Atomistry » Calcium » PDB 3ti4-3tvc » 3tmn
Atomistry »
  Calcium »
    PDB 3ti4-3tvc »
      3tmn »

Calcium in PDB 3tmn: The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis

Enzymatic activity of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis

All present enzymatic activity of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis:
3.4.24.27;

Protein crystallography data

The structure of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis, PDB code: 3tmn was solved by H.M.Holden, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.100, 94.100, 131.400, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 3tmn:

The structure of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis (pdb code 3tmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis, PDB code: 3tmn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3tmn

Go back to Calcium Binding Sites List in 3tmn
Calcium binding site 1 out of 4 in the The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:10.8
occ:1.00
 O E:GLU187 2.2 8.7 1.0
OE1 E:GLU190 2.4 10.9 1.0
OD1 E:ASP138 2.4 13.8 1.0
OE2 E:GLU190 2.5 11.8 1.0
OD2 E:ASP185 2.5 9.8 1.0
O E:HOH346 2.6 11.7 1.0
OE1 E:GLU177 2.6 13.1 1.0
CD E:GLU190 2.8 10.3 1.0
OE2 E:GLU177 2.9 11.2 1.0
CD E:GLU177 3.1 13.1 1.0
C E:GLU187 3.4 11.6 1.0
CG E:ASP138 3.4 15.9 1.0
CG E:ASP185 3.5 14.6 1.0
OD1 E:ASP185 3.7 13.4 1.0
CA E:CA320 3.9 12.9 1.0
CB E:ASP138 4.1 9.2 1.0
N E:GLU187 4.2 14.1 1.0
N E:ILE188 4.2 9.1 1.0
CG E:GLU190 4.2 8.6 1.0
OD2 E:ASP138 4.3 13.7 1.0
O E:ASP185 4.3 13.8 1.0
CA E:GLU187 4.3 11.3 1.0
CA E:ILE188 4.4 13.2 1.0
O E:HOH469 4.4 31.4 1.0
N E:GLY189 4.5 18.0 1.0
CG E:GLU177 4.5 9.6 1.0
CB E:GLU187 4.5 11.0 1.0
O E:HOH350 4.5 15.6 1.0
C E:ASP185 4.6 14.3 1.0
CB E:ASP185 4.8 13.4 1.0
N E:ASP185 4.8 12.8 1.0
C E:ILE188 4.9 17.3 1.0
CA E:ASP185 5.0 9.4 1.0
CB E:GLU177 5.0 11.3 1.0
N E:GLU190 5.0 10.4 1.0

Calcium binding site 2 out of 4 in 3tmn

Go back to Calcium Binding Sites List in 3tmn
Calcium binding site 2 out of 4 in the The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:12.9
occ:1.00
 O E:HOH475 2.0 24.2 1.0
OE2 E:GLU177 2.3 11.2 1.0
OE2 E:GLU190 2.3 11.8 1.0
O E:HOH353 2.4 14.5 1.0
O E:ASN183 2.4 17.7 1.0
OD1 E:ASP185 2.4 13.4 1.0
CD E:GLU177 3.3 13.1 1.0
CG E:ASP185 3.3 14.6 1.0
CD E:GLU190 3.4 10.3 1.0
C E:ASN183 3.6 19.7 1.0
OD2 E:ASP185 3.7 9.8 1.0
CG E:GLU190 3.8 8.6 1.0
OE1 E:GLU177 3.8 13.1 1.0
CA E:CA319 3.9 10.8 1.0
O E:LYS182 4.0 25.9 1.0
CB E:ASN183 4.1 22.2 1.0
OD2 E:ASP191 4.1 16.2 1.0
CA E:PRO184 4.2 16.3 1.0
C E:PRO184 4.3 21.4 1.0
CG E:GLU177 4.3 9.6 1.0
N E:ASP185 4.3 12.8 1.0
N E:PRO184 4.3 12.1 1.0
OE1 E:GLU190 4.4 10.9 1.0
OD1 E:ASP191 4.4 15.0 1.0
CB E:ASP185 4.5 13.4 1.0
CG E:ASP191 4.5 18.9 1.0
CA E:ASN183 4.6 15.8 1.0
O E:HOH469 4.6 31.4 1.0
O E:PRO184 4.8 17.3 1.0
ND2 E:ASN183 4.8 51.3 1.0
CA E:ASP185 5.0 9.4 1.0

