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: Sat Dec 12 05:44:38 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy