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Calcium in PDB 3qgo: Structure of Thermolysin in Complex with L-Phenylalanine Methylester

Enzymatic activity of Structure of Thermolysin in Complex with L-Phenylalanine Methylester

All present enzymatic activity of Structure of Thermolysin in Complex with L-Phenylalanine Methylester:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin in Complex with L-Phenylalanine Methylester, PDB code: 3qgo 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) 40.30 / 1.45
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.066, 93.066, 128.171, 90.00, 90.00, 120.00
R / Rfree (%) 11.1 / 14.2

Other elements in 3qgo:

The structure of Structure of Thermolysin in Complex with L-Phenylalanine Methylester 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 L-Phenylalanine Methylester (pdb code 3qgo). 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 L-Phenylalanine Methylester, PDB code: 3qgo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3qgo

Go back to Calcium Binding Sites List in 3qgo
Calcium binding site 1 out of 4 in the Structure of Thermolysin in Complex with L-Phenylalanine Methylester


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 L-Phenylalanine Methylester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.5
occ:1.00
 O A:GLU187 2.3 14.1 1.0
OD2 A:ASP138 2.4 14.3 1.0
O A:HOH465 2.5 13.9 1.0
OE1 A:GLU177 2.5 13.7 1.0
OE1 A:GLU190 2.5 14.6 1.0
OD1 A:ASP185 2.5 13.7 1.0
OE2 A:GLU190 2.5 15.1 1.0
OE2 A:GLU177 2.8 14.9 1.0
CD A:GLU190 2.8 13.0 1.0
CD A:GLU177 3.0 13.7 1.0
C A:GLU187 3.4 14.0 1.0
CG A:ASP138 3.4 14.7 1.0
CG A:ASP185 3.5 14.5 1.0
CA A:CA402 3.8 16.5 1.0
OD2 A:ASP185 3.8 15.7 1.0
CB A:ASP138 4.0 12.8 1.0
O A:ASP185 4.1 14.7 1.0
O A:HOH586 4.2 21.6 1.0
N A:GLU187 4.2 14.1 1.0
N A:ILE188 4.3 13.7 1.0
CA A:GLU187 4.3 14.8 1.0
CG A:GLU190 4.3 14.4 1.0
CA A:ILE188 4.3 14.0 1.0
OD1 A:ASP138 4.4 20.7 1.0
CG A:GLU177 4.4 13.6 1.0
N A:GLY189 4.4 14.7 1.0
O A:HOH488 4.5 22.9 1.0
C A:ASP185 4.6 14.8 1.0
CB A:GLU187 4.7 14.8 1.0
CB A:ASP185 4.8 14.1 1.0
N A:ASP185 4.8 14.4 1.0
C A:ILE188 4.8 13.8 1.0
CB A:GLU177 4.9 13.2 1.0
N A:GLU190 4.9 14.2 1.0
O A:HOH493 4.9 18.3 1.0
CA A:ASP185 5.0 13.7 1.0

Calcium binding site 2 out of 4 in 3qgo

Go back to Calcium Binding Sites List in 3qgo
Calcium binding site 2 out of 4 in the Structure of Thermolysin in Complex with L-Phenylalanine Methylester


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 L-Phenylalanine Methylester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.5
occ:1.00
 O A:ASN183 2.3 16.5 1.0
OE2 A:GLU190 2.3 15.1 1.0
O A:HOH502 2.3 19.7 1.0
O A:HOH493 2.3 18.3 1.0
OD2 A:ASP185 2.3 15.7 1.0
OE2 A:GLU177 2.4 14.9 1.0
CG A:ASP185 3.2 14.5 1.0
CD A:GLU177 3.2 13.7 1.0
CD A:GLU190 3.3 13.0 1.0
C A:ASN183 3.4 16.7 1.0
OD1 A:ASP185 3.6 13.7 1.0
OE1 A:GLU177 3.7 13.7 1.0
CG A:GLU190 3.8 14.4 1.0
CA A:CA401 3.8 13.5 1.0
CA A:PRO184 4.1 15.2 1.0
CB A:ASN183 4.1 19.5 1.0
OD1 A:ASP191 4.1 21.1 1.0
OD2 A:ASP191 4.2 19.0 1.0
N A:ASP185 4.2 14.4 1.0
CG A:GLU177 4.2 13.6 1.0
C A:PRO184 4.3 15.3 1.0
N A:PRO184 4.3 15.5 1.0
OE1 A:GLU190 4.3 14.6 1.0
O A:LYS182 4.3 20.6 1.0
CB A:ASP185 4.4 14.1 1.0
CA A:ASN183 4.4 18.7 1.0
CG A:ASP191 4.5 17.9 1.0
O A:HOH715 4.5 74.1 1.0
O A:HOH586 4.6 21.6 1.0
CA A:ASP185 4.9 13.7 1.0
O A:PRO184 5.0 17.4 1.0

Calcium binding site 3 out of 4 in 3qgo

Go back to Calcium Binding Sites List in 3qgo
Calcium binding site 3 out of 4 in the Structure of Thermolysin in Complex with L-Phenylalanine Methylester


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 L-Phenylalanine Methylester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:13.4
occ:1.00
 O A:GLN61 2.3 13.2 1.0
O A:HOH471 2.3 15.6 1.0
OD1 A:ASP57 2.4 12.8 1.0
OD1 A:ASP59 2.4 14.2 1.0
O A:HOH462 2.4 14.9 1.0
O A:HOH470 2.4 13.8 1.0
OD2 A:ASP57 2.6 13.3 1.0
CG A:ASP57 2.8 12.4 1.0
CG A:ASP59 3.4 14.3 1.0
C A:GLN61 3.4 12.3 1.0
OD2 A:ASP59 3.8 18.5 1.0
O A:HOH491 4.0 18.9 1.0
N A:GLN61 4.0 12.1 1.0
CA A:GLN61 4.1 12.9 0.5
CA A:GLN61 4.2 11.8 0.5
CB A:GLN61 4.3 14.2 0.5
N A:ASP59 4.3 13.3 1.0
CB A:ASP57 4.3 12.2 1.0
CB A:GLN61 4.4 12.2 0.5
O A:HOH477 4.5 14.9 1.0
N A:PHE62 4.5 12.1 1.0
O A:HOH492 4.6 18.4 1.0
O A:HOH431 4.6 12.4 1.0
CB A:ASP59 4.6 13.4 1.0
OD2 A:ASP67 4.6 13.2 1.0
N A:ASN60 4.7 12.2 1.0
O A:HOH564 4.7 26.3 1.0
CA A:PHE62 4.8 12.0 1.0
N A:ALA58 4.8 12.8 1.0
CA A:ASP59 4.8 13.2 1.0
O A:HOH443 4.8 27.2 1.0
C A:ASP59 4.9 13.0 1.0

Calcium binding site 4 out of 4 in 3qgo

Go back to Calcium Binding Sites List in 3qgo
Calcium binding site 4 out of 4 in the Structure of Thermolysin in Complex with L-Phenylalanine Methylester


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 L-Phenylalanine Methylester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:20.5
occ:1.00
 O A:ILE197 2.3 24.6 1.0
OD1 A:ASP200 2.4 19.6 1.0
OG1 A:THR194 2.4 20.9 1.0
O A:TYR193 2.4 18.1 1.0
O A:HOH510 2.4 19.4 1.0
O A:THR194 2.4 22.2 1.0
O A:HOH524 2.4 24.0 1.0
C A:THR194 3.2 22.0 1.0
C A:TYR193 3.3 18.2 1.0
CG A:ASP200 3.4 19.3 1.0
CB A:THR194 3.4 20.8 1.0
C A:ILE197 3.5 25.8 1.0
CA A:THR194 3.6 20.6 1.0
OD2 A:ASP200 3.8 21.2 1.0
N A:THR194 3.9 19.3 1.0
CB A:ILE197 4.2 24.8 1.0
CA A:ILE197 4.2 25.2 1.0
N A:ILE197 4.2 26.7 1.0
N A:PRO195 4.3 23.3 1.0
O A:HOH769 4.3 38.1 1.0
O A:HOH732 4.4 46.6 1.0
O A:ASP200 4.5 17.5 1.0
N A:SER198 4.5 25.8 1.0
CA A:TYR193 4.5 17.0 1.0
O A:GLU190 4.6 16.7 1.0
N A:ASP200 4.6 19.5 1.0
CD2 A:TYR193 4.6 20.8 1.0
CB A:TYR193 4.6 17.7 1.0
O A:HOH666 4.6 34.7 1.0
CA A:PRO195 4.7 24.6 1.0
CB A:ASP200 4.7 18.9 1.0
CG2 A:THR194 4.7 22.5 1.0
CG2 A:ILE197 4.8 25.2 1.0
CA A:SER198 4.8 25.8 0.5
CA A:SER198 4.8 26.1 0.5
C A:ASP200 4.8 17.5 1.0
N A:GLY199 4.9 23.0 1.0
C A:SER198 4.9 25.1 1.0
CA A:ASP200 5.0 18.4 1.0
C A:PRO195 5.0 25.2 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 17:32:12 2024

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