Zinc in PDB 5uu7: Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
Enzymatic activity of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
All present enzymatic activity of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd:
3.4.24.27;
Protein crystallography data
The structure of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd, PDB code: 5uu7
was solved by
D.H.Juers,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
20.76 /
1.60
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.026,
98.026,
107.522,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.4 /
15.6
|
Other elements in 5uu7:
The structure of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
(pdb code 5uu7). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd, PDB code: 5uu7:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 1 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:16.1
occ:0.93
|
OD2
|
A:ASP185
|
2.0
|
15.8
|
1.0
|
|
OE2
|
A:GLU190
|
2.1
|
14.2
|
1.0
|
|
O
|
A:HOH538
|
2.1
|
15.7
|
1.0
|
|
O
|
A:HOH525
|
2.1
|
15.6
|
1.0
|
|
OE2
|
A:GLU177
|
2.1
|
15.4
|
1.0
|
|
O
|
A:ASN183
|
2.3
|
15.6
|
1.0
|
|
CG
|
A:ASP185
|
3.0
|
17.4
|
1.0
|
|
CD
|
A:GLU177
|
3.0
|
15.9
|
1.0
|
|
CD
|
A:GLU190
|
3.1
|
13.2
|
1.0
|
|
OD1
|
A:ASP185
|
3.3
|
14.9
|
1.0
|
|
HG3
|
A:GLU190
|
3.5
|
17.8
|
1.0
|
|
C
|
A:ASN183
|
3.5
|
15.2
|
1.0
|
|
HA
|
A:PRO184
|
3.5
|
22.4
|
1.0
|
|
OE1
|
A:GLU177
|
3.5
|
15.2
|
1.0
|
|
CA
|
A:CA401
|
3.6
|
14.4
|
1.0
|
|
HB2
|
A:ASN183
|
3.6
|
24.3
|
1.0
|
|
CG
|
A:GLU190
|
3.7
|
14.8
|
1.0
|
|
HG2
|
A:GLU190
|
3.7
|
17.8
|
1.0
|
|
O
|
A:LYS182
|
3.9
|
20.5
|
1.0
|
|
OD1
|
A:ASP191
|
4.1
|
18.5
|
1.0
|
|
OD2
|
A:ASP191
|
4.1
|
20.8
|
1.0
|
|
OE1
|
A:GLU190
|
4.1
|
16.1
|
1.0
|
|
H
|
A:ASP185
|
4.1
|
17.7
|
1.0
|
|
CG
|
A:GLU177
|
4.1
|
14.7
|
1.0
|
|
CA
|
A:PRO184
|
4.1
|
18.6
|
1.0
|
|
HG2
|
A:GLU177
|
4.1
|
17.6
|
1.0
|
|
N
|
A:ASP185
|
4.2
|
14.7
|
1.0
|
|
HG3
|
A:GLU177
|
4.2
|
17.6
|
1.0
|
|
HB3
|
A:ASN183
|
4.2
|
24.3
|
1.0
|
|
C
|
A:PRO184
|
4.2
|
18.4
|
1.0
|
|
CB
|
A:ASN183
|
4.2
|
20.2
|
1.0
|
|
CB
|
A:ASP185
|
4.3
|
16.2
|
1.0
|
|
N
|
A:PRO184
|
4.3
|
16.6
|
1.0
|
|
HB3
|
A:ASP185
|
4.3
|
19.4
|
1.0
|
|
O
|
A:HOH561
|
4.3
|
31.1
|
1.0
|
|
CG
|
A:ASP191
|
4.4
|
18.2
|
1.0
|
|
CA
|
A:ASN183
|
4.5
|
17.4
|
1.0
|
|
CA
|
A:ASP185
|
4.8
|
14.9
|
1.0
|
|
O
|
A:PRO184
|
4.8
|
18.7
|
1.0
|
|
C
|
A:LYS182
|
4.9
|
20.8
|
1.0
|
|
HB2
|
A:ASP185
|
5.0
|
19.4
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 2 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn405
b:15.6
occ:0.93
|
O
|
A:HOH620
|
1.8
|
19.6
|
1.0
|
|
OE2
|
A:GLU166
|
1.9
|
18.2
|
0.6
|
|
OE1
|
A:GLU166
|
2.0
|
11.6
|
0.4
|
|
NE2
|
A:HIS146
|
2.0
|
14.9
|
1.0
|
|
NE2
|
A:HIS142
|
2.0
|
12.4
|
1.0
|
|
CD
|
A:GLU166
|
2.8
|
19.2
|
0.6
|
|
CD
|
A:GLU166
|
2.9
|
13.6
|
0.4
|
|
CE1
|
A:HIS146
|
2.9
|
15.1
|
1.0
|
|
CE1
|
A:HIS142
|
3.0
|
12.8
|
1.0
|
|
CD2
|
A:HIS142
|
3.0
|
13.7
|
1.0
|
|
CD2
|
A:HIS146
|
3.1
|
14.5
|
1.0
|
|
OE1
|
A:GLU166
|
3.1
|
19.9
|
0.6
|
|
OE2
|
A:GLU166
|
3.1
|
18.7
|
0.4
|
|
HE1
|
A:HIS146
|
3.1
|
18.1
|
1.0
|
|
HE1
|
A:HIS142
|
3.2
|
15.3
|
1.0
|
|
HD2
|
A:HIS142
|
3.2
|
16.5
|
1.0
|
|
HMC1
|
A:MRD416
|
3.3
|
45.6
|
0.2
|
|
HD2
|
A:HIS146
|
3.3
|
17.4
|
1.0
|
|
ZN
|
A:ZN406
|
3.4
|
32.1
|
0.7
|
|
HH
|
A:TYR157
|
3.4
|
32.6
|
0.5
|
|
HA
|
A:MRD416
|
3.5
|
47.6
|
0.8
|
|
HE2
|
A:HIS231
|
3.6
|
40.5
|
1.0
|
|
ZN
|
A:ZN406
|
3.6
|
29.6
|
0.3
|
|
O
|
A:HOH509
|
3.7
|
44.4
|
1.0
|
|
HA
|
A:GLU166
|
3.8
|
15.9
|
0.6
|
|
HA
|
A:GLU166
|
3.8
|
15.1
|
0.4
|
|
OE2
|
A:GLU143
|
3.8
|
30.0
|
1.0
|
|
O
|
A:HOH625
|
4.1
|
35.3
|
0.7
|
|
ND1
|
A:HIS146
|
4.1
|
15.0
|
1.0
|
|
OH
|
A:TYR157
|
4.1
|
27.2
|
0.5
|
|
ND1
|
A:HIS142
|
4.1
|
14.0
|
1.0
|
|
HB2
|
A:SER169
|
4.1
|
16.8
|
1.0
|
|
CG
|
A:GLU166
|
4.1
|
18.0
|
0.6
|
|
CG
|
A:HIS142
|
4.1
|
13.4
|
1.0
|
|
CM
|
A:MRD416
|
4.2
|
38.0
|
0.2
|
|
CG
|
A:HIS146
|
4.2
|
14.4
|
1.0
|
|
HG2
|
A:GLU166
|
4.2
|
21.6
|
0.6
|
|
HE1
|
A:TYR157
|
4.2
|
30.9
|
0.5
|
|
HB3
|
A:SER169
|
4.2
|
16.8
|
1.0
|
|
HMC3
|
A:MRD416
|
4.2
|
45.6
|
0.2
|
|
CG
|
A:GLU166
|
4.3
|
13.3
|
0.4
|
|
NE2
|
A:HIS231
|
4.3
|
33.8
|
1.0
|
|
O4
|
A:MRD416
|
4.3
|
39.6
|
0.8
|
|
O
|
A:HOH633
|
4.5
|
38.5
|
1.0
|
|
H4
|
A:MRD416
|
4.5
|
43.9
|
0.8
|
|
HB3
|
A:GLU166
|
4.5
|
15.8
|
0.4
|
|
CD
|
A:GLU143
|
4.5
|
19.8
|
1.0
|
|
CB
|
A:SER169
|
4.5
|
14.0
|
1.0
|
|
CA
|
A:GLU166
|
4.7
|
12.6
|
0.4
|
|
H1C3
|
A:MRD416
|
4.7
|
44.5
|
0.2
|
|
H1C1
|
A:MRD416
|
4.7
|
51.5
|
0.8
|
|
CA
|
A:GLU166
|
4.7
|
13.2
|
0.6
|
|
OE1
|
A:GLU143
|
4.7
|
24.8
|
1.0
|
|
HG3
|
A:GLU166
|
4.7
|
15.9
|
0.4
|
|
HG3
|
A:GLU166
|
4.7
|
21.6
|
0.6
|
|
HMC2
|
A:MRD416
|
4.7
|
45.6
|
0.2
|
|
O2
|
A:MRD416
|
4.8
|
39.1
|
0.2
|
|
CB
|
A:GLU166
|
4.8
|
13.2
|
0.4
|
|
HH22
|
A:ARG203
|
4.8
|
23.4
|
1.0
|
|
OG
|
A:SER169
|
4.8
|
14.2
|
1.0
|
|
HD1
|
A:HIS146
|
4.8
|
18.0
|
1.0
|
|
HD1
|
A:HIS142
|
4.9
|
16.8
|
1.0
|
|
HG2
|
A:GLU166
|
4.9
|
15.9
|
0.4
|
|
CE1
|
A:TYR157
|
4.9
|
25.7
|
0.5
|
|
CB
|
A:GLU166
|
4.9
|
15.8
|
0.6
|
|
HA
|
A:GLU143
|
4.9
|
19.1
|
1.0
|
|
C4
|
A:MRD416
|
5.0
|
36.6
|
0.8
|
|
HD2
|
A:HIS231
|
5.0
|
37.5
|
1.0
|
|
H5C2
|
A:MRD416
|
5.0
|
39.0
|
0.8
|
|
CZ
|
A:TYR157
|
5.0
|
24.9
|
0.5
|
|
Zinc binding site 3 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 3 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn406
b:32.1
occ:0.70
|
ZN
|
A:ZN406
|
0.0
|
32.1
|
0.7
|
|
ZN
|
A:ZN406
|
1.9
|
29.6
|
0.3
|
|
O
|
A:HOH535
|
2.0
|
26.0
|
1.0
|
|
O
|
A:HOH620
|
2.0
|
19.6
|
1.0
|
|
OE2
|
A:GLU143
|
2.1
|
30.0
|
1.0
|
|
O
|
A:HOH633
|
2.2
|
38.5
|
1.0
|
|
OE1
|
A:GLU143
|
2.6
|
24.8
|
1.0
|
|
CD
|
A:GLU143
|
2.6
|
19.8
|
1.0
|
|
ZN
|
A:ZN405
|
3.4
|
15.6
|
0.9
|
|
O
|
A:HOH509
|
3.4
|
44.4
|
1.0
|
|
HD2
|
A:HIS146
|
3.4
|
17.4
|
1.0
|
|
H1C1
|
A:MRD416
|
3.5
|
51.5
|
0.8
|
|
HA
|
A:PHE114
|
3.8
|
20.7
|
1.0
|
|
H2
|
A:MRD416
|
3.8
|
58.6
|
0.8
|
|
CD2
|
A:HIS146
|
3.9
|
14.5
|
1.0
|
|
O2
|
A:MRD416
|
3.9
|
39.1
|
0.2
|
|
NE2
|
A:HIS146
|
4.0
|
14.9
|
1.0
|
|
HD2
|
A:HIS142
|
4.0
|
16.5
|
1.0
|
|
O
|
A:ALA113
|
4.0
|
20.7
|
1.0
|
|
H4
|
A:MRD416
|
4.1
|
43.9
|
0.8
|
|
CG
|
A:GLU143
|
4.1
|
17.6
|
1.0
|
|
HMC3
|
A:MRD416
|
4.1
|
45.6
|
0.2
|
|
HMC1
|
A:MRD416
|
4.2
|
45.6
|
0.2
|
|
HB3
|
A:PHE114
|
4.3
|
22.5
|
1.0
|
|
NE2
|
A:HIS142
|
4.4
|
12.4
|
1.0
|
|
HG3
|
A:GLU143
|
4.4
|
21.2
|
1.0
|
|
HG2
|
A:GLU143
|
4.4
|
21.2
|
1.0
|
|
C1
|
A:MRD416
|
4.4
|
42.9
|
0.8
|
|
HA
|
A:MRD416
|
4.5
|
47.6
|
0.8
|
|
CD2
|
A:HIS142
|
4.5
|
13.7
|
1.0
|
|
H2
|
A:MRD416
|
4.5
|
46.9
|
0.2
|
|
CM
|
A:MRD416
|
4.6
|
38.0
|
0.2
|
|
O2
|
A:MRD416
|
4.6
|
48.8
|
0.8
|
|
H
|
A:TRP115
|
4.6
|
21.2
|
1.0
|
|
H1C3
|
A:MRD416
|
4.6
|
51.5
|
0.8
|
|
HA
|
A:GLU143
|
4.6
|
19.1
|
1.0
|
|
HB2
|
A:PHE114
|
4.6
|
22.5
|
1.0
|
|
O
|
A:HOH711
|
4.6
|
59.1
|
1.0
|
|
CA
|
A:PHE114
|
4.6
|
17.3
|
1.0
|
|
OE2
|
A:GLU166
|
4.6
|
18.2
|
0.6
|
|
H4
|
A:MRD416
|
4.7
|
43.6
|
0.2
|
|
CB
|
A:PHE114
|
4.7
|
18.7
|
1.0
|
|
HE2
|
A:HIS231
|
4.8
|
40.5
|
1.0
|
|
O4
|
A:MRD416
|
4.8
|
39.6
|
0.8
|
|
HH
|
A:TYR157
|
4.9
|
32.6
|
0.5
|
|
C4
|
A:MRD416
|
4.9
|
36.6
|
0.8
|
|
C2
|
A:MRD416
|
4.9
|
37.9
|
0.2
|
|
Zinc binding site 4 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 4 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn406
b:29.6
occ:0.30
|
ZN
|
A:ZN406
|
0.0
|
29.6
|
0.3
|
|
OE2
|
A:GLU143
|
1.8
|
30.0
|
1.0
|
|
ZN
|
A:ZN406
|
1.9
|
32.1
|
0.7
|
|
H1C1
|
A:MRD416
|
1.9
|
51.5
|
0.8
|
|
O
|
A:HOH620
|
2.2
|
19.6
|
1.0
|
|
O2
|
A:MRD416
|
2.2
|
39.1
|
0.2
|
|
H2
|
A:MRD416
|
2.3
|
58.6
|
0.8
|
|
O
|
A:HOH535
|
2.3
|
26.0
|
1.0
|
|
H4
|
A:MRD416
|
2.4
|
43.9
|
0.8
|
|
HMC3
|
A:MRD416
|
2.5
|
45.6
|
0.2
|
|
HMC1
|
A:MRD416
|
2.8
|
45.6
|
0.2
|
|
C1
|
A:MRD416
|
2.8
|
42.9
|
0.8
|
|
H2
|
A:MRD416
|
2.9
|
46.9
|
0.2
|
|
CM
|
A:MRD416
|
2.9
|
38.0
|
0.2
|
|
CD
|
A:GLU143
|
3.0
|
19.8
|
1.0
|
|
H4
|
A:MRD416
|
3.0
|
43.6
|
0.2
|
|
HA
|
A:MRD416
|
3.0
|
47.6
|
0.8
|
|
O2
|
A:MRD416
|
3.0
|
48.8
|
0.8
|
|
C2
|
A:MRD416
|
3.1
|
37.9
|
0.2
|
|
C4
|
A:MRD416
|
3.1
|
36.6
|
0.8
|
|
O4
|
A:MRD416
|
3.1
|
39.6
|
0.8
|
|
H1C3
|
A:MRD416
|
3.2
|
51.5
|
0.8
|
|
O
|
A:HOH509
|
3.3
|
44.4
|
1.0
|
|
C2
|
A:MRD416
|
3.3
|
43.4
|
0.8
|
|
H1C2
|
A:MRD416
|
3.5
|
51.5
|
0.8
|
|
ZN
|
A:ZN405
|
3.6
|
15.6
|
0.9
|
|
OE1
|
A:GLU143
|
3.6
|
24.8
|
1.0
|
|
HD2
|
A:HIS142
|
3.6
|
16.5
|
1.0
|
|
O
|
A:HOH625
|
3.7
|
35.3
|
0.7
|
|
C4
|
A:MRD416
|
3.7
|
36.3
|
0.2
|
|
C3
|
A:MRD416
|
3.8
|
37.7
|
0.8
|
|
O
|
A:ALA113
|
3.8
|
20.7
|
1.0
|
|
HMC2
|
A:MRD416
|
3.8
|
45.6
|
0.2
|
|
NE2
|
A:HIS142
|
3.9
|
12.4
|
1.0
|
|
O4
|
A:MRD416
|
3.9
|
35.5
|
0.2
|
|
CD2
|
A:HIS142
|
4.0
|
13.7
|
1.0
|
|
C3
|
A:MRD416
|
4.0
|
36.9
|
0.2
|
|
HG2
|
A:GLU143
|
4.0
|
21.2
|
1.0
|
|
O
|
A:HOH633
|
4.0
|
38.5
|
1.0
|
|
HA
|
A:MRD416
|
4.1
|
42.6
|
0.2
|
|
CG
|
A:GLU143
|
4.1
|
17.6
|
1.0
|
|
H1C3
|
A:MRD416
|
4.1
|
44.5
|
0.2
|
|
C1
|
A:MRD416
|
4.2
|
37.1
|
0.2
|
|
H3C2
|
A:MRD416
|
4.3
|
45.2
|
0.8
|
|
HE2
|
A:HIS231
|
4.3
|
40.5
|
1.0
|
|
HG3
|
A:GLU143
|
4.3
|
21.2
|
1.0
|
|
C5
|
A:MRD416
|
4.3
|
32.5
|
0.8
|
|
H5C2
|
A:MRD416
|
4.5
|
39.0
|
0.8
|
|
H3C2
|
A:MRD416
|
4.5
|
44.2
|
0.2
|
|
H3C1
|
A:MRD416
|
4.5
|
45.2
|
0.8
|
|
HD2
|
A:HIS146
|
4.5
|
17.4
|
1.0
|
|
H5C1
|
A:MRD416
|
4.6
|
39.0
|
0.8
|
|
HA
|
A:PHE114
|
4.6
|
20.7
|
1.0
|
|
H1C1
|
A:MRD416
|
4.6
|
44.5
|
0.2
|
|
H3C1
|
A:MRD416
|
4.7
|
44.2
|
0.2
|
|
CM
|
A:MRD416
|
4.8
|
42.6
|
0.8
|
|
OD1
|
A:ASN112
|
4.8
|
29.5
|
1.0
|
|
NE2
|
A:HIS146
|
4.9
|
14.9
|
1.0
|
|
OE2
|
A:GLU166
|
4.9
|
18.2
|
0.6
|
|
HMC1
|
A:MRD416
|
4.9
|
51.1
|
0.8
|
|
H1C2
|
A:MRD416
|
4.9
|
44.5
|
0.2
|
|
CE1
|
A:HIS142
|
5.0
|
12.8
|
1.0
|
|
C
|
A:ALA113
|
5.0
|
20.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 5 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn407
b:49.5
occ:0.70
|
ND1
|
A:HIS231
|
1.9
|
33.7
|
1.0
|
|
OD1
|
A:ASP226
|
2.0
|
32.7
|
1.0
|
|
O
|
A:HOH721
|
2.1
|
54.3
|
1.0
|
|
O
|
A:HOH736
|
2.5
|
54.6
|
1.0
|
|
HB2
|
A:HIS231
|
2.7
|
32.6
|
1.0
|
|
CE1
|
A:HIS231
|
2.8
|
30.0
|
1.0
|
|
CG
|
A:HIS231
|
2.8
|
28.2
|
1.0
|
|
CG
|
A:ASP226
|
2.9
|
36.0
|
1.0
|
|
HE1
|
A:HIS231
|
3.0
|
36.0
|
1.0
|
|
OD2
|
A:ASP226
|
3.2
|
35.2
|
1.0
|
|
CB
|
A:HIS231
|
3.3
|
27.2
|
1.0
|
|
H
|
A:HIS231
|
3.8
|
25.3
|
1.0
|
|
NE2
|
A:HIS231
|
3.8
|
33.8
|
1.0
|
|
HB3
|
A:HIS231
|
3.8
|
32.6
|
1.0
|
|
CD2
|
A:HIS231
|
3.9
|
31.3
|
1.0
|
|
HG23
|
A:VAL230
|
4.0
|
30.0
|
1.0
|
|
HG22
|
A:VAL230
|
4.1
|
30.0
|
1.0
|
|
CB
|
A:ASP226
|
4.3
|
34.9
|
1.0
|
|
HA
|
A:ASP226
|
4.3
|
43.0
|
1.0
|
|
N
|
A:HIS231
|
4.3
|
21.1
|
1.0
|
|
CA
|
A:HIS231
|
4.4
|
22.4
|
1.0
|
|
HB2
|
A:ASP226
|
4.5
|
41.9
|
1.0
|
|
CG2
|
A:VAL230
|
4.5
|
25.0
|
1.0
|
|
HE2
|
A:HIS231
|
4.6
|
40.5
|
1.0
|
|
HD2
|
A:HIS231
|
4.7
|
37.5
|
1.0
|
|
CA
|
A:ASP226
|
4.8
|
35.8
|
1.0
|
|
HG21
|
A:VAL230
|
4.8
|
30.0
|
1.0
|
|
HB3
|
A:ASP226
|
4.9
|
41.9
|
1.0
|
|
HA
|
A:HIS231
|
5.0
|
26.9
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 6 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn408
b:19.4
occ:0.54
|
HZ1
|
A:LYS239
|
1.2
|
33.3
|
1.0
|
|
O
|
A:HOH636
|
1.8
|
19.0
|
1.0
|
|
NZ
|
A:LYS239
|
2.1
|
27.8
|
1.0
|
|
CL
|
A:CL411
|
2.2
|
29.4
|
0.6
|
|
CL
|
A:CL412
|
2.3
|
69.1
|
1.0
|
|
HZ3
|
A:LYS239
|
2.4
|
33.3
|
1.0
|
|
HZ2
|
A:LYS239
|
2.4
|
33.3
|
1.0
|
|
CE
|
A:LYS239
|
3.2
|
21.9
|
1.0
|
|
HE2
|
A:LYS239
|
3.3
|
26.2
|
1.0
|
|
HE3
|
A:LYS239
|
3.3
|
26.2
|
1.0
|
|
ZN
|
A:ZN409
|
3.4
|
20.2
|
0.9
|
|
HD21
|
A:LEU243
|
3.8
|
23.1
|
1.0
|
|
CL
|
A:CL413
|
3.8
|
24.8
|
0.9
|
|
O
|
A:SER206
|
4.0
|
19.2
|
1.0
|
|
HE2
|
A:TYR242
|
4.0
|
26.1
|
1.0
|
|
HB2
|
A:HIS250
|
4.2
|
19.1
|
1.0
|
|
ND1
|
A:HIS250
|
4.4
|
17.5
|
1.0
|
|
O
|
A:THR249
|
4.4
|
26.6
|
1.0
|
|
CD
|
A:LYS239
|
4.5
|
21.0
|
1.0
|
|
O
|
A:HOH698
|
4.5
|
38.8
|
1.0
|
|
HD23
|
A:LEU243
|
4.6
|
23.1
|
1.0
|
|
CD2
|
A:LEU243
|
4.6
|
19.2
|
1.0
|
|
HD3
|
A:LYS239
|
4.7
|
25.2
|
1.0
|
|
HD2
|
A:LYS239
|
4.7
|
25.2
|
1.0
|
|
CE2
|
A:TYR242
|
4.8
|
21.8
|
1.0
|
|
HD2
|
A:TYR242
|
4.8
|
22.8
|
1.0
|
|
HA3
|
A:GLY248
|
4.8
|
23.9
|
1.0
|
|
O
|
A:HOH610
|
4.9
|
50.1
|
1.0
|
|
HA
|
A:HIS250
|
4.9
|
20.7
|
1.0
|
|
CB
|
A:HIS250
|
4.9
|
15.9
|
1.0
|
|
CG
|
A:HIS250
|
5.0
|
15.7
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 7 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn409
b:20.2
occ:0.88
|
ND1
|
A:HIS250
|
2.0
|
17.5
|
1.0
|
|
O
|
A:HOH636
|
2.1
|
19.0
|
1.0
|
|
CL
|
A:CL414
|
2.2
|
19.9
|
0.9
|
|
CL
|
A:CL413
|
2.2
|
24.8
|
0.9
|
|
HA
|
A:HIS250
|
2.9
|
20.7
|
1.0
|
|
CE1
|
A:HIS250
|
2.9
|
16.7
|
1.0
|
|
HE1
|
A:HIS250
|
3.0
|
20.1
|
1.0
|
|
CG
|
A:HIS250
|
3.2
|
15.7
|
1.0
|
|
HE2
|
A:LYS239
|
3.4
|
26.2
|
1.0
|
|
ZN
|
A:ZN408
|
3.4
|
19.4
|
0.5
|
|
HZ1
|
A:LYS239
|
3.5
|
33.3
|
1.0
|
|
HB2
|
A:HIS250
|
3.5
|
19.1
|
1.0
|
|
CB
|
A:HIS250
|
3.6
|
15.9
|
1.0
|
|
CA
|
A:HIS250
|
3.7
|
17.2
|
1.0
|
|
H
|
A:TYR251
|
3.8
|
20.6
|
1.0
|
|
HZ3
|
A:LYS239
|
3.9
|
33.3
|
1.0
|
|
O
|
A:THR249
|
3.9
|
26.6
|
1.0
|
|
NZ
|
A:LYS239
|
4.0
|
27.8
|
1.0
|
|
NE2
|
A:HIS250
|
4.1
|
16.6
|
1.0
|
|
CE
|
A:LYS239
|
4.1
|
21.9
|
1.0
|
|
CD2
|
A:HIS250
|
4.2
|
17.0
|
1.0
|
|
N
|
A:TYR251
|
4.4
|
17.2
|
1.0
|
|
HE3
|
A:LYS239
|
4.5
|
26.2
|
1.0
|
|
CL
|
A:CL412
|
4.6
|
69.1
|
1.0
|
|
C
|
A:HIS250
|
4.6
|
16.7
|
1.0
|
|
HB3
|
A:HIS250
|
4.6
|
19.1
|
1.0
|
|
N
|
A:HIS250
|
4.7
|
18.0
|
1.0
|
|
C
|
A:THR249
|
4.7
|
22.2
|
1.0
|
|
O
|
A:HOH610
|
4.7
|
50.1
|
1.0
|
|
OD2
|
A:ASP215
|
4.8
|
18.0
|
1.0
|
|
HE2
|
A:HIS250
|
4.8
|
20.0
|
1.0
|
|
HD2
|
A:TYR251
|
4.8
|
21.9
|
1.0
|
|
HZ2
|
A:LYS239
|
4.8
|
33.3
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5uu7
Go back to
Zinc Binding Sites List in 5uu7
Zinc binding site 8 out
of 8 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn410
b:24.2
occ:0.42
|
O
|
A:HOH666
|
1.8
|
48.7
|
1.0
|
|
O
|
A:HOH744
|
2.0
|
40.3
|
1.0
|
|
O
|
A:HOH604
|
2.0
|
45.2
|
1.0
|
|
O
|
A:HOH515
|
2.1
|
34.8
|
1.0
|
|
O
|
A:HOH614
|
2.1
|
36.6
|
1.0
|
|
OD2
|
A:ASP213
|
2.2
|
27.8
|
1.0
|
|
OD1
|
A:ASP213
|
2.2
|
25.7
|
1.0
|
|
CG
|
A:ASP213
|
2.5
|
25.1
|
1.0
|
|
HO4
|
A:MPD417
|
3.3
|
74.4
|
0.9
|
|
H51
|
A:MPD417
|
3.9
|
72.5
|
0.9
|
|
HB3
|
A:ARG203
|
4.0
|
27.9
|
1.0
|
|
CB
|
A:ASP213
|
4.0
|
18.6
|
1.0
|
|
O
|
A:HOH630
|
4.1
|
28.9
|
1.0
|
|
HA
|
A:ILE232
|
4.1
|
27.5
|
1.0
|
|
O
|
A:HOH742
|
4.2
|
51.1
|
1.0
|
|
O4
|
A:MPD417
|
4.2
|
62.0
|
0.9
|
|
HB2
|
A:TYR211
|
4.3
|
26.1
|
1.0
|
|
HG12
|
A:ILE232
|
4.3
|
36.2
|
1.0
|
|
HB3
|
A:TYR211
|
4.3
|
26.1
|
1.0
|
|
O
|
A:TYR211
|
4.4
|
26.4
|
1.0
|
|
HB2
|
A:ASP213
|
4.4
|
22.3
|
1.0
|
|
O
|
A:LEU202
|
4.4
|
19.4
|
1.0
|
|
HB3
|
A:ASP213
|
4.5
|
22.3
|
1.0
|
|
O
|
A:HIS231
|
4.5
|
30.1
|
1.0
|
|
HA
|
A:ASP213
|
4.6
|
21.3
|
1.0
|
|
O
|
A:HOH581
|
4.6
|
19.4
|
1.0
|
|
H
|
A:ASP213
|
4.7
|
23.6
|
1.0
|
|
O
|
A:HOH722
|
4.7
|
25.9
|
1.0
|
|
CA
|
A:ASP213
|
4.8
|
17.7
|
1.0
|
|
CB
|
A:TYR211
|
4.8
|
21.8
|
1.0
|
|
H31
|
A:MPD417
|
4.8
|
78.9
|
0.9
|
|
C5
|
A:MPD417
|
4.8
|
60.5
|
0.9
|
|
N
|
A:ASP213
|
4.8
|
19.7
|
1.0
|
|
CB
|
A:ARG203
|
4.9
|
23.2
|
1.0
|
|
HD3
|
A:ARG203
|
4.9
|
24.0
|
1.0
|
|
H53
|
A:MPD417
|
4.9
|
72.5
|
0.9
|
|
HB2
|
A:ARG203
|
4.9
|
27.9
|
1.0
|
|
Reference:
D.H.Juers,
C.A.Farley,
C.P.Saxby,
R.A.Cotter,
J.K.B.Cahn,
R.C.Holton-Burke,
K.Harrison,
Z.Wu.
The Impact of Cryosolution Thermal Contraction on Proteins and Protein Crystals: Volumes, Conformation and Order. Acta Crystallogr D Struct V. 74 922 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198901
DOI: 10.1107/S2059798318008793
Page generated: Mon Oct 28 12:19:00 2024
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