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:
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
|