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Calcium in PDB 5tmn: Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues

Enzymatic activity of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues

All present enzymatic activity of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues:
3.4.24.27;

Protein crystallography data

The structure of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues, PDB code: 5tmn was solved by H.M.Holden, D.E.Tronrud, A.F.Monzingo, L.H.Weaver, 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 5tmn:

The structure of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues (pdb code 5tmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues, PDB code: 5tmn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5tmn

Go back to Calcium Binding Sites List in 5tmn
Calcium binding site 1 out of 4 in the Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:10.7
occ:1.00
 O E:GLU187 2.3 10.2 1.0
OD1 E:ASP138 2.4 12.0 1.0
OE2 E:GLU190 2.4 12.9 1.0
OD2 E:ASP185 2.4 8.6 1.0
OE1 E:GLU190 2.5 9.2 1.0
OE1 E:GLU177 2.5 11.3 1.0
O E:HOH334 2.6 10.6 1.0
CD E:GLU190 2.8 9.1 1.0
OE2 E:GLU177 2.9 11.3 1.0
CD E:GLU177 3.1 8.3 1.0
CG E:ASP138 3.4 10.8 1.0
C E:GLU187 3.4 11.7 1.0
CG E:ASP185 3.5 12.3 1.0
OD1 E:ASP185 3.7 12.2 1.0
CA E:CA319 3.8 14.0 1.0
CB E:ASP138 4.1 5.1 1.0
CG E:GLU190 4.2 6.3 1.0
N E:GLU187 4.3 13.0 1.0
OD2 E:ASP138 4.3 13.5 1.0
N E:ILE188 4.3 8.0 1.0
O E:ASP185 4.3 14.0 1.0
CA E:ILE188 4.4 6.9 1.0
CA E:GLU187 4.4 9.0 1.0
O E:HOH418 4.4 34.2 1.0
O E:HOH338 4.5 13.3 1.0
CG E:GLU177 4.5 6.0 1.0
N E:GLY189 4.6 18.4 1.0
CB E:GLU187 4.6 9.8 1.0
C E:ASP185 4.7 12.5 1.0
CB E:ASP185 4.8 10.9 1.0
N E:ASP185 4.8 8.9 1.0
C E:ILE188 4.8 17.1 1.0
CB E:GLU177 4.9 5.7 1.0
N E:GLU190 5.0 8.8 1.0
CD1 E:ILE188 5.0 16.4 1.0

Calcium binding site 2 out of 4 in 5tmn

Go back to Calcium Binding Sites List in 5tmn
Calcium binding site 2 out of 4 in the Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:14.0
occ:1.00
 O E:HOH423 2.1 20.8 1.0
OE2 E:GLU190 2.4 12.9 1.0
O E:ASN183 2.4 18.3 1.0
O E:HOH341 2.4 15.1 1.0
OD1 E:ASP185 2.4 12.2 1.0
OE2 E:GLU177 2.5 11.3 1.0
CG E:ASP185 3.3 12.3 1.0
CD E:GLU177 3.4 8.3 1.0
CD E:GLU190 3.4 9.1 1.0
C E:ASN183 3.6 16.8 1.0
OD2 E:ASP185 3.7 8.6 1.0
CG E:GLU190 3.8 6.3 1.0
CA E:CA318 3.8 10.7 1.0
OE1 E:GLU177 3.9 11.3 1.0
O E:LYS182 3.9 23.7 1.0
CB E:ASN183 4.1 22.6 1.0
CA E:PRO184 4.2 15.8 1.0
OD2 E:ASP191 4.2 14.9 1.0
C E:PRO184 4.3 18.4 1.0
N E:ASP185 4.3 8.9 1.0
CG E:GLU177 4.3 6.0 1.0
N E:PRO184 4.3 11.7 1.0
OD1 E:ASP191 4.4 17.7 1.0
OE1 E:GLU190 4.4 9.2 1.0
CA E:ASN183 4.5 16.5 1.0
CB E:ASP185 4.5 10.9 1.0
CG E:ASP191 4.6 18.1 1.0
O E:HOH418 4.7 34.2 1.0
ND2 E:ASN183 4.7 43.1 1.0
O E:PRO184 4.8 17.4 1.0
C E:LYS182 4.9 22.2 1.0

Calcium binding site 3 out of 4 in 5tmn

Go back to Calcium Binding Sites List in 5tmn
Calcium binding site 3 out of 4 in the Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:12.2
occ:1.00
 OD1 E:ASP57 2.2 12.6 1.0
O E:HOH430 2.2 12.3 1.0
O E:GLN61 2.3 10.4 1.0
O E:HOH446 2.5 15.0 1.0
OD1 E:ASP59 2.5 13.2 1.0
O E:HOH387 2.5 13.0 1.0
OD2 E:ASP57 2.7 10.8 1.0
CG E:ASP57 2.8 13.7 1.0
CG E:ASP59 3.4 13.7 1.0
C E:GLN61 3.5 16.6 1.0
OD2 E:ASP59 3.8 15.0 1.0
O E:HOH432 3.9 23.0 1.0
N E:GLN61 4.1 14.0 1.0
CA E:GLN61 4.2 13.4 1.0
CB E:ASP57 4.3 4.9 1.0
N E:ASP59 4.4 11.1 1.0
CB E:GLN61 4.4 11.5 1.0
O E:HOH451 4.5 12.3 1.0
N E:PHE62 4.5 13.7 1.0
OD2 E:ASP67 4.6 9.6 1.0
O E:HOH344 4.6 8.3 1.0
CA E:PHE62 4.6 7.8 1.0
CB E:ASP59 4.7 8.7 1.0
N E:ASN60 4.8 9.3 1.0
N E:ALA58 4.8 7.4 1.0
CA E:ASP59 4.9 11.3 1.0
C E:ASP59 4.9 12.1 1.0

Calcium binding site 4 out of 4 in 5tmn

Go back to Calcium Binding Sites List in 5tmn
Calcium binding site 4 out of 4 in the Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Slow-and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding. Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca321

b:17.0
occ:1.00
 O E:HOH428 2.1 25.8 1.0
O E:ILE197 2.1 29.6 1.0
OD1 E:ASP200 2.3 14.9 1.0
O E:HOH342 2.4 12.7 1.0
OG1 E:THR194 2.5 15.0 1.0
O E:THR194 2.5 15.3 1.0
O E:TYR193 2.5 14.0 1.0
C E:THR194 3.3 17.2 1.0
C E:ILE197 3.3 29.4 1.0
CG E:ASP200 3.4 12.2 1.0
C E:TYR193 3.4 11.1 1.0
CB E:THR194 3.6 13.5 1.0
CA E:THR194 3.8 15.2 1.0
OD2 E:ASP200 3.8 16.9 1.0
N E:THR194 4.0 15.6 1.0
CA E:ILE197 4.1 22.4 1.0
N E:ILE197 4.1 33.2 1.0
N E:PRO195 4.3 19.4 1.0
N E:SER198 4.3 28.0 1.0
CB E:ILE197 4.3 26.6 1.0
O E:ASP200 4.4 16.7 1.0
CA E:SER198 4.5 29.8 1.0
O E:GLU190 4.5 15.6 1.0
N E:ASP200 4.6 16.6 1.0
CA E:TYR193 4.6 10.1 1.0
CD2 E:TYR193 4.7 12.1 1.0
CB E:ASP200 4.7 12.2 1.0
CA E:PRO195 4.7 19.2 1.0
C E:ASP200 4.8 7.3 1.0
CG2 E:THR194 4.8 10.6 1.0
CB E:TYR193 4.8 14.1 1.0
C E:SER198 4.9 25.4 1.0
O E:HOH448 4.9 50.1 1.0
CA E:ASP200 5.0 11.0 1.0
C E:PRO195 5.0 25.6 1.0

Reference:

H.M.Holden, D.E.Tronrud, A.F.Monzingo, L.H.Weaver, B.W.Matthews. Slow- and Fast-Binding Inhibitors of Thermolysin Display Different Modes of Binding: Crystallographic Analysis of Extended Phosphonamidate Transition-State Analogues. Biochemistry V. 26 8542 1987.
ISSN: ISSN 0006-2960
PubMed: 3442675
DOI: 10.1021/BI00400A008
Page generated: Mon Jul 15 11:20:52 2024

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