Calcium binding site 3 out of 4 in 3tmn

Go back to Calcium Binding Sites List in 3tmn
Calcium binding site 3 out of 4 in the The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca321

b:11.2
occ:1.00
 O E:HOH482 2.2 15.6 1.0
OD1 E:ASP57 2.2 14.1 1.0
O E:GLN61 2.2 12.3 1.0
OD1 E:ASP59 2.4 17.4 1.0
O E:HOH503 2.4 14.8 1.0
O E:HOH419 2.5 13.6 1.0
OD2 E:ASP57 2.6 11.5 1.0
CG E:ASP57 2.8 13.6 1.0
CG E:ASP59 3.4 19.1 1.0
C E:GLN61 3.4 15.5 1.0
OD2 E:ASP59 3.9 16.1 1.0
N E:GLN61 4.0 12.7 1.0
O E:HOH484 4.0 23.9 1.0
CA E:GLN61 4.2 15.8 1.0
CB E:ASP57 4.3 5.1 1.0
N E:ASP59 4.4 11.8 1.0
CB E:GLN61 4.4 13.7 1.0
N E:PHE62 4.5 13.1 1.0
O E:HOH508 4.6 18.0 1.0
OD2 E:ASP67 4.6 15.0 1.0
O E:HOH356 4.7 11.8 1.0
CB E:ASP59 4.7 9.7 1.0
N E:ASN60 4.7 8.6 1.0
CA E:PHE62 4.7 10.9 1.0
N E:ALA58 4.8 9.6 1.0
CA E:ASP59 4.9 11.5 1.0
C E:ASP59 4.9 14.0 1.0

Calcium binding site 4 out of 4 in 3tmn

Go back to Calcium Binding Sites List in 3tmn
Calcium binding site 4 out of 4 in the The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca322

b:15.1
occ:1.00
 O E:HOH480 2.1 28.9 1.0
O E:ILE197 2.2 28.8 1.0
OD1 E:ASP200 2.3 18.9 1.0
OG1 E:THR194 2.4 15.8 1.0
O E:THR194 2.4 18.7 1.0
O E:TYR193 2.5 15.4 1.0
O E:HOH354 2.6 13.8 1.0
C E:THR194 3.2 18.3 1.0
CG E:ASP200 3.3 10.1 1.0
C E:ILE197 3.3 26.1 1.0
C E:TYR193 3.4 14.8 1.0
CB E:THR194 3.5 12.7 1.0
CA E:THR194 3.7 15.8 1.0
OD2 E:ASP200 3.8 14.9 1.0
N E:THR194 3.9 14.0 1.0
CA E:ILE197 4.1 18.0 1.0
N E:ILE197 4.1 31.8 1.0
N E:PRO195 4.2 22.1 1.0
N E:SER198 4.4 28.4 1.0
CB E:ILE197 4.4 31.1 1.0
O E:ASP200 4.4 15.6 1.0
O E:GLU190 4.5 15.0 1.0
N E:ASP200 4.6 17.6 1.0
CA E:SER198 4.6 30.3 1.0
CA E:TYR193 4.6 10.7 1.0
CB E:ASP200 4.7 13.2 1.0
CA E:PRO195 4.7 15.1 1.0
CD2 E:TYR193 4.8 14.5 1.0
CG2 E:THR194 4.8 13.3 1.0
C E:ASP200 4.8 9.5 1.0
O E:HOH505 4.9 53.4 1.0
CB E:TYR193 4.9 13.2 1.0
C E:PRO195 4.9 30.7 1.0
C E:SER198 4.9 23.9 1.0
CA E:ASP200 5.0 9.4 1.0

Reference:

H.M.Holden, B.W.Matthews. The Binding of L-Valyl-L-Tryptophan to Crystalline Thermolysin Illustrates the Mode of Interaction of A Product of Peptide Hydrolysis. J.Biol.Chem. V. 263 3256 1988.
ISSN: ISSN 0021-9258
PubMed: 3343246
Page generated: Sat Jul 13 19:49:29 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