Atomistry » Calcium » PDB 3qgv-3r3t » 3qh1
Atomistry »
  Calcium »
    PDB 3qgv-3r3t »
      3qh1 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy