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Calcium in PDB 1fjw: Thermolysin (50 Mm Phenol Soaked)

Enzymatic activity of Thermolysin (50 Mm Phenol Soaked)

All present enzymatic activity of Thermolysin (50 Mm Phenol Soaked):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin (50 Mm Phenol Soaked), PDB code: 1fjw was solved by A.C.English, C.R.Groom, R.E.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.960, 93.960, 130.915, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 19.4

Other elements in 1fjw:

The structure of Thermolysin (50 Mm Phenol Soaked) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin (50 Mm Phenol Soaked) (pdb code 1fjw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin (50 Mm Phenol Soaked), PDB code: 1fjw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1fjw

Go back to Calcium Binding Sites List in 1fjw
Calcium binding site 1 out of 4 in the Thermolysin (50 Mm Phenol Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin (50 Mm Phenol Soaked) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:22.8
occ:1.00
O A:GLU187 2.5 21.1 1.0
OD2 A:ASP138 2.6 24.6 1.0
O A:HOH522 2.6 22.1 1.0
OE1 A:GLU190 2.6 20.0 1.0
OE2 A:GLU190 2.6 19.3 1.0
OE1 A:GLU177 2.6 21.9 1.0
OD1 A:ASP185 2.6 21.7 1.0
OE2 A:GLU177 2.8 21.9 1.0
CD A:GLU190 3.1 25.9 1.0
CD A:GLU177 3.1 24.5 1.0
CG A:ASP138 3.5 24.9 1.0
C A:GLU187 3.6 22.9 1.0
CG A:ASP185 3.6 30.2 1.0
CA A:CA503 3.9 27.9 1.0
OD2 A:ASP185 3.9 23.7 1.0
CB A:ASP138 4.0 19.0 1.0
O A:ASP185 4.2 24.4 1.0
N A:GLU187 4.3 25.0 1.0
CA A:ILE188 4.3 20.4 1.0
OD1 A:ASP138 4.3 22.9 1.0
O A:HOH643 4.3 41.1 1.0
N A:ILE188 4.4 19.4 1.0
CA A:GLU187 4.4 25.1 1.0
O A:HOH537 4.5 28.2 1.0
N A:GLY189 4.5 22.6 1.0
CG A:GLU177 4.5 19.2 1.0
CG A:GLU190 4.6 23.3 1.0
C A:ASP185 4.7 25.3 1.0
CB A:GLU187 4.7 25.8 1.0
N A:ASP185 4.7 24.2 1.0
C A:ILE188 4.8 21.2 1.0
CB A:ASP185 4.9 23.3 1.0
N A:GLU190 4.9 21.4 1.0
CB A:GLU177 5.0 21.6 1.0
O A:HOH538 5.0 52.4 1.0

Calcium binding site 2 out of 4 in 1fjw

Go back to Calcium Binding Sites List in 1fjw
Calcium binding site 2 out of 4 in the Thermolysin (50 Mm Phenol Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin (50 Mm Phenol Soaked) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:27.9
occ:1.00
O A:HOH538 2.5 52.4 1.0
O A:HOH521 2.5 35.8 1.0
OD2 A:ASP185 2.6 23.7 1.0
OE2 A:GLU190 2.6 19.3 1.0
O A:ASN183 2.6 29.2 1.0
OE2 A:GLU177 2.6 21.9 1.0
CG A:ASP185 3.3 30.2 1.0
CD A:GLU177 3.4 24.5 1.0
CD A:GLU190 3.5 25.9 1.0
OD1 A:ASP185 3.7 21.7 1.0
C A:ASN183 3.8 33.4 1.0
O A:LYS182 3.9 33.0 1.0
CA A:CA502 3.9 22.8 1.0
OE1 A:GLU177 3.9 21.9 1.0
CG A:GLU190 4.1 23.3 1.0
N A:ASP185 4.1 24.2 1.0
C A:PRO184 4.2 30.0 1.0
CA A:PRO184 4.2 29.9 1.0
OD2 A:ASP191 4.2 24.6 1.0
CB A:ASN183 4.3 37.5 1.0
OD1 A:ASP191 4.3 25.8 1.0
CG A:GLU177 4.3 19.2 1.0
OE1 A:GLU190 4.4 20.0 1.0
N A:PRO184 4.4 32.4 1.0
CB A:ASP185 4.5 23.3 1.0
O A:HOH643 4.6 41.1 1.0
CG A:ASP191 4.6 30.9 1.0
CA A:ASN183 4.7 30.5 1.0
O A:PRO184 4.9 28.0 1.0
C A:LYS182 4.9 35.1 1.0
CA A:ASP185 4.9 23.4 1.0
O A:HOH612 5.0 47.1 1.0

Calcium binding site 3 out of 4 in 1fjw

Go back to Calcium Binding Sites List in 1fjw
Calcium binding site 3 out of 4 in the Thermolysin (50 Mm Phenol Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin (50 Mm Phenol Soaked) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:24.4
occ:1.00
O A:HOH535 2.5 23.0 1.0
O A:GLN61 2.5 22.2 1.0
O A:HOH524 2.5 29.4 1.0
OD1 A:ASP59 2.5 22.0 1.0
OD1 A:ASP57 2.6 21.6 1.0
O A:HOH555 2.6 33.4 1.0
OD2 A:ASP57 2.7 23.9 1.0
CG A:ASP57 3.1 25.3 1.0
CG A:ASP59 3.6 32.3 1.0
C A:GLN61 3.7 24.5 1.0
OD2 A:ASP59 3.8 27.4 1.0
N A:GLN61 3.9 23.7 1.0
O A:HOH560 4.1 38.3 1.0
CA A:GLN61 4.2 24.1 1.0
N A:ASP59 4.3 25.2 1.0
CB A:GLN61 4.3 27.6 1.0
CB A:ASP57 4.6 21.2 1.0
O A:HOH608 4.6 65.4 1.0
N A:PHE62 4.6 22.0 1.0
N A:ASN60 4.6 22.1 1.0
O A:HOH552 4.6 28.0 1.0
OD2 A:ASP67 4.7 23.0 1.0
CA A:PHE62 4.7 21.5 1.0
O A:HOH517 4.7 21.4 1.0
CB A:ASP59 4.7 22.5 1.0
N A:ALA58 4.8 20.3 1.0
C A:ASP59 4.8 25.5 1.0
CA A:ASP59 4.8 23.9 1.0

Calcium binding site 4 out of 4 in 1fjw

Go back to Calcium Binding Sites List in 1fjw
Calcium binding site 4 out of 4 in the Thermolysin (50 Mm Phenol Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin (50 Mm Phenol Soaked) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:28.9
occ:1.00
O A:TYR193 2.5 23.8 1.0
O A:HOH546 2.6 38.1 1.0
O A:ILE197 2.6 34.6 1.0
O A:THR194 2.6 30.8 1.0
OD1 A:ASP200 2.7 29.3 1.0
O A:HOH573 2.8 35.3 1.0
OG1 A:THR194 2.8 32.3 1.0
C A:THR194 3.4 30.0 1.0
C A:TYR193 3.5 27.6 1.0
CB A:THR194 3.6 32.4 1.0
CG A:ASP200 3.7 26.0 1.0
C A:ILE197 3.8 42.2 1.0
OD2 A:ASP200 3.8 29.9 1.0
CA A:THR194 3.9 27.1 1.0
N A:THR194 4.0 25.1 1.0
CB A:ILE197 4.2 46.0 1.0
N A:ILE197 4.3 42.4 1.0
CA A:ILE197 4.4 42.1 1.0
N A:PRO195 4.4 29.6 1.0
O A:ASP200 4.5 26.0 1.0
N A:ASP200 4.6 31.6 1.0
CA A:TYR193 4.7 23.6 1.0
CA A:SER198 4.7 41.7 1.0
CD2 A:TYR193 4.7 27.6 1.0
CB A:TYR193 4.7 23.5 1.0
N A:SER198 4.7 40.6 1.0
O A:GLU190 4.8 24.2 1.0
CA A:PRO195 4.8 34.4 1.0
O A:HOH613 4.8 51.6 1.0
C A:ASP200 4.9 26.0 1.0
CG2 A:ILE197 4.9 41.1 1.0
CB A:ASP200 4.9 26.5 1.0
C A:SER198 4.9 40.2 1.0
CG2 A:THR194 5.0 28.1 1.0

Reference:

A.C.English, C.R.Groom, R.E.Hubbard. Experimental and Computational Mapping of the Binding Surface of A Crystalline Protein. Protein Eng. V. 14 47 2001.
ISSN: ISSN 0269-2139
PubMed: 11287678
DOI: 10.1093/PROTEIN/14.1.47
Page generated: Sat Dec 12 02:55:46 2020

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