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Calcium in PDB 3qh5: Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester

Enzymatic activity of Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester

All present enzymatic activity of Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester, PDB code: 3qh5 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) 27.44 / 1.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.686, 92.686, 128.764, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 18.7

Other elements in 3qh5:

The structure of Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester 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-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester (pdb code 3qh5). 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-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester, PDB code: 3qh5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3qh5

Go back to Calcium Binding Sites List in 3qh5
Calcium binding site 1 out of 4 in the Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester


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-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca317

b:16.9
occ:1.00
 O A:GLU187 2.3 18.1 1.0
OD1 A:ASP138 2.4 15.6 1.0
O A:HOH331 2.4 17.2 1.0
OD2 A:ASP185 2.5 17.9 1.0
OE1 A:GLU190 2.5 19.1 1.0
OE1 A:GLU177 2.5 18.5 1.0
OE2 A:GLU190 2.5 17.6 1.0
OE2 A:GLU177 2.7 20.5 1.0
CD A:GLU190 2.8 16.6 1.0
CD A:GLU177 2.9 16.3 1.0
CG A:ASP138 3.4 17.6 1.0
C A:GLU187 3.4 17.9 1.0
CG A:ASP185 3.5 19.8 1.0
CA A:CA318 3.8 28.2 1.0
OD1 A:ASP185 3.9 23.9 1.0
CB A:ASP138 4.0 14.4 1.0
O A:ASP185 4.1 17.5 1.0
N A:GLU187 4.2 18.8 1.0
O A:HOH579 4.2 34.8 1.0
N A:ILE188 4.3 18.6 1.0
OD2 A:ASP138 4.3 21.1 1.0
CG A:GLU190 4.3 18.6 1.0
CA A:GLU187 4.3 19.0 1.0
CA A:ILE188 4.3 17.7 1.0
CG A:GLU177 4.4 15.4 1.0
N A:GLY189 4.4 16.4 1.0
O A:HOH333 4.5 23.4 1.0
C A:ASP185 4.5 18.6 1.0
O A:HOH497 4.7 36.0 1.0
CB A:GLU187 4.7 19.7 1.0
N A:ASP185 4.7 19.3 1.0
CB A:ASP185 4.8 17.7 1.0
C A:ILE188 4.9 17.9 1.0
CB A:GLU177 4.9 15.6 1.0
CA A:ASP185 4.9 18.2 1.0
N A:GLU190 4.9 17.8 1.0

Calcium binding site 2 out of 4 in 3qh5

Go back to Calcium Binding Sites List in 3qh5
Calcium binding site 2 out of 4 in the Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester


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-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca318

b:28.2
occ:1.00
 OE2 A:GLU190 2.3 17.6 1.0
O A:HOH497 2.4 36.0 1.0
O A:HOH489 2.4 27.4 1.0
O A:ASN183 2.5 27.3 1.0
OD1 A:ASP185 2.5 23.9 1.0
OE2 A:GLU177 2.5 20.5 1.0
CD A:GLU177 3.3 16.3 1.0
CG A:ASP185 3.3 19.8 1.0
CD A:GLU190 3.3 16.6 1.0
C A:ASN183 3.6 26.5 1.0
OD2 A:ASP185 3.7 17.9 1.0
OE1 A:GLU177 3.7 18.5 1.0
CA A:CA317 3.8 16.9 1.0
CG A:GLU190 3.8 18.6 1.0
OD1 A:ASP191 3.9 27.0 1.0
N A:ASP185 4.1 19.3 1.0
CA A:PRO184 4.1 21.4 1.0
OD2 A:ASP191 4.2 27.1 1.0
CB A:ASN183 4.2 29.6 1.0
OE1 A:GLU190 4.3 19.1 1.0
CG A:GLU177 4.3 15.4 1.0
C A:PRO184 4.3 20.2 1.0
CB A:ASP185 4.3 17.7 1.0
N A:PRO184 4.4 23.4 1.0
CG A:ASP191 4.4 23.2 1.0
O A:LYS182 4.4 31.2 1.0
O A:HOH579 4.5 34.8 1.0
CA A:ASN183 4.6 29.1 1.0
CA A:ASP185 4.9 18.2 1.0

Calcium binding site 3 out of 4 in 3qh5

Go back to Calcium Binding Sites List in 3qh5
Calcium binding site 3 out of 4 in the Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester


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-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca319

b:14.8
occ:1.00
 O A:GLN61 2.3 14.2 1.0
O A:HOH351 2.3 18.4 1.0
OD1 A:ASP59 2.4 15.4 1.0
O A:HOH337 2.4 17.1 1.0
OD1 A:ASP57 2.4 14.8 1.0
O A:HOH359 2.4 15.8 1.0
OD2 A:ASP57 2.6 14.9 1.0
CG A:ASP57 2.9 13.4 1.0
CG A:ASP59 3.4 15.4 1.0
C A:GLN61 3.4 14.2 1.0
OD2 A:ASP59 3.8 19.3 1.0
O A:HOH389 3.9 20.0 1.0
N A:GLN61 4.0 14.6 1.0
CA A:GLN61 4.1 14.8 1.0
N A:ASP59 4.3 14.5 1.0
CB A:ASP57 4.4 13.2 1.0
CB A:GLN61 4.4 16.5 1.0
N A:PHE62 4.5 13.4 1.0
O A:HOH353 4.5 16.4 1.0
O A:HOH334 4.6 13.6 1.0
OD2 A:ASP67 4.6 13.4 1.0
CB A:ASP59 4.6 14.7 1.0
O A:HOH410 4.6 24.2 1.0
N A:ASN60 4.6 14.7 1.0
O A:HOH508 4.7 30.3 1.0
CA A:PHE62 4.7 13.7 1.0
N A:ALA58 4.8 14.5 1.0
CA A:ASP59 4.8 14.7 1.0
O A:HOH422 4.8 28.9 1.0
C A:ASP59 4.9 14.5 1.0

Calcium binding site 4 out of 4 in 3qh5

Go back to Calcium Binding Sites List in 3qh5
Calcium binding site 4 out of 4 in the Structure of Thermolysin in Complex with N-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester


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-Carbobenzyloxy-L-Aspartic Acid and L-Phenylalanine Methyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca320

b:29.0
occ:1.00
 O A:ILE197 2.3 35.7 1.0
O A:HOH347 2.3 30.6 1.0
O A:TYR193 2.3 24.6 1.0
O A:HOH348 2.4 25.3 1.0
O A:THR194 2.4 29.8 1.0
OD1 A:ASP200 2.5 28.1 1.0
OG1 A:THR194 2.5 28.8 1.0
C A:THR194 3.2 29.8 1.0
C A:TYR193 3.3 25.1 1.0
C A:ILE197 3.5 36.7 1.0
CB A:THR194 3.5 28.9 1.0
CG A:ASP200 3.5 27.2 1.0
CA A:THR194 3.7 28.6 1.0
N A:THR194 3.9 26.9 1.0
OD2 A:ASP200 3.9 28.0 1.0
CA A:ILE197 4.2 36.8 1.0
N A:ILE197 4.2 37.0 1.0
CB A:ILE197 4.3 37.0 1.0
N A:PRO195 4.3 31.4 1.0
O A:ASP200 4.3 27.2 1.0
CA A:TYR193 4.5 23.3 1.0
N A:SER198 4.5 36.5 1.0
O A:HOH349 4.5 56.2 1.0
O A:GLU190 4.6 20.2 1.0
N A:ASP200 4.6 28.5 1.0
CB A:TYR193 4.6 24.5 1.0
CA A:PRO195 4.6 32.7 1.0
CD2 A:TYR193 4.7 27.1 1.0
O A:HOH583 4.7 57.7 1.0
CA A:SER198 4.8 36.6 1.0
CG2 A:THR194 4.8 29.2 1.0
CB A:ASP200 4.8 27.3 1.0
C A:ASP200 4.8 26.7 1.0
N A:GLY199 4.9 33.8 1.0
C A:SER198 4.9 35.3 1.0
C A:PRO195 4.9 34.5 1.0
CG2 A:ILE197 4.9 37.2 1.0
N A:TYR193 5.0 21.6 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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