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Calcium in PDB 6d5u: Hexagonal Thermolysin Cryocooled to 100 K with 50% Methanol As Cryoprotectant

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

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

Protein crystallography data

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 50% Methanol As Cryoprotectant, PDB code: 6d5u 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) 13.92 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.812, 92.812, 127.699, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 22.3

Other elements in 6d5u:

The structure of Hexagonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant (pdb code 6d5u). 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% Methanol As Cryoprotectant, PDB code: 6d5u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6d5u

Go back to Calcium Binding Sites List in 6d5u
Calcium binding site 1 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:13.1
occ:1.00
 O A:GLU187 2.2 10.2 0.5
O A:GLU187 2.4 10.0 0.5
OD2 A:ASP138 2.5 14.9 1.0
O A:HOH590 2.5 16.3 1.0
OE1 A:GLU177 2.5 15.3 1.0
OD1 A:ASP185 2.5 14.2 1.0
OE2 A:GLU190 2.5 16.7 1.0
OE1 A:GLU190 2.6 19.8 1.0
OE2 A:GLU177 2.8 14.8 1.0
CD A:GLU190 2.9 19.6 1.0
CD A:GLU177 3.0 12.9 1.0
C A:GLU187 3.4 16.8 0.5
C A:GLU187 3.4 16.8 0.5
CG A:ASP138 3.5 13.2 1.0
CG A:ASP185 3.5 15.9 1.0
HB3 A:ASP138 3.6 11.1 1.0
HA A:ILE188 3.6 12.7 1.0
H A:GLU187 3.7 20.5 0.5
OD2 A:ASP185 3.8 12.1 1.0
H A:GLU187 3.8 20.5 0.5
H A:GLY189 3.8 11.3 1.0
CA A:CA407 3.8 13.8 1.0
CB A:ASP138 4.0 11.1 1.0
HB2 A:GLU187 4.0 21.4 0.5
O A:ASP185 4.1 18.3 1.0
H A:GLU190 4.1 15.2 1.0
N A:GLU187 4.2 20.5 0.5
N A:ILE188 4.2 11.4 1.0
HB2 A:ASP138 4.2 11.1 1.0
N A:GLU187 4.3 20.5 0.5
HB2 A:GLU187 4.3 21.4 0.5
HD13 A:ILE188 4.3 15.7 1.0
H A:ASP185 4.3 15.6 1.0
CA A:ILE188 4.3 12.7 1.0
CA A:GLU187 4.3 18.1 0.5
CA A:GLU187 4.3 18.1 0.5
CG A:GLU190 4.4 19.2 1.0
OD1 A:ASP138 4.4 11.3 1.0
N A:GLY189 4.4 11.3 1.0
CG A:GLU177 4.4 13.6 1.0
O A:HOH569 4.5 16.8 1.0
C A:ASP185 4.6 17.4 1.0
HG3 A:GLU190 4.6 19.2 1.0
CB A:GLU187 4.7 21.4 0.5
CB A:ASP185 4.8 19.5 1.0
HB2 A:GLU177 4.8 14.4 1.0
C A:ILE188 4.8 14.1 1.0
N A:ASP185 4.8 15.6 1.0
HB3 A:GLU177 4.8 14.4 1.0
CB A:GLU187 4.8 22.3 0.5
HA A:THR174 4.9 14.5 1.0
HG2 A:GLU190 4.9 19.2 1.0
HG2 A:GLU177 4.9 13.6 1.0
N A:GLU190 4.9 15.2 1.0
HG3 A:GLU177 4.9 13.6 1.0
O A:HOH523 5.0 16.8 1.0
CB A:GLU177 5.0 14.4 1.0
CA A:ASP185 5.0 12.6 1.0
HB3 A:GLU190 5.0 9.3 1.0
H A:ILE188 5.0 11.4 0.5

Calcium binding site 2 out of 4 in 6d5u

Go back to Calcium Binding Sites List in 6d5u
Calcium binding site 2 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:15.3
occ:1.00
 O A:GLN61 2.2 10.6 1.0
O A:HOH733 2.4 11.6 1.0
OD1 A:ASP57 2.4 17.1 1.0
OD1 A:ASP59 2.4 11.4 1.0
OD2 A:ASP57 2.5 12.4 1.0
O A:HOH587 2.5 14.5 1.0
O A:HOH525 2.6 17.3 1.0
CG A:ASP57 2.8 20.2 1.0
H A:GLN61 3.2 14.9 1.0
CG A:ASP59 3.3 16.3 1.0
C A:GLN61 3.4 15.5 1.0
H A:ASP59 3.5 19.8 1.0
HB2 A:GLN61 3.6 14.9 1.0
OD2 A:ASP59 3.7 14.9 1.0
N A:GLN61 3.9 14.9 1.0
HA A:PHE62 4.0 17.8 1.0
CA A:GLN61 4.0 20.6 1.0
H A:ALA58 4.1 13.8 1.0
O A:HOH619 4.2 16.4 1.0
N A:ASP59 4.3 19.8 1.0
CB A:GLN61 4.3 14.9 1.0
CB A:ASP57 4.3 13.6 1.0
H A:ASN60 4.4 15.9 1.0
N A:PHE62 4.5 12.5 1.0
O A:HOH792 4.6 31.1 1.0
CB A:ASP59 4.6 10.7 1.0
O A:HOH538 4.6 12.6 1.0
N A:ALA58 4.6 13.8 1.0
N A:ASN60 4.6 15.9 1.0
OD2 A:ASP67 4.6 13.1 1.0
HB2 A:ASP57 4.7 13.6 1.0
HB3 A:GLN61 4.7 14.9 1.0
HB3 A:ASP57 4.7 13.6 1.0
CA A:PHE62 4.7 17.8 1.0
CA A:ASP59 4.8 10.3 1.0
O A:HOH815 4.8 39.6 1.0
C A:ASP59 4.8 15.1 1.0
HB3 A:ALA58 4.8 20.7 1.0
HA A:ASP57 4.9 15.7 1.0
H A:PHE63 4.9 14.6 1.0
HB3 A:ASP59 4.9 10.7 1.0
HA A:GLN61 5.0 20.6 1.0
C A:ASN60 5.0 21.3 1.0

Calcium binding site 3 out of 4 in 6d5u

Go back to Calcium Binding Sites List in 6d5u
Calcium binding site 3 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:20.1
occ:1.00
 O A:TYR193 2.3 15.3 1.0
OD1 A:ASP200 2.3 20.3 1.0
O A:ILE197 2.3 17.5 1.0
O A:THR194 2.3 20.9 1.0
OG1 A:THR194 2.4 18.6 1.0
O A:HOH527 2.4 12.6 1.0
O A:HOH722 2.5 16.9 1.0
C A:THR194 3.2 19.8 1.0
C A:TYR193 3.3 12.9 1.0
CG A:ASP200 3.3 14.3 1.0
HB A:ILE197 3.4 31.5 1.0
H A:ILE197 3.5 31.8 1.0
C A:ILE197 3.5 28.1 1.0
CB A:THR194 3.5 21.1 1.0
OD2 A:ASP200 3.6 19.6 1.0
CA A:THR194 3.7 19.7 1.0
HB A:THR194 3.8 21.1 1.0
H A:ASP200 3.9 24.3 1.0
N A:THR194 3.9 19.3 1.0
HD2 A:TYR193 4.0 19.1 1.0
HB3 A:TYR193 4.0 19.6 1.0
CA A:ILE197 4.2 20.7 1.0
N A:ILE197 4.2 31.8 1.0
CB A:ILE197 4.2 31.5 1.0
O A:ASP200 4.2 22.2 1.0
HA A:PRO195 4.2 25.9 1.0
O A:HOH679 4.3 30.1 1.0
N A:PRO195 4.3 19.4 1.0
HA A:SER198 4.4 29.4 1.0
O A:HOH752 4.5 26.3 1.0
CA A:TYR193 4.5 20.1 1.0
HG22 A:ILE197 4.6 26.7 1.0
CD2 A:TYR193 4.6 19.1 1.0
N A:ASP200 4.6 24.3 1.0
O A:GLU190 4.6 17.3 1.0
N A:SER198 4.6 16.9 1.0
CB A:TYR193 4.6 19.6 1.0
CB A:ASP200 4.7 15.6 1.0
CA A:PRO195 4.7 25.9 1.0
HA A:THR194 4.7 19.7 1.0
H A:TYR193 4.7 15.9 1.0
C A:ASP200 4.7 26.7 1.0
H A:GLY199 4.7 24.4 1.0
H A:THR194 4.8 19.3 1.0
CG2 A:THR194 4.8 16.7 1.0
CA A:SER198 4.9 29.4 1.0
HG23 A:THR194 4.9 16.7 1.0
CA A:ASP200 4.9 14.9 1.0
CG2 A:ILE197 4.9 26.7 1.0
C A:PRO195 5.0 26.5 1.0
CG A:TYR193 5.0 27.0 1.0
N A:TYR193 5.0 15.9 1.0
C A:SER198 5.0 16.9 1.0
N A:GLY199 5.0 24.4 1.0

Calcium binding site 4 out of 4 in 6d5u

Go back to Calcium Binding Sites List in 6d5u
Calcium binding site 4 out of 4 in the Hexagonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:13.8
occ:1.00
 OE2 A:GLU190 2.3 16.7 1.0
OD2 A:ASP185 2.3 12.1 1.0
O A:ASN183 2.3 14.8 1.0
O A:HOH574 2.4 16.9 1.0
O A:HOH523 2.4 16.8 1.0
OE2 A:GLU177 2.5 14.8 1.0
CG A:ASP185 3.2 15.9 1.0
CD A:GLU177 3.3 12.9 1.0
CD A:GLU190 3.3 19.6 1.0
HA A:PRO184 3.5 13.8 1.0
C A:ASN183 3.5 14.2 1.0
HG3 A:GLU190 3.6 19.2 1.0
OD1 A:ASP185 3.7 14.2 1.0
CA A:CA404 3.8 13.1 1.0
OE1 A:GLU177 3.8 15.3 1.0
HG2 A:GLU190 3.8 19.2 1.0
CG A:GLU190 3.9 19.2 1.0
HB2 A:ASN183 3.9 18.9 1.0
HB3 A:ASN183 4.0 18.9 1.0
OD2 A:ASP191 4.0 16.4 1.0
OD1 A:ASP191 4.1 17.6 1.0
CA A:PRO184 4.1 13.8 1.0
H A:ASP185 4.2 15.6 1.0
C A:PRO184 4.2 21.6 1.0
N A:ASP185 4.2 15.6 1.0
HB3 A:ASP185 4.2 19.5 1.0
N A:PRO184 4.3 18.3 1.0
HG2 A:GLU177 4.3 13.6 1.0
CG A:GLU177 4.3 13.6 1.0
CB A:ASN183 4.3 18.9 1.0
CB A:ASP185 4.3 19.5 1.0
OE1 A:GLU190 4.3 19.8 1.0
HG3 A:GLU177 4.4 13.6 1.0
CG A:ASP191 4.4 19.0 1.0
O A:LYS182 4.5 27.9 1.0
CA A:ASN183 4.6 17.2 1.0
O A:PRO184 4.8 24.5 1.0
CA A:ASP185 4.9 12.6 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: Mon Jul 15 17:39:25 2024

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