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Calcium in PDB 3qh1: Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid

Enzymatic activity of Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid

All present enzymatic activity of Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid, PDB code: 3qh1 was solved by G.Birrane, B.Bhyravbhatla, M.Navia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.11 / 1.55
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.503, 92.503, 130.102, 90.00, 90.00, 120.00
R / Rfree (%) 11.3 / 15

Other elements in 3qh1:

The structure of Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid (pdb code 3qh1). 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 in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid, PDB code: 3qh1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3qh1

Go back to Calcium Binding Sites List in 3qh1
Calcium binding site 1 out of 4 in the Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid


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 in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:17.0
occ:1.00
 O A:GLU187 2.3 17.4 1.0
OD2 A:ASP138 2.3 17.4 1.0
O A:HOH447 2.4 16.2 1.0
OE1 A:GLU177 2.4 17.8 1.0
OD1 A:ASP185 2.5 16.3 1.0
OE2 A:GLU190 2.5 18.0 1.0
OE1 A:GLU190 2.5 18.4 1.0
OE2 A:GLU177 2.8 18.6 1.0
CD A:GLU190 2.8 17.4 1.0
CD A:GLU177 2.9 16.4 1.0
CG A:ASP138 3.4 17.8 1.0
C A:GLU187 3.4 17.4 1.0
CG A:ASP185 3.5 18.0 1.0
CA A:CA402 3.8 19.6 1.0
OD2 A:ASP185 3.9 20.4 1.0
CB A:ASP138 4.0 16.0 1.0
O A:ASP185 4.1 17.4 1.0
O A:HOH576 4.2 27.6 1.0
N A:GLU187 4.2 18.2 1.0
N A:ILE188 4.3 17.7 1.0
CA A:GLU187 4.3 18.6 1.0
CG A:GLU190 4.3 18.7 1.0
OD1 A:ASP138 4.3 22.1 1.0
CA A:ILE188 4.3 17.7 1.0
CG A:GLU177 4.4 16.5 1.0
N A:GLY189 4.4 17.2 1.0
O A:HOH516 4.5 25.1 1.0
C A:ASP185 4.6 17.7 1.0
CB A:GLU187 4.7 20.2 1.0
CB A:ASP185 4.8 17.0 1.0
N A:ASP185 4.8 17.7 1.0
C A:ILE188 4.8 17.5 1.0
CB A:GLU177 4.9 15.8 1.0
N A:GLU190 5.0 18.1 1.0
O A:HOH504 5.0 21.4 1.0
CA A:ASP185 5.0 17.8 1.0

Calcium binding site 2 out of 4 in 3qh1

Go back to Calcium Binding Sites List in 3qh1
Calcium binding site 2 out of 4 in the Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid


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 in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:19.6
occ:1.00
 O A:ASN183 2.3 21.4 1.0
O A:HOH462 2.3 23.0 1.0
OE2 A:GLU190 2.3 18.0 1.0
O A:HOH504 2.4 21.4 1.0
OD2 A:ASP185 2.4 20.4 1.0
OE2 A:GLU177 2.4 18.6 1.0
CG A:ASP185 3.2 18.0 1.0
CD A:GLU177 3.2 16.4 1.0
CD A:GLU190 3.3 17.4 1.0
C A:ASN183 3.5 21.1 1.0
OD1 A:ASP185 3.6 16.3 1.0
OE1 A:GLU177 3.7 17.8 1.0
CG A:GLU190 3.8 18.7 1.0
CA A:CA401 3.8 17.0 1.0
O A:HOH337 4.1 74.2 1.0
CA A:PRO184 4.1 18.2 1.0
OD2 A:ASP191 4.1 25.3 1.0
OD1 A:ASP191 4.1 24.2 1.0
CB A:ASN183 4.1 23.4 1.0
N A:ASP185 4.2 17.7 1.0
CG A:GLU177 4.2 16.5 1.0
C A:PRO184 4.3 18.2 1.0
N A:PRO184 4.3 19.4 1.0
OE1 A:GLU190 4.3 18.4 1.0
O A:LYS182 4.3 24.2 1.0
CB A:ASP185 4.4 17.0 1.0
CG A:ASP191 4.5 21.8 1.0
CA A:ASN183 4.5 22.6 1.0
O A:HOH576 4.6 27.6 1.0
O A:HOH335 4.6 48.2 1.0
CA A:ASP185 4.9 17.8 1.0
O A:PRO184 5.0 21.1 1.0

Calcium binding site 3 out of 4 in 3qh1

Go back to Calcium Binding Sites List in 3qh1
Calcium binding site 3 out of 4 in the Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid


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 in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:17.2
occ:1.00
 O A:GLN61 2.3 16.3 1.0
OD1 A:ASP59 2.3 18.5 1.0
O A:HOH477 2.4 19.4 1.0
O A:HOH476 2.4 19.4 1.0
OD1 A:ASP57 2.4 17.6 1.0
O A:HOH459 2.5 18.4 1.0
OD2 A:ASP57 2.6 17.1 1.0
CG A:ASP57 2.8 16.4 1.0
CG A:ASP59 3.4 17.4 1.0
C A:GLN61 3.4 14.9 1.0
OD2 A:ASP59 3.8 20.8 1.0
O A:HOH514 4.0 23.3 1.0
N A:GLN61 4.0 17.1 1.0
CA A:GLN61 4.2 16.2 0.5
CA A:GLN61 4.2 16.3 0.5
N A:ASP59 4.3 16.4 1.0
CB A:GLN61 4.3 17.1 0.5
CB A:ASP57 4.4 16.8 1.0
CB A:GLN61 4.4 17.1 0.5
O A:HOH454 4.5 19.1 1.0
N A:PHE62 4.5 15.4 1.0
OD2 A:ASP67 4.6 17.9 1.0
CB A:ASP59 4.6 17.4 1.0
O A:HOH442 4.6 17.1 1.0
O A:HOH535 4.6 24.0 1.0
N A:ASN60 4.7 16.9 1.0
CA A:PHE62 4.7 15.8 1.0
O A:HOH601 4.7 34.0 1.0
N A:ALA58 4.8 17.3 1.0
CA A:ASP59 4.8 17.0 1.0
C A:ASP59 4.9 17.0 1.0

Calcium binding site 4 out of 4 in 3qh1

Go back to Calcium Binding Sites List in 3qh1
Calcium binding site 4 out of 4 in the Structure of Thermolysin in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid


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 in Complex with N-Benzyloxycarbonyl-L- Aspartic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:22.7
occ:1.00
 O A:ILE197 2.3 27.0 1.0
O A:TYR193 2.4 20.5 1.0
OD1 A:ASP200 2.4 21.0 1.0
O A:HOH479 2.4 21.5 1.0
O A:THR194 2.4 23.0 1.0
O A:HOH495 2.4 26.6 1.0
OG1 A:THR194 2.4 23.1 1.0
C A:THR194 3.2 22.6 1.0
C A:TYR193 3.4 20.1 1.0
CG A:ASP200 3.4 21.9 1.0
CB A:THR194 3.5 22.4 1.0
C A:ILE197 3.5 29.0 1.0
CA A:THR194 3.6 22.3 1.0
OD2 A:ASP200 3.8 23.5 1.0
N A:THR194 3.9 20.9 1.0
CA A:ILE197 4.2 29.2 1.0
CB A:ILE197 4.2 29.3 1.0
N A:PRO195 4.3 24.1 1.0
N A:ILE197 4.3 30.2 1.0
O A:HOH663 4.4 52.8 1.0
O A:ASP200 4.5 21.5 1.0
N A:SER198 4.5 29.1 1.0
CA A:TYR193 4.6 19.0 1.0
O A:HOH411 4.6 44.3 1.0
O A:GLU190 4.6 19.8 1.0
CA A:SER198 4.6 30.2 1.0
N A:ASP200 4.6 24.7 1.0
CD2 A:TYR193 4.7 24.6 1.0
CB A:TYR193 4.7 19.8 1.0
CA A:PRO195 4.7 25.9 1.0
CB A:ASP200 4.7 22.3 1.0
O A:HOH394 4.7 48.4 1.0
CG2 A:THR194 4.8 24.9 1.0
C A:ASP200 4.8 21.1 1.0
CG2 A:ILE197 4.9 29.2 1.0
N A:GLY199 4.9 28.7 1.0
C A:SER198 4.9 30.0 1.0
CA A:ASP200 4.9 22.8 1.0
C A:PRO195 5.0 27.3 1.0

Reference:

G.Birrane, B.Bhyravbhatla, M.A.Navia. Synthesis of Aspartame By Thermolysin: An X-Ray Structural Study. Acs Med.Chem.Lett. V. 5 706 2014.
ISSN: ISSN 1948-5875
PubMed: 24944748
DOI: 10.1021/ML500101Z
Page generated: Sat Jul 13 17:34:27 2024

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