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Calcium in PDB 5tln: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis

Enzymatic activity of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis

All present enzymatic activity of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis:
3.4.24.27;

Protein crystallography data

The structure of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis, PDB code: 5tln was solved by B.W.Matthews, M.A.Holmes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.200, 94.200, 131.400, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 5tln:

The structure of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis (pdb code 5tln). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis, PDB code: 5tln:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5tln

Go back to Calcium Binding Sites List in 5tln
Calcium binding site 1 out of 4 in the Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca317

b:9.7
occ:1.00
 O A:GLU187 2.3 9.2 1.0
OD2 A:ASP185 2.4 12.3 1.0
OE1 A:GLU177 2.5 7.0 1.0
OE2 A:GLU190 2.5 4.6 1.0
OD1 A:ASP138 2.6 7.5 1.0
OE1 A:GLU190 2.6 4.0 1.0
O A:HOH346 2.7 6.6 1.0
OE2 A:GLU177 2.8 4.8 1.0
CD A:GLU190 2.9 5.4 1.0
CD A:GLU177 3.1 5.1 1.0
CG A:ASP185 3.3 11.5 1.0
C A:GLU187 3.4 8.8 1.0
CG A:ASP138 3.5 7.0 1.0
OD1 A:ASP185 3.7 13.7 1.0
CA A:CA318 3.8 13.5 1.0
CB A:GLU187 4.1 11.8 1.0
CA A:GLU187 4.1 9.7 1.0
CB A:ASP138 4.1 5.1 1.0
N A:GLU187 4.2 8.1 1.0
O A:ASP185 4.3 10.7 1.0
OD2 A:ASP138 4.3 8.0 1.0
N A:ILE188 4.3 8.6 1.0
O A:HOH469 4.3 25.8 1.0
CG A:GLU190 4.4 3.8 1.0
CA A:ILE188 4.5 8.8 1.0
CG A:GLU177 4.5 1.9 1.0
O A:HOH350 4.5 9.9 1.0
C A:ASP185 4.6 10.7 1.0
CB A:ASP185 4.6 11.7 1.0
N A:GLY189 4.7 8.4 1.0
N A:ASP185 4.8 12.2 1.0
OG1 A:THR174 4.9 8.9 1.0
CA A:ASP185 5.0 9.7 1.0

Calcium binding site 2 out of 4 in 5tln

Go back to Calcium Binding Sites List in 5tln
Calcium binding site 2 out of 4 in the Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca318

b:13.5
occ:1.00
 O A:HOH475 2.0 54.3 1.0
OE2 A:GLU177 2.3 4.8 1.0
O A:HOH353 2.4 8.0 1.0
OE2 A:GLU190 2.4 4.6 1.0
O A:ASN183 2.5 16.2 1.0
OD1 A:ASP185 2.7 13.7 1.0
CD A:GLU177 3.4 5.1 1.0
CG A:ASP185 3.5 11.5 1.0
CD A:GLU190 3.5 5.4 1.0
C A:ASN183 3.7 15.7 1.0
CA A:CA317 3.8 9.7 1.0
O A:LYS182 3.8 17.5 1.0
OE1 A:GLU177 3.9 7.0 1.0
OD2 A:ASP185 3.9 12.3 1.0
CG A:GLU190 4.0 3.8 1.0
OD2 A:ASP191 4.1 11.3 1.0
CA A:PRO184 4.2 12.5 1.0
CG A:GLU177 4.3 1.9 1.0
C A:PRO184 4.4 12.8 1.0
N A:PRO184 4.4 14.4 1.0
N A:ASP185 4.4 12.2 1.0
CB A:ASN183 4.4 19.4 1.0
OE1 A:GLU190 4.4 4.0 1.0
OD1 A:ASP191 4.6 6.6 1.0
ND2 A:ASN183 4.6 25.1 1.0
CG A:ASP191 4.6 8.4 1.0
CA A:ASN183 4.7 16.8 1.0
CB A:ASP185 4.7 11.7 1.0
O A:HOH469 4.8 25.8 1.0
O A:PRO184 4.9 12.6 1.0
C A:LYS182 4.9 18.3 1.0
CG A:ASN183 5.0 23.1 1.0

Calcium binding site 3 out of 4 in 5tln

Go back to Calcium Binding Sites List in 5tln
Calcium binding site 3 out of 4 in the Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca319

b:11.8
occ:1.00
 O A:GLN61 2.1 7.0 1.0
O A:HOH419 2.2 17.9 1.0
O A:HOH482 2.3 32.1 1.0
OD1 A:ASP57 2.4 5.7 1.0
OD1 A:ASP59 2.4 15.9 1.0
OD2 A:ASP57 2.5 7.2 1.0
CG A:ASP57 2.8 6.7 1.0
C A:GLN61 3.3 9.5 1.0
CG A:ASP59 3.4 13.1 1.0
OD2 A:ASP59 3.6 13.3 1.0
O A:HOH421 4.0 42.1 1.0
N A:GLN61 4.1 9.0 1.0
O A:HOH484 4.1 24.3 1.0
CA A:GLN61 4.2 8.8 1.0
CB A:ASP57 4.3 7.8 1.0
N A:ASP59 4.3 9.4 1.0
N A:PHE62 4.4 9.3 1.0
CB A:GLN61 4.5 12.4 1.0
N A:ALA58 4.6 9.2 1.0
CB A:ASP59 4.6 11.9 1.0
N A:ASN60 4.7 8.1 1.0
O A:HOH356 4.8 11.8 1.0
CA A:PHE62 4.8 7.5 1.0
CA A:ASP59 4.8 8.2 1.0
OD2 A:ASP67 4.9 7.4 1.0
CA A:ASP57 4.9 7.8 1.0
C A:ASP59 4.9 8.1 1.0

Calcium binding site 4 out of 4 in 5tln

Go back to Calcium Binding Sites List in 5tln
Calcium binding site 4 out of 4 in the Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca320

b:13.6
occ:1.00
 O A:HOH480 1.8 21.2 1.0
OD1 A:ASP200 2.1 11.8 1.0
O A:HOH354 2.3 3.5 1.0
OG1 A:THR194 2.4 9.6 1.0
O A:THR194 2.5 12.2 1.0
O A:TYR193 2.6 10.3 1.0
O A:ILE197 2.8 18.6 1.0
CG A:ASP200 3.3 11.1 1.0
C A:THR194 3.4 13.2 1.0
C A:ILE197 3.5 18.2 1.0
C A:TYR193 3.6 10.9 1.0
CB A:THR194 3.7 12.1 1.0
OD2 A:ASP200 3.8 13.7 1.0
CA A:THR194 3.9 12.3 1.0
N A:THR194 4.1 11.6 1.0
CA A:ILE197 4.2 17.9 1.0
CB A:ILE197 4.3 17.9 1.0
O A:ASP200 4.3 12.3 1.0
N A:SER198 4.3 18.8 1.0
N A:ILE197 4.4 18.8 1.0
O A:GLU190 4.4 7.0 1.0
N A:ASP200 4.4 14.8 1.0
CA A:SER198 4.5 18.7 1.0
N A:PRO195 4.5 13.2 1.0
CB A:ASP200 4.6 10.2 1.0
C A:ASP200 4.6 12.1 1.0
CA A:TYR193 4.7 10.9 1.0
CD2 A:TYR193 4.7 12.5 1.0
CB A:TYR193 4.8 10.0 1.0
CA A:ASP200 4.8 12.4 1.0
C A:SER198 4.9 18.0 1.0
CA A:PRO195 4.9 14.7 1.0
CG2 A:THR194 5.0 9.9 1.0
N A:GLY199 5.0 16.9 1.0

Reference:

M.A.Holmes, B.W.Matthews. Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests A Pentacoordinate Zinc Intermediate in Catalysis. Biochemistry V. 20 6912 1981.
ISSN: ISSN 0006-2960
PubMed: 7317361
DOI: 10.1021/BI00527A026
Page generated: Wed Jul 9 10:20:51 2025

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