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Calcium in PDB 1hyt: Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A

Enzymatic activity of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A

All present enzymatic activity of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A:
3.4.24.27;

Protein crystallography data

The structure of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A, PDB code: 1hyt was solved by A.C.Hausrath, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.691, 93.691, 131.503, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 1hyt:

The structure of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A (pdb code 1hyt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A, PDB code: 1hyt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1hyt

Go back to Calcium Binding Sites List in 1hyt
Calcium binding site 1 out of 4 in the Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:12.7
occ:1.00
 O A:GLU187 2.3 12.9 1.0
OD2 A:ASP138 2.3 15.2 1.0
OD1 A:ASP185 2.4 12.7 1.0
OE1 A:GLU177 2.4 12.2 1.0
OE1 A:GLU190 2.5 10.7 1.0
OE2 A:GLU190 2.5 14.3 1.0
O A:HOH346 2.6 11.1 1.0
OE2 A:GLU177 2.8 15.1 1.0
CD A:GLU190 2.8 16.1 1.0
CD A:GLU177 2.9 12.7 1.0
CG A:ASP138 3.3 18.0 1.0
C A:GLU187 3.4 19.1 1.0
CG A:ASP185 3.4 16.8 1.0
OD2 A:ASP185 3.8 14.1 1.0
CA A:CA802 3.8 14.4 1.0
CB A:ASP138 4.0 9.4 1.0
N A:GLU187 4.2 17.2 1.0
O A:ASP185 4.2 19.1 1.0
O A:HOH469 4.2 45.9 1.0
N A:ILE188 4.2 13.1 1.0
CG A:GLU190 4.3 11.4 1.0
CA A:GLU187 4.3 15.0 1.0
OD1 A:ASP138 4.3 14.9 1.0
CA A:ILE188 4.3 12.3 1.0
N A:GLY189 4.4 18.4 1.0
CG A:GLU177 4.4 9.8 1.0
O A:HOH350 4.5 23.8 1.0
CB A:GLU187 4.5 16.2 1.0
C A:ASP185 4.6 13.2 1.0
CB A:ASP185 4.7 20.7 1.0
C A:ILE188 4.7 19.6 1.0
N A:ASP185 4.8 17.0 1.0
N A:GLU190 4.9 13.4 1.0
O A:HOH353 4.9 16.9 1.0
CB A:GLU177 4.9 8.8 1.0

Calcium binding site 2 out of 4 in 1hyt

Go back to Calcium Binding Sites List in 1hyt
Calcium binding site 2 out of 4 in the Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:14.4
occ:1.00
 OE2 A:GLU190 2.3 14.3 1.0
OD2 A:ASP185 2.3 14.1 1.0
OE2 A:GLU177 2.3 15.1 1.0
O A:HOH475 2.3 18.6 1.0
O A:HOH353 2.4 16.9 1.0
O A:ASN183 2.4 19.8 1.0
CG A:ASP185 3.2 16.8 1.0
CD A:GLU177 3.3 12.7 1.0
CD A:GLU190 3.4 16.1 1.0
C A:ASN183 3.6 21.4 1.0
OD1 A:ASP185 3.7 12.7 1.0
CG A:GLU190 3.8 11.4 1.0
CA A:CA801 3.8 12.7 1.0
OE1 A:GLU177 3.8 12.2 1.0
O A:LYS182 3.9 24.4 1.0
N A:ASP185 4.2 17.0 1.0
CA A:PRO184 4.2 17.1 1.0
OD2 A:ASP191 4.2 17.4 1.0
CG A:GLU177 4.2 9.8 1.0
C A:PRO184 4.2 27.1 1.0
OD1 A:ASP191 4.3 18.7 1.0
OE1 A:GLU190 4.3 10.7 1.0
CB A:ASN183 4.3 19.0 1.0
N A:PRO184 4.3 18.1 1.0
CB A:ASP185 4.4 20.7 1.0
CG A:ASP191 4.6 20.8 1.0
CA A:ASN183 4.6 14.5 1.0
O A:HOH469 4.6 45.9 1.0
O A:PRO184 4.9 23.7 1.0
CA A:ASP185 4.9 10.2 1.0
C A:LYS182 5.0 31.5 1.0

Calcium binding site 3 out of 4 in 1hyt

Go back to Calcium Binding Sites List in 1hyt
Calcium binding site 3 out of 4 in the Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:13.4
occ:1.00
 O A:GLN61 2.3 12.3 1.0
O A:HOH482 2.3 20.5 1.0
OD1 A:ASP59 2.4 15.2 1.0
O A:HOH503 2.4 16.4 1.0
O A:HOH419 2.4 13.0 1.0
OD1 A:ASP57 2.4 15.1 1.0
OD2 A:ASP57 2.5 16.5 1.0
CG A:ASP57 2.8 17.6 1.0
CG A:ASP59 3.3 20.6 1.0
C A:GLN61 3.4 22.9 1.0
OD2 A:ASP59 3.8 19.8 1.0
O A:HOH484 3.9 35.0 1.0
N A:GLN61 4.0 13.7 1.0
CA A:GLN61 4.2 11.9 1.0
N A:ASP59 4.3 13.1 1.0
CB A:ASP57 4.3 9.3 1.0
O A:HOH628 4.4 52.2 1.0
CB A:GLN61 4.4 12.8 1.0
N A:PHE62 4.4 13.1 1.0
O A:HOH508 4.5 18.4 1.0
OD2 A:ASP67 4.6 13.1 1.0
O A:HOH356 4.6 14.4 1.0
CA A:PHE62 4.6 13.4 1.0
CB A:ASP59 4.6 11.2 1.0
N A:ALA58 4.7 12.5 1.0
N A:ASN60 4.7 15.2 1.0
CA A:ASP59 4.8 12.1 1.0
O A:HOH671 4.8 55.8 1.0
C A:ASP59 4.9 12.9 1.0

Calcium binding site 4 out of 4 in 1hyt

Go back to Calcium Binding Sites List in 1hyt
Calcium binding site 4 out of 4 in the Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Re-Determination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:18.8
occ:1.00
 O A:ILE197 2.2 29.9 1.0
OG1 A:THR194 2.2 16.9 1.0
OD1 A:ASP200 2.3 18.8 1.0
O A:HOH480 2.3 28.7 1.0
O A:THR194 2.4 19.0 1.0
O A:TYR193 2.4 13.9 1.0
O A:HOH354 2.4 16.2 1.0
C A:THR194 3.2 25.5 1.0
CG A:ASP200 3.3 15.8 1.0
C A:TYR193 3.4 16.2 1.0
C A:ILE197 3.4 46.4 1.0
CB A:THR194 3.4 16.9 1.0
CA A:THR194 3.7 18.5 1.0
OD2 A:ASP200 3.7 19.4 1.0
N A:THR194 3.9 16.5 1.0
CA A:ILE197 4.1 24.0 1.0
N A:PRO195 4.2 24.4 1.0
N A:ILE197 4.2 46.3 1.0
CB A:ILE197 4.2 34.3 1.0
O A:ASP200 4.4 20.5 1.0
N A:SER198 4.4 30.1 1.0
O A:GLU190 4.5 18.9 1.0
N A:ASP200 4.5 18.7 1.0
CA A:SER198 4.6 37.0 1.0
CA A:TYR193 4.6 15.4 1.0
CA A:PRO195 4.6 25.5 1.0
CG2 A:THR194 4.6 14.3 1.0
CD2 A:TYR193 4.6 20.4 1.0
CB A:ASP200 4.6 18.2 1.0
C A:ASP200 4.7 11.8 1.0
CB A:TYR193 4.7 19.2 1.0
C A:PRO195 4.9 46.6 1.0
CG2 A:ILE197 4.9 23.0 1.0
O A:HOH476 4.9 52.0 1.0
C A:SER198 4.9 32.8 1.0
CA A:ASP200 4.9 14.9 1.0

Reference:

A.C.Hausrath, B.W.Matthews. Redetermination and Refinement of the Complex of Benzylsuccinic Acid with Thermolysin and Its Relation to the Complex with Carboxypeptidase A. J.Biol.Chem. V. 269 18839 1994.
ISSN: ISSN 0021-9258
PubMed: 8034637
Page generated: Thu Jul 11 10:12:43 2024

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