Atomistry » Calcium » PDB 6cl6-6d73 » 6d5s
Atomistry »
  Calcium »
    PDB 6cl6-6d73 »
      6d5s »

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: Mon Jul 15 17:39:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy