Atomistry » Calcium » PDB 5npf-5odc » 5o8n
Atomistry »
  Calcium »
    PDB 5npf-5odc »
      5o8n »

Calcium in PDB 5o8n: Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.

Enzymatic activity of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.

All present enzymatic activity of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation., PDB code: 5o8n was solved by D.N.Axford, C.Burton, P.Docker, M.Prince, P.D.Topham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.552, 93.552, 129.753, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 25.9

Other elements in 5o8n:

The structure of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 3 atoms
Sodium (Na) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. (pdb code 5o8n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation., PDB code: 5o8n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5o8n

Go back to Calcium Binding Sites List in 5o8n
Calcium binding site 1 out of 4 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:43.3
occ:1.00
 O A:GLU187 2.3 42.6 1.0
O A:HOH524 2.5 39.7 1.0
OD1 A:ASP185 2.5 50.2 1.0
OE2 A:GLU190 2.6 48.7 1.0
OD2 A:ASP138 2.6 44.7 1.0
OE2 A:GLU177 2.7 51.9 1.0
OE1 A:GLU177 2.7 42.6 1.0
OE1 A:GLU190 2.8 45.5 1.0
CD A:GLU190 3.0 47.4 1.0
CD A:GLU177 3.0 47.8 1.0
C A:GLU187 3.4 48.2 1.0
CG A:ASP138 3.5 37.3 1.0
CG A:ASP185 3.6 54.0 1.0
OD2 A:ASP185 4.0 57.6 1.0
CB A:ASP138 4.1 34.4 1.0
N A:GLU187 4.1 45.9 1.0
O A:ASP185 4.2 46.7 1.0
CA A:GLU187 4.2 43.9 1.0
CA A:CA413 4.3 69.4 1.0
N A:ILE188 4.3 44.5 1.0
OD1 A:ASP138 4.3 45.5 1.0
CA A:ILE188 4.4 42.1 1.0
CG A:GLU177 4.4 39.0 1.0
N A:GLY189 4.4 40.2 1.0
CG A:GLU190 4.4 38.9 1.0
C A:ASP185 4.5 49.4 1.0
CB A:GLU187 4.6 49.0 1.0
N A:ASP185 4.6 46.5 1.0
CB A:ASP185 4.8 51.2 1.0
O A:HOH526 4.9 44.8 1.0
C A:ILE188 4.9 43.1 1.0
CA A:ASP185 4.9 47.4 1.0
OG1 A:THR174 4.9 43.0 1.0
CD1 A:ILE188 4.9 43.7 1.0
CB A:GLU177 4.9 36.9 1.0

Calcium binding site 2 out of 4 in 5o8n

Go back to Calcium Binding Sites List in 5o8n
Calcium binding site 2 out of 4 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:40.9
occ:1.00
 O A:HOH550 2.3 43.1 1.0
O A:GLN61 2.3 37.0 1.0
OD1 A:ASP59 2.4 45.5 1.0
OD2 A:ASP57 2.4 43.1 1.0
O A:HOH564 2.4 41.6 1.0
OD1 A:ASP57 2.5 41.5 1.0
O A:HOH504 2.6 44.1 1.0
CG A:ASP57 2.8 43.6 1.0
C A:GLN61 3.4 41.2 1.0
CG A:ASP59 3.5 45.2 1.0
OD2 A:ASP59 3.9 47.8 1.0
N A:GLN61 3.9 41.4 1.0
O A:HOH577 4.0 43.8 1.0
CA A:GLN61 4.1 41.1 1.0
N A:ASP59 4.3 42.5 1.0
CB A:ASP57 4.3 36.1 1.0
O A:HOH561 4.3 45.7 1.0
CB A:GLN61 4.4 46.4 1.0
N A:PHE62 4.5 39.5 1.0
OD1 A:ASP67 4.6 43.5 1.0
N A:ALA58 4.6 39.0 1.0
CB A:ASP59 4.7 38.1 1.0
N A:ASN60 4.7 40.2 1.0
CA A:PHE62 4.8 35.9 1.0
CA A:ASP59 4.9 39.4 1.0
O A:HOH509 4.9 35.2 1.0
C A:ASP59 4.9 37.7 1.0

