3.4 26.0 0.5
CG A:ASP138 3.6 28.2 1.0
HB3 A:ASP138 3.6 38.8 1.0
H A:GLU187 3.6 35.6 0.5
H A:GLU187 3.7 35.6 0.5
OD2 A:ASP185 3.7 32.0 1.0
HA A:ILE188 3.8 34.8 1.0
CA A:CA407 3.8 29.4 0.9
H A:GLY189 3.9 30.6 1.0
H A:ASP185 4.0 40.7 1.0
CB A:ASP138 4.0 32.4 1.0
O A:ASP185 4.1 23.1 1.0
HB2 A:GLU187 4.1 38.2 0.5
HB2 A:GLU187 4.1 38.1 0.5
H A:GLU190 4.2 36.3 1.0
N A:GLU187 4.2 29.7 0.5
N A:GLU187 4.2 29.6 0.5
HB2 A:ASP138 4.2 38.8 1.0
O A:HOH525 4.3 23.3 1.0
CA A:GLU187 4.3 29.1 0.5
CA A:GLU187 4.3 29.1 0.5
N A:ILE188 4.3 24.3 1.0
CG A:GLU190 4.3 23.4 1.0
CG A:GLU177 4.4 24.1 1.0
CA A:ILE188 4.5 29.0 1.0
HD13 A:ILE188 4.5 33.0 1.0
OD1 A:ASP138 4.5 30.4 1.0
C A:ASP185 4.5 27.1 1.0
N A:GLY189 4.5 25.5 1.0
N A:ASP185 4.6 33.9 1.0
HG3 A:GLU190 4.6 28.1 1.0
CB A:ASP185 4.7 40.1 1.0
HB3 A:GLU177 4.7 26.7 1.0
HB2 A:GLU177 4.7 26.7 1.0
CB A:GLU187 4.7 31.8 0.5
HA A:THR174 4.7 38.1 1.0
CB A:GLU187 4.7 31.8 0.5
HG2 A:GLU190 4.8 28.1 1.0
HG2 A:GLU177 4.8 28.9 1.0
CA A:ASP185 4.8 28.7 1.0
CB A:GLU177 4.9 22.3 1.0
C A:ILE188 4.9 36.2 1.0
O A:HOH586 4.9 31.7 1.0
HG3 A:GLU177 4.9 28.9 1.0
HA A:PRO184 5.0 34.0 1.0

Calcium binding site 2 out of 4 in 6d5q

Go back to Calcium Binding Sites List in 6d5q
Calcium binding site 2 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 30% 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 30% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:28.6
occ:1.00
 O A:GLN61 2.3 22.6 1.0
O A:HOH672 2.4 32.5 1.0
O A:HOH512 2.4 34.9 1.0
O A:HOH567 2.4 27.9 1.0
OD1 A:ASP59 2.4 24.8 1.0
OD1 A:ASP57 2.5 35.4 1.0
OD2 A:ASP57 2.5 23.2 1.0
CG A:ASP57 2.8 34.4 1.0
H A:GLN61 3.3 33.7 1.0
CG A:ASP59 3.4 25.0 1.0
C A:GLN61 3.5 28.5 1.0
H A:ASP59 3.5 44.7 1.0
OD2 A:ASP59 3.7 29.8 1.0
HB2 A:GLN61 3.8 32.4 1.0
O A:HOH599 3.8 27.3 1.0
N A:GLN61 3.9 28.1 1.0
HA A:PHE62 4.0 40.5 1.0
H A:ALA58 4.0 34.3 1.0
CA A:GLN61 4.2 30.5 1.0
N A:ASP59 4.3 37.2 1.0
CB A:ASP57 4.3 22.8 1.0
O A:HOH721 4.3 40.7 1.0
H A:ASN60 4.4 32.1 1.0
O A:HOH598 4.4 30.3 1.0
CB A:GLN61 4.5 27.0 1.0
N A:PHE62 4.5 27.4 1.0
N A:ALA58 4.6 28.6 1.0
CB A:ASP59 4.7 25.4 1.0
N A:ASN60 4.7 26.8 1.0
OD2 A:ASP67 4.7 29.5 1.0
CA A:PHE62 4.7 33.8 1.0
O A:HOH532 4.7 24.0 1.0
O A:HOH733 4.7 37.1 1.0
HB2 A:ASP57 4.7 27.4 1.0
HB3 A:ASP57 4.7 27.4 1.0
HB3 A:ALA58 4.8 36.0 1.0
H A:PHE63 4.8 30.5 1.0
HA A:ASP57 4.8 29.1 1.0
CA A:ASP59 4.8 26.2 1.0
C A:ASP59 4.9 36.0 1.0

Calcium binding site 3 out of 4 in 6d5q

Go back to Calcium Binding Sites List in 6d5q
Calcium binding site 3 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 30% 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 30% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:32.5
occ:1.00
 O A:THR194 2.3 31.6 1.0
OG1 A:THR194 2.3 32.5 1.0
O A:TYR193 2.4 35.3 1.0
OD1 A:ASP200 2.4 33.2 1.0
O A:HOH614 2.4 36.0 1.0
O A:ILE197 2.4 36.8 1.0
O A:HOH510 2.4 25.9 1.0
C A:THR194 3.1 35.7 1.0
C A:TYR193 3.2 24.6 1.0
CB A:THR194 3.3 34.7 1.0
CG A:ASP200 3.4 27.2 1.0
HB A:ILE197 3.5 54.0 1.0
H A:ILE197 3.5 36.3 1.0
C A:ILE197 3.6 32.9 1.0
CA A:THR194 3.6 31.6 1.0
HB A:THR194 3.6 41.6 1.0
OD2 A:ASP200 3.7 28.3 1.0
N A:THR194 3.7 25.9 1.0
HB3 A:TYR193 3.9 36.2 1.0
H A:ASP200 3.9 43.2 1.0
HD2 A:TYR193 4.0 30.8 1.0
N A:ILE197 4.2 30.2 1.0
N A:PRO195 4.2 21.0 1.0
CA A:ILE197 4.2 30.4 1.0
O A:ASP200 4.3 31.3 1.0
CB A:ILE197 4.3 45.0 1.0
HA A:PRO195 4.3 34.0 1.0
HA A:SER198 4.3 42.6 1.0
CA A:TYR193 4.4 24.1 1.0
HA A:THR194 4.5 38.0 1.0
CD2 A:TYR193 4.5 25.7 1.0
CB A:TYR193 4.5 30.2 1.0
H A:THR194 4.5 31.0 1.0
O A:GLU190 4.6 25.8 1.0
HG22 A:ILE197 4.6 34.5 1.0
N A:SER198 4.6 40.2 1.0
CG2 A:THR194 4.6 41.3 1.0
CA A:PRO195 4.6 28.3 1.0
N A:ASP200 4.7 36.0 1.0
CB A:ASP200 4.7 31.6 1.0
O A:HOH674 4.7 44.1 1.0
C A:ASP200 4.8 33.2 1.0
HG23 A:THR194 4.8 49.5 1.0
CA A:SER198 4.9 35.5 1.0
H A:TYR193 4.9 34.7 1.0
CG A:TYR193 4.9 34.9 1.0
HG21 A:THR194 4.9 49.5 1.0
C A:PRO195 4.9 36.3 1.0
H A:GLY199 4.9 35.0 1.0
CA A:ASP200 5.0 25.8 1.0
N A:TYR193 5.0 28.9 1.0

Calcium binding site 4 out of 4 in 6d5q

Go back to Calcium Binding Sites List in 6d5q
Calcium binding site 4 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 30% 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 30% Xylose As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:29.4
occ:0.89
 OE2 A:GLU190 2.3 24.4 1.0
O A:ASN183 2.4 34.8 1.0
OD2 A:ASP185 2.4 32.0 1.0
O A:HOH588 2.4 27.2 1.0
OE2 A:GLU177 2.5 30.4 1.0
O A:HOH586 2.5 31.7 1.0
CD A:GLU190 3.2 33.7 1.0
CG A:ASP185 3.3 27.8 1.0
HG3 A:GLU190 3.3 28.1 1.0
CD A:GLU177 3.4 21.7 1.0
HA A:PRO184 3.5 34.0 1.0
C A:ASN183 3.6 40.8 1.0
HG2 A:GLU190 3.6 28.1 1.0
CG A:GLU190 3.6 23.4 1.0
OD1 A:ASP185 3.7 25.6 1.0
CA A:CA404 3.8 27.2 1.0
HB3 A:ASN183 4.0 62.7 1.0
OE1 A:GLU177 4.0 21.8 1.0
HB2 A:ASN183 4.0 62.7 1.0
OD1 A:ASP191 4.1 28.9 1.0
H A:ASP185 4.1 40.7 1.0
CA A:PRO184 4.1 28.3 1.0
N A:ASP185 4.2 33.9 1.0
HB3 A:ASP185 4.2 48.1 1.0
OD2 A:ASP191 4.2 27.2 1.0
C A:PRO184 4.3 39.3 1.0
OE1 A:GLU190 4.3 24.1 1.0
CB A:ASP185 4.3 40.1 1.0
N A:PRO184 4.3 36.9 1.0
O A:HOH665 4.3 56.8 1.0
CB A:ASN183 4.4 52.2 1.0
HG2 A:GLU177 4.4 28.9 1.0
O A:HOH726 4.4 44.5 1.0
CG A:ASP191 4.5 37.0 1.0
O A:LYS182 4.5 41.0 1.0
CG A:GLU177 4.5 24.1 1.0
CA A:ASN183 4.6 48.5 1.0
HG3 A:GLU177 4.7 28.9 1.0
CA A:ASP185 4.9 28.7 1.0
O A:PRO184 4.9 35.7 1.0
O A:HOH525 5.0 23.3 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 17:36:55 2024

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