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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: Tue Jul 8 17:01:42 2025

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