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Calcium in PDB 1gxw: The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate

Enzymatic activity of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate

All present enzymatic activity of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate:
3.4.24.27;

Protein crystallography data

The structure of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate, PDB code: 1gxw was solved by J.F.Gaucher, M.Selkti, T.Prange, A.Tomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.46 / 2.18
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.170, 93.170, 130.630, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 21.5

Other elements in 1gxw:

The structure of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate (pdb code 1gxw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate, PDB code: 1gxw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1gxw

Go back to Calcium Binding Sites List in 1gxw
Calcium binding site 1 out of 4 in the The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1317

b:16.4
occ:1.00
 O A:GLU187 2.5 9.9 1.0
OD2 A:ASP138 2.6 8.9 1.0
OE1 A:GLU177 2.7 11.2 1.0
OD1 A:ASP185 2.7 10.0 1.0
OE1 A:GLU190 2.7 12.9 1.0
OE2 A:GLU190 2.7 9.5 1.0
OE2 A:GLU177 2.8 9.7 1.0
O A:HOH2100 2.8 13.7 1.0
CD A:GLU190 3.0 14.7 1.0
CD A:GLU177 3.1 8.8 1.0
CG A:ASP138 3.5 12.2 1.0
C A:GLU187 3.5 13.5 1.0
CG A:ASP185 3.6 15.3 1.0
CA A:CA1318 3.8 14.9 1.0
OD2 A:ASP185 3.9 10.4 1.0
CB A:ASP138 4.0 9.4 1.0
N A:GLU187 4.2 15.1 1.0
O A:ASP185 4.3 13.3 1.0
CA A:GLU187 4.3 15.8 1.0
O A:HOH2102 4.3 36.0 1.0
N A:ILE188 4.3 11.6 1.0
CA A:ILE188 4.4 11.5 1.0
OD1 A:ASP138 4.4 13.6 1.0
N A:GLY189 4.5 9.3 1.0
CG A:GLU177 4.5 5.8 1.0
CG A:GLU190 4.5 12.5 1.0
CB A:GLU187 4.6 16.2 1.0
O A:HOH2088 4.6 13.4 1.0
C A:ASP185 4.7 13.6 1.0
C A:ILE188 4.8 12.3 1.0
N A:ASP185 4.8 15.4 1.0
CB A:ASP185 4.9 12.7 1.0
CB A:GLU177 5.0 9.2 1.0
N A:GLU190 5.0 11.8 1.0

Calcium binding site 2 out of 4 in 1gxw

Go back to Calcium Binding Sites List in 1gxw
Calcium binding site 2 out of 4 in the The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1318

b:14.9
occ:1.00
 O A:ASN183 2.5 15.4 1.0
OD2 A:ASP185 2.5 10.4 1.0
OE2 A:GLU177 2.5 9.7 1.0
OE2 A:GLU190 2.5 9.5 1.0
O A:HOH2108 2.6 16.0 1.0
O A:HOH2109 2.7 20.6 1.0
CD A:GLU177 3.3 8.8 1.0
CG A:ASP185 3.3 15.3 1.0
CD A:GLU190 3.5 14.7 1.0
C A:ASN183 3.6 19.9 1.0
CA A:CA1317 3.8 16.4 1.0
OD1 A:ASP185 3.8 10.0 1.0
OE1 A:GLU177 3.8 11.2 1.0
CG A:GLU190 4.0 12.5 1.0
O A:LYS182 4.1 25.4 1.0
OD2 A:ASP191 4.2 10.9 1.0
CB A:ASN183 4.2 26.6 1.0
OD1 A:ASP191 4.2 13.6 1.0
CA A:PRO184 4.3 16.7 1.0
N A:ASP185 4.3 15.4 1.0
CG A:GLU177 4.3 5.8 1.0
C A:PRO184 4.3 17.2 1.0
OE1 A:GLU190 4.4 12.9 1.0
N A:PRO184 4.4 17.0 1.0
CB A:ASP185 4.5 12.7 1.0
CG A:ASP191 4.5 11.9 1.0
O A:HOH2102 4.5 36.0 1.0
CA A:ASN183 4.5 23.5 1.0
O A:PRO184 4.9 19.5 1.0

Calcium binding site 3 out of 4 in 1gxw

Go back to Calcium Binding Sites List in 1gxw
Calcium binding site 3 out of 4 in the The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1319

b:20.1
occ:1.00
 O A:GLN61 2.4 18.3 1.0
OD1 A:ASP59 2.6 17.3 1.0
OD1 A:ASP57 2.6 16.1 1.0
OD2 A:ASP57 2.7 13.9 1.0
O A:HOH2052 2.7 9.8 1.0
O A:HOH2041 2.8 27.4 1.0
O A:HOH2014 2.8 46.4 1.0
CG A:ASP57 3.0 15.4 1.0
CG A:ASP59 3.5 16.9 1.0
C A:GLN61 3.5 18.8 1.0
OD2 A:ASP59 3.8 16.7 1.0
O A:HOH2045 3.9 36.4 1.0
N A:GLN61 4.0 16.5 1.0
CA A:GLN61 4.2 19.7 1.0
N A:ASP59 4.3 14.5 1.0
CB A:GLN61 4.4 24.4 1.0
O A:HOH2040 4.5 15.8 1.0
CB A:ASP57 4.5 11.3 1.0
N A:PHE62 4.6 16.5 1.0
O A:HOH2053 4.6 8.1 1.0
CA A:PHE62 4.7 14.9 1.0
CB A:ASP59 4.7 15.0 1.0
OD2 A:ASP67 4.7 14.0 1.0
N A:ASN60 4.7 15.4 1.0
N A:ALA58 4.8 11.2 1.0
CA A:ASP59 4.8 14.8 1.0
C A:ASP59 4.9 15.7 1.0

Calcium binding site 4 out of 4 in 1gxw

Go back to Calcium Binding Sites List in 1gxw
Calcium binding site 4 out of 4 in the The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The 2.2 A Resolution Structure of Thermolysin Crystallized in Presence of Potassium Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1320

b:20.2
occ:1.00
 O A:ILE197 2.5 40.3 1.0
OD1 A:ASP200 2.5 20.7 1.0
O A:THR194 2.5 17.5 1.0
O A:TYR193 2.6 8.9 1.0
OG1 A:THR194 2.6 19.3 1.0
O A:HOH2107 2.7 14.7 1.0
O A:HOH2112 2.9 30.3 1.0
C A:THR194 3.3 18.8 1.0
C A:TYR193 3.4 12.8 1.0
CG A:ASP200 3.5 19.7 1.0
C A:ILE197 3.6 36.5 1.0
CB A:THR194 3.7 20.0 1.0
OD2 A:ASP200 3.7 20.5 1.0
CA A:THR194 3.8 16.7 1.0
N A:THR194 4.0 15.1 1.0
CB A:ILE197 4.1 36.4 1.0
CA A:ILE197 4.2 35.6 1.0
N A:ILE197 4.2 34.7 1.0
N A:PRO195 4.3 19.6 1.0
O A:ASP200 4.4 15.7 1.0
O A:GLU190 4.6 12.2 1.0
CA A:TYR193 4.6 12.9 1.0
CB A:TYR193 4.6 11.5 1.0
N A:SER198 4.6 34.8 1.0
CD2 A:TYR193 4.7 15.4 1.0
N A:ASP200 4.7 20.1 1.0
CA A:PRO195 4.7 22.9 1.0
CB A:ASP200 4.8 19.2 1.0
C A:ASP200 4.8 17.1 1.0
CA A:SER198 4.8 32.9 1.0
CG2 A:ILE197 4.9 35.6 1.0
CG2 A:THR194 4.9 19.2 1.0
C A:PRO195 5.0 25.5 1.0
CG A:TYR193 5.0 15.3 1.0

Reference:

J.Gaucher, M.Selkti, T.Prange, A.Tomas. The 2.2 A Resolution Structure of Thermolysin (Tln) Crystallized in the Presence of Potassium Thiocyanate. Acta Crystallogr.,Sect.D V. 58 2198 2002.
ISSN: ISSN 0907-4449
PubMed: 12454500
DOI: 10.1107/S0907444902015457
Page generated: Thu Jul 11 09:48:16 2024

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