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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: Mon Jul 15 09:44:00 2024

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