Calcium binding site 3 out of 4 in 5o8n

Go back to Calcium Binding Sites List in 5o8n
Calcium binding site 3 out of 4 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca412

b:47.3
occ:1.00
 O A:ILE197 2.3 75.0 1.0
O A:TYR193 2.4 55.5 1.0
O A:HOH549 2.4 57.1 1.0
OG1 A:THR194 2.4 55.0 1.0
O A:THR194 2.5 56.5 1.0
O A:HOH502 2.5 33.4 1.0
OD1 A:ASP200 2.6 53.9 1.0
C A:THR194 3.3 54.4 1.0
C A:TYR193 3.4 50.6 1.0
C A:ILE197 3.4 67.2 1.0
CB A:THR194 3.6 51.2 1.0
CG A:ASP200 3.6 55.3 1.0
CA A:THR194 3.8 50.8 1.0
N A:THR194 4.0 50.3 1.0
OD2 A:ASP200 4.0 49.8 1.0
N A:ILE197 4.1 63.6 1.0
CA A:ILE197 4.1 60.2 1.0
CB A:ILE197 4.2 57.0 1.0
N A:PRO195 4.3 55.1 1.0
N A:SER198 4.4 65.0 1.0
O A:GLU190 4.5 48.4 1.0
O A:ASP200 4.5 42.3 1.0
O A:HOH574 4.5 49.5 1.0
CA A:TYR193 4.5 48.0 1.0
CA A:SER198 4.5 69.5 1.0
CA A:PRO195 4.6 53.6 1.0
CB A:TYR193 4.7 47.8 1.0
CG2 A:THR194 4.7 45.8 1.0
N A:ASP200 4.9 46.0 1.0
CG2 A:ILE197 4.9 57.9 1.0
CD1 A:TYR193 4.9 48.4 1.0
C A:SER198 5.0 66.4 1.0
C A:PRO195 5.0 57.0 1.0
CB A:ASP200 5.0 47.8 1.0
C A:ASP200 5.0 46.6 1.0
N A:TYR193 5.0 47.2 1.0

Calcium binding site 4 out of 4 in 5o8n

Go back to Calcium Binding Sites List in 5o8n
Calcium binding site 4 out of 4 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:69.4
occ:1.00
 O A:ASN183 2.5 56.6 1.0
OE2 A:GLU190 2.5 48.7 1.0
OD2 A:ASP185 3.1 57.6 1.0
OE2 A:GLU177 3.2 51.9 1.0
CD A:GLU190 3.4 47.4 1.0
CG A:GLU190 3.6 38.9 1.0
OD1 A:ASP191 3.7 49.7 1.0
C A:ASN183 3.7 54.0 1.0
OD2 A:ASP191 3.8 53.6 1.0
CG A:ASP185 3.8 54.0 1.0
CD A:GLU177 3.9 47.8 1.0
CB A:ASN183 4.0 65.7 1.0
CG A:ASP191 4.1 49.2 1.0
OD1 A:ASP185 4.2 50.2 1.0
CA A:CA401 4.3 43.3 1.0
OE1 A:GLU177 4.3 42.6 1.0
O A:LYS182 4.4 62.2 1.0
CA A:ASN183 4.5 61.5 1.0
OE1 A:GLU190 4.5 45.5 1.0
N A:PRO184 4.6 46.2 1.0
CA A:PRO184 4.6 48.2 1.0
N A:ASP185 4.7 46.5 1.0
C A:PRO184 4.8 51.3 1.0
CB A:ASP185 4.9 51.2 1.0
CG A:GLU177 4.9 39.0 1.0

Reference:

C.G.Burton, D.Axford, A.M.J.Edwards, R.J.Gildea, R.H.Morris, M.I.Newton, A.M.Orville, M.Prince, P.D.Topham, P.T.Docker. An Acoustic on-Chip Goniometer For Room Temperature Macromolecular Crystallography. Lab Chip V. 17 4225 2017.
ISSN: ISSN 1473-0189
PubMed: 29124258
DOI: 10.1039/C7LC00812K
Page generated: Wed Jul 9 09:15:12 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy