Atomistry » Calcium » PDB 5tae-5tua » 5tln
Atomistry »
  Calcium »
    PDB 5tae-5tua »
      5tln »

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: Mon Jul 15 11:20:45 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy