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Calcium in PDB 6tmn: Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond

Enzymatic activity of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond

All present enzymatic activity of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond:
3.4.24.27;

Protein crystallography data

The structure of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond, PDB code: 6tmn was solved by D.E.Tronrud, 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) N/A / 1.60
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 6tmn:

The structure of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond (pdb code 6tmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond, PDB code: 6tmn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6tmn

Go back to Calcium Binding Sites List in 6tmn
Calcium binding site 1 out of 4 in the Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:8.7
occ:1.00
 O E:GLU187 2.3 7.5 1.0
OD1 E:ASP138 2.4 10.7 1.0
OD2 E:ASP185 2.4 8.2 1.0
OE2 E:GLU190 2.4 12.9 1.0
OE1 E:GLU190 2.5 8.5 1.0
OE1 E:GLU177 2.5 12.5 1.0
O E:HOH335 2.6 9.7 1.0
CD E:GLU190 2.8 8.1 1.0
OE2 E:GLU177 2.9 10.2 1.0
CD E:GLU177 3.1 10.5 1.0
CG E:ASP138 3.3 10.8 1.0
C E:GLU187 3.4 9.3 1.0
CG E:ASP185 3.4 12.0 1.0
OD1 E:ASP185 3.7 12.1 1.0
CA E:CA319 3.8 13.4 1.0
CB E:ASP138 4.0 8.8 1.0
OD2 E:ASP138 4.2 11.3 1.0
CG E:GLU190 4.2 8.5 1.0
O E:ASP185 4.3 13.5 1.0
N E:ILE188 4.3 9.6 1.0
N E:GLU187 4.3 10.9 1.0
N E:GLY189 4.3 18.5 1.0
CA E:ILE188 4.3 10.0 1.0
O E:HOH419 4.4 32.4 1.0
CA E:GLU187 4.4 8.7 1.0
CG E:GLU177 4.5 5.9 1.0
O E:HOH339 4.5 16.5 1.0
CB E:GLU187 4.6 12.7 1.0
C E:ASP185 4.7 10.6 1.0
CB E:ASP185 4.7 11.6 1.0
N E:ASP185 4.8 11.4 1.0
C E:ILE188 4.8 18.9 1.0
N E:GLU190 4.9 9.6 1.0
O E:HOH342 5.0 13.7 1.0
CB E:GLU177 5.0 6.0 1.0

Calcium binding site 2 out of 4 in 6tmn

Go back to Calcium Binding Sites List in 6tmn
Calcium binding site 2 out of 4 in the Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:13.4
occ:1.00
 O E:HOH424 2.1 21.0 1.0
OE2 E:GLU177 2.3 10.2 1.0
OE2 E:GLU190 2.3 12.9 1.0
O E:HOH342 2.4 13.7 1.0
OD1 E:ASP185 2.4 12.1 1.0
O E:ASN183 2.5 18.1 1.0
CG E:ASP185 3.3 12.0 1.0
CD E:GLU177 3.3 10.5 1.0
CD E:GLU190 3.4 8.1 1.0
C E:ASN183 3.7 14.5 1.0
OD2 E:ASP185 3.7 8.2 1.0
CA E:CA318 3.8 8.7 1.0
CG E:GLU190 3.8 8.5 1.0
OE1 E:GLU177 3.8 12.5 1.0
O E:LYS182 3.9 24.5 1.0
CA E:PRO184 4.2 14.4 1.0
CB E:ASN183 4.2 22.8 1.0
OD2 E:ASP191 4.2 18.2 1.0
N E:ASP185 4.3 11.4 1.0
C E:PRO184 4.3 18.7 1.0
CG E:GLU177 4.3 5.9 1.0
OE1 E:GLU190 4.4 8.5 1.0
OD1 E:ASP191 4.4 15.6 1.0
N E:PRO184 4.4 13.9 1.0
CB E:ASP185 4.5 11.6 1.0
CG E:ASP191 4.6 18.7 1.0
CA E:ASN183 4.6 13.5 1.0
O E:HOH419 4.7 32.4 1.0
ND2 E:ASN183 4.8 45.0 1.0
O E:PRO184 4.8 16.0 1.0

Calcium binding site 3 out of 4 in 6tmn

Go back to Calcium Binding Sites List in 6tmn
Calcium binding site 3 out of 4 in the Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:11.9
occ:1.00
 O E:GLN61 2.2 11.7 1.0
OD1 E:ASP57 2.3 10.9 1.0
O E:HOH431 2.3 14.6 1.0
O E:HOH447 2.4 15.0 1.0
OD1 E:ASP59 2.4 15.6 1.0
O E:HOH388 2.5 11.6 1.0
OD2 E:ASP57 2.6 15.7 1.0
CG E:ASP57 2.8 11.7 1.0
CG E:ASP59 3.4 14.3 1.0
C E:GLN61 3.5 14.7 1.0
OD2 E:ASP59 3.9 15.8 1.0
O E:HOH433 3.9 22.8 1.0
N E:GLN61 4.0 13.1 1.0
CA E:GLN61 4.2 12.8 1.0
CB E:ASP57 4.3 6.9 1.0
N E:ASP59 4.3 9.3 1.0
CB E:GLN61 4.4 10.6 1.0
O E:HOH452 4.5 15.0 1.0
N E:PHE62 4.5 13.6 1.0
O E:HOH345 4.6 9.8 1.0
OD2 E:ASP67 4.6 10.3 1.0
CA E:PHE62 4.7 6.5 1.0
CB E:ASP59 4.7 8.1 1.0
N E:ASN60 4.7 9.9 1.0
N E:ALA58 4.8 7.2 1.0
CA E:ASP59 4.9 9.8 1.0
C E:ASP59 4.9 10.3 1.0

Calcium binding site 4 out of 4 in 6tmn

Go back to Calcium Binding Sites List in 6tmn
Calcium binding site 4 out of 4 in the Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca321

b:16.2
occ:1.00
 O E:HOH429 2.2 29.9 1.0
OD1 E:ASP200 2.3 13.0 1.0
O E:ILE197 2.3 28.8 1.0
O E:HOH343 2.5 15.5 1.0
O E:TYR193 2.5 10.5 1.0
OG1 E:THR194 2.5 12.8 1.0
O E:THR194 2.5 16.4 1.0
C E:THR194 3.3 16.4 1.0
CG E:ASP200 3.3 7.2 1.0
C E:ILE197 3.4 26.4 1.0
C E:TYR193 3.4 12.4 1.0
CB E:THR194 3.7 11.2 1.0
OD2 E:ASP200 3.8 14.7 1.0
CA E:THR194 3.8 11.3 1.0
N E:THR194 4.0 12.2 1.0
N E:ILE197 4.1 29.7 1.0
CA E:ILE197 4.2 20.8 1.0
N E:PRO195 4.3 20.1 1.0
CB E:ILE197 4.3 26.7 1.0
O E:ASP200 4.4 16.1 1.0
N E:SER198 4.4 24.4 1.0
O E:GLU190 4.5 13.2 1.0
CA E:SER198 4.6 26.5 1.0
N E:ASP200 4.6 16.5 1.0
CA E:TYR193 4.6 10.2 1.0
CB E:ASP200 4.6 11.3 1.0
CD2 E:TYR193 4.7 12.5 1.0
CA E:PRO195 4.7 16.2 1.0
CB E:TYR193 4.8 13.5 1.0
C E:ASP200 4.8 7.3 1.0
CG2 E:THR194 4.9 9.2 1.0
O E:HOH449 4.9 49.5 1.0
C E:SER198 4.9 21.9 1.0
CG2 E:ILE197 4.9 26.3 1.0
N E:GLY199 4.9 19.1 1.0
CA E:ASP200 5.0 7.5 1.0

Reference:

D.E.Tronrud, H.M.Holden, B.W.Matthews. Structures of Two Thermolysin-Inhibitor Complexes That Differ By A Single Hydrogen Bond. Science V. 235 571 1987.
ISSN: ISSN 0036-8075
PubMed: 3810156
Page generated: Tue Jul 16 15:22:17 2024

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