Manganese in PDB 3wvp: Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
Enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
All present enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking:
3.1.21.4;
Protein crystallography data
The structure of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking, PDB code: 3wvp
was solved by
T.Kawamura,
T.Kobayashi,
N.Watanabe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.71 /
2.30
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.495,
140.704,
96.467,
90.00,
112.07,
90.00
|
|
R / Rfree (%)
|
18.2 /
23
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
(pdb code 3wvp). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking, PDB code: 3wvp:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 1 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn302
b:28.6
occ:1.00
|
OP1
|
F:DA5
|
1.8
|
24.4
|
0.5
|
|
OP3
|
R:DA1
|
1.9
|
27.8
|
0.5
|
|
O
|
C:ALA109
|
2.0
|
27.1
|
1.0
|
|
OD2
|
C:ASP93
|
2.1
|
27.6
|
1.0
|
|
O
|
C:HOH466
|
2.2
|
23.4
|
1.0
|
|
O
|
F:HOH106
|
2.4
|
21.0
|
0.5
|
|
OD1
|
C:ASP108
|
2.4
|
37.4
|
1.0
|
|
OP2
|
R:DA1
|
2.7
|
28.1
|
0.5
|
|
P
|
R:DA1
|
2.8
|
30.1
|
0.5
|
|
CG
|
C:ASP108
|
3.0
|
44.0
|
1.0
|
|
CG
|
C:ASP93
|
3.1
|
28.2
|
1.0
|
|
C
|
C:ALA109
|
3.1
|
29.1
|
1.0
|
|
OD2
|
C:ASP108
|
3.1
|
63.2
|
1.0
|
|
P
|
F:DA5
|
3.2
|
27.2
|
0.5
|
|
OD1
|
C:ASP93
|
3.4
|
26.1
|
1.0
|
|
N
|
C:ALA109
|
3.5
|
31.1
|
1.0
|
|
CA
|
C:ALA109
|
3.8
|
30.9
|
1.0
|
|
OP1
|
R:DA1
|
3.8
|
29.3
|
0.5
|
|
O5'
|
R:DA1
|
3.9
|
29.4
|
0.5
|
|
O
|
C:HOH469
|
3.9
|
43.2
|
1.0
|
|
O5'
|
F:DA5
|
3.9
|
26.5
|
0.5
|
|
OP2
|
F:DA5
|
4.1
|
26.2
|
0.5
|
|
MN
|
C:MN303
|
4.1
|
33.3
|
0.7
|
|
O
|
C:HOH472
|
4.1
|
33.1
|
1.0
|
|
C
|
C:ASP108
|
4.1
|
30.7
|
1.0
|
|
C5'
|
F:DA5
|
4.2
|
25.9
|
0.5
|
|
C5'
|
R:DA1
|
4.2
|
28.7
|
0.5
|
|
N
|
C:LYS110
|
4.2
|
29.3
|
1.0
|
|
CB
|
C:ASP108
|
4.2
|
33.3
|
1.0
|
|
O3'
|
F:DA4
|
4.3
|
27.0
|
0.5
|
|
O
|
C:HOH468
|
4.3
|
44.0
|
1.0
|
|
CA
|
C:ASP108
|
4.4
|
31.5
|
1.0
|
|
OD1
|
C:ASP68
|
4.4
|
41.9
|
1.0
|
|
CB
|
C:ASP93
|
4.4
|
28.9
|
1.0
|
|
CB
|
C:ALA109
|
4.5
|
31.0
|
1.0
|
|
CA
|
C:LYS110
|
4.6
|
27.9
|
1.0
|
|
O
|
C:HOH467
|
4.8
|
30.7
|
1.0
|
|
OG
|
C:SER64
|
4.8
|
30.0
|
1.0
|
|
Manganese binding site 2 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 2 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn303
b:33.3
occ:0.71
|
O
|
C:HOH467
|
2.0
|
30.7
|
1.0
|
|
OP2
|
R:DA1
|
2.0
|
28.1
|
0.5
|
|
O
|
C:HOH468
|
2.1
|
44.0
|
1.0
|
|
OD1
|
C:ASP93
|
2.3
|
26.1
|
1.0
|
|
O
|
C:HOH470
|
2.3
|
26.3
|
0.6
|
|
OE1
|
C:GLN87
|
2.4
|
22.4
|
0.3
|
|
O3'
|
S:DA4
|
2.4
|
16.9
|
0.5
|
|
O3'
|
F:DA4
|
2.5
|
27.0
|
0.5
|
|
OP1
|
F:DA5
|
3.0
|
24.4
|
0.5
|
|
NE2
|
C:GLN87
|
3.0
|
20.9
|
0.3
|
|
CD
|
C:GLN87
|
3.1
|
23.3
|
0.3
|
|
C3'
|
S:DA4
|
3.3
|
17.3
|
0.5
|
|
P
|
F:DA5
|
3.4
|
27.2
|
0.5
|
|
CG
|
C:ASP93
|
3.4
|
28.2
|
1.0
|
|
P
|
R:DA1
|
3.4
|
30.1
|
0.5
|
|
C3'
|
F:DA4
|
3.6
|
27.9
|
0.5
|
|
O
|
C:HOH471
|
3.7
|
42.1
|
0.6
|
|
C4'
|
F:DA4
|
3.8
|
28.8
|
0.5
|
|
OD2
|
C:ASP93
|
3.9
|
27.6
|
1.0
|
|
O
|
C:ALA91
|
4.0
|
37.9
|
1.0
|
|
MN
|
C:MN302
|
4.1
|
28.6
|
1.0
|
|
C5'
|
F:DA5
|
4.2
|
25.9
|
0.5
|
|
C5'
|
R:DA1
|
4.2
|
28.7
|
0.5
|
|
O5'
|
R:DA1
|
4.2
|
29.4
|
0.5
|
|
OD2
|
C:ASP108
|
4.2
|
63.2
|
1.0
|
|
C4'
|
S:DA4
|
4.2
|
18.1
|
0.5
|
|
O5'
|
F:DA5
|
4.2
|
26.5
|
0.5
|
|
OP1
|
R:DA1
|
4.2
|
29.3
|
0.5
|
|
O
|
C:HOH466
|
4.3
|
23.4
|
1.0
|
|
C2'
|
F:DA4
|
4.3
|
29.6
|
0.5
|
|
OP3
|
R:DA1
|
4.4
|
27.8
|
0.5
|
|
O
|
C:ARG88
|
4.4
|
24.7
|
0.6
|
|
O
|
C:HOH450
|
4.4
|
33.9
|
1.0
|
|
C
|
C:GLY92
|
4.5
|
27.9
|
1.0
|
|
C2'
|
S:DA4
|
4.5
|
17.8
|
0.5
|
|
O
|
C:GLY92
|
4.5
|
29.8
|
1.0
|
|
C5'
|
F:DA4
|
4.5
|
28.5
|
0.5
|
|
CG
|
C:GLN87
|
4.6
|
25.0
|
0.3
|
|
OP2
|
F:DA5
|
4.6
|
26.2
|
0.5
|
|
CB
|
C:ASP93
|
4.6
|
28.9
|
1.0
|
|
N
|
C:ASP93
|
4.6
|
25.3
|
1.0
|
|
CA
|
C:ASP93
|
4.6
|
26.5
|
1.0
|
|
O4'
|
F:DA4
|
4.9
|
28.1
|
0.5
|
|
CA
|
C:GLY92
|
5.0
|
27.8
|
1.0
|
|
Manganese binding site 3 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 3 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn302
b:32.5
occ:1.00
|
OP1
|
E:DA5
|
1.9
|
20.4
|
0.5
|
|
O
|
D:ALA109
|
2.1
|
27.9
|
1.0
|
|
OD2
|
D:ASP93
|
2.1
|
33.7
|
1.0
|
|
OD1
|
D:ASP108
|
2.1
|
42.8
|
1.0
|
|
OP3
|
Q:DA1
|
2.2
|
33.2
|
0.5
|
|
O
|
D:HOH471
|
2.2
|
26.5
|
1.0
|
|
O
|
D:HOH474
|
2.4
|
21.3
|
0.5
|
|
OP2
|
Q:DA1
|
2.7
|
29.0
|
0.5
|
|
CG
|
D:ASP108
|
3.0
|
47.1
|
1.0
|
|
P
|
Q:DA1
|
3.0
|
33.4
|
0.5
|
|
CG
|
D:ASP93
|
3.1
|
31.6
|
1.0
|
|
C
|
D:ALA109
|
3.2
|
30.9
|
1.0
|
|
P
|
E:DA5
|
3.3
|
21.4
|
0.5
|
|
OD1
|
D:ASP93
|
3.4
|
33.4
|
1.0
|
|
OD2
|
D:ASP108
|
3.5
|
71.2
|
1.0
|
|
N
|
D:ALA109
|
3.5
|
34.4
|
1.0
|
|
CA
|
D:ALA109
|
3.9
|
31.5
|
1.0
|
|
O5'
|
E:DA5
|
4.0
|
21.1
|
0.5
|
|
O
|
E:HOH101
|
4.0
|
26.5
|
1.0
|
|
O5'
|
Q:DA1
|
4.1
|
29.9
|
0.5
|
|
O
|
D:HOH473
|
4.1
|
50.8
|
1.0
|
|
OP1
|
Q:DA1
|
4.1
|
33.9
|
0.5
|
|
MN
|
D:MN303
|
4.1
|
40.5
|
0.8
|
|
OP2
|
E:DA5
|
4.1
|
21.7
|
0.5
|
|
C5'
|
E:DA5
|
4.1
|
21.6
|
0.5
|
|
O
|
D:HOH472
|
4.2
|
33.8
|
1.0
|
|
C5'
|
Q:DA1
|
4.2
|
30.1
|
0.5
|
|
C
|
D:ASP108
|
4.2
|
34.5
|
1.0
|
|
CB
|
D:ASP108
|
4.2
|
37.6
|
1.0
|
|
OD1
|
D:ASP68
|
4.3
|
42.1
|
1.0
|
|
CA
|
D:ASP108
|
4.3
|
33.2
|
1.0
|
|
N
|
D:LYS110
|
4.3
|
30.2
|
1.0
|
|
O3'
|
E:DA4
|
4.4
|
21.6
|
0.5
|
|
CB
|
D:ALA109
|
4.4
|
34.8
|
1.0
|
|
CB
|
D:ASP93
|
4.4
|
29.8
|
1.0
|
|
CA
|
D:LYS110
|
4.6
|
30.3
|
1.0
|
|
O
|
D:HOH432
|
5.0
|
33.0
|
1.0
|
|
Manganese binding site 4 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 4 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn303
b:40.5
occ:0.77
|
OP2
|
Q:DA1
|
2.0
|
29.0
|
0.5
|
|
OD1
|
D:ASP93
|
2.2
|
33.4
|
1.0
|
|
O
|
D:HOH477
|
2.2
|
19.0
|
0.6
|
|
O3'
|
T:DA4
|
2.4
|
28.3
|
0.5
|
|
O
|
T:HOH104
|
2.4
|
39.8
|
1.0
|
|
O3'
|
E:DA4
|
2.5
|
21.6
|
0.5
|
|
O
|
D:HOH472
|
2.5
|
33.8
|
1.0
|
|
OE1
|
D:GLN87
|
2.7
|
26.4
|
0.3
|
|
OP1
|
E:DA5
|
2.8
|
20.4
|
0.5
|
|
C3'
|
T:DA4
|
3.1
|
25.9
|
0.5
|
|
P
|
E:DA5
|
3.3
|
21.4
|
0.5
|
|
CG
|
D:ASP93
|
3.3
|
31.6
|
1.0
|
|
P
|
Q:DA1
|
3.4
|
33.4
|
0.5
|
|
CD
|
D:GLN87
|
3.4
|
26.1
|
0.3
|
|
NE2
|
D:GLN87
|
3.4
|
26.4
|
0.3
|
|
O
|
D:HOH478
|
3.4
|
38.6
|
0.6
|
|
C3'
|
E:DA4
|
3.6
|
22.3
|
0.5
|
|
C4'
|
E:DA4
|
3.8
|
23.3
|
0.5
|
|
OD2
|
D:ASP93
|
3.8
|
33.7
|
1.0
|
|
O
|
D:ALA91
|
4.0
|
43.1
|
1.0
|
|
MN
|
D:MN302
|
4.1
|
32.5
|
1.0
|
|
O5'
|
Q:DA1
|
4.1
|
29.9
|
0.5
|
|
C4'
|
T:DA4
|
4.1
|
26.7
|
0.5
|
|
OP1
|
Q:DA1
|
4.1
|
33.9
|
0.5
|
|
C5'
|
Q:DA1
|
4.2
|
30.1
|
0.5
|
|
O
|
D:ARG88
|
4.2
|
23.3
|
0.6
|
|
C2'
|
T:DA4
|
4.2
|
26.3
|
0.5
|
|
C5'
|
E:DA5
|
4.3
|
21.6
|
0.5
|
|
C2'
|
E:DA4
|
4.3
|
23.4
|
0.5
|
|
O5'
|
E:DA5
|
4.3
|
21.1
|
0.5
|
|
OP3
|
Q:DA1
|
4.3
|
33.2
|
0.5
|
|
O
|
D:GLY92
|
4.4
|
30.7
|
1.0
|
|
OP2
|
E:DA5
|
4.4
|
21.7
|
0.5
|
|
C5'
|
E:DA4
|
4.4
|
25.2
|
0.5
|
|
C
|
D:GLY92
|
4.5
|
29.4
|
1.0
|
|
CB
|
D:ASP93
|
4.5
|
29.8
|
1.0
|
|
N
|
D:ASP93
|
4.5
|
29.8
|
1.0
|
|
O
|
D:HOH471
|
4.5
|
26.5
|
1.0
|
|
O
|
D:HOH432
|
4.6
|
33.0
|
1.0
|
|
CA
|
D:ASP93
|
4.6
|
31.2
|
1.0
|
|
OD2
|
D:ASP108
|
4.7
|
71.2
|
1.0
|
|
C5'
|
T:DA4
|
4.8
|
26.8
|
0.5
|
|
CG
|
D:GLN87
|
4.9
|
27.9
|
0.3
|
|
O4'
|
E:DA4
|
5.0
|
24.8
|
0.5
|
|
Manganese binding site 5 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 5 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn303
b:33.1
occ:1.00
|
OP2
|
M:DA1
|
2.0
|
31.7
|
0.5
|
|
OP1
|
H:DA5
|
2.0
|
25.0
|
0.5
|
|
O
|
A:ALA109
|
2.1
|
28.5
|
1.0
|
|
OD2
|
A:ASP93
|
2.1
|
33.2
|
1.0
|
|
O
|
A:HOH452
|
2.3
|
30.1
|
1.0
|
|
OD1
|
A:ASP108
|
2.3
|
39.2
|
1.0
|
|
O
|
H:HOH107
|
2.8
|
26.2
|
0.5
|
|
P
|
M:DA1
|
2.8
|
32.8
|
0.5
|
|
OP1
|
M:DA1
|
2.9
|
30.6
|
0.5
|
|
CG
|
A:ASP108
|
3.0
|
43.5
|
1.0
|
|
OD2
|
A:ASP108
|
3.1
|
53.2
|
1.0
|
|
C
|
A:ALA109
|
3.2
|
30.7
|
1.0
|
|
CG
|
A:ASP93
|
3.3
|
35.8
|
1.0
|
|
P
|
H:DA5
|
3.4
|
25.5
|
0.5
|
|
N
|
A:ALA109
|
3.5
|
32.0
|
1.0
|
|
O
|
M:HOH106
|
3.7
|
44.6
|
1.0
|
|
OD1
|
A:ASP93
|
3.8
|
32.8
|
1.0
|
|
OP3
|
M:DA1
|
3.9
|
33.5
|
0.5
|
|
O5'
|
M:DA1
|
3.9
|
30.2
|
0.5
|
|
CA
|
A:ALA109
|
4.0
|
32.8
|
1.0
|
|
O5'
|
H:DA5
|
4.1
|
25.4
|
0.5
|
|
OP2
|
H:DA5
|
4.1
|
27.4
|
0.5
|
|
C5'
|
H:DA5
|
4.2
|
27.1
|
0.5
|
|
O
|
H:HOH105
|
4.2
|
41.4
|
1.0
|
|
CB
|
A:ASP108
|
4.2
|
36.1
|
1.0
|
|
MN
|
A:MN304
|
4.2
|
34.6
|
0.7
|
|
C
|
A:ASP108
|
4.3
|
32.2
|
1.0
|
|
N
|
A:LYS110
|
4.3
|
30.7
|
1.0
|
|
C5'
|
M:DA1
|
4.3
|
30.4
|
0.5
|
|
CA
|
A:ASP108
|
4.4
|
31.7
|
1.0
|
|
OD1
|
A:ASP68
|
4.4
|
48.1
|
1.0
|
|
O
|
A:HOH454
|
4.5
|
49.5
|
1.0
|
|
O3'
|
H:DA4
|
4.5
|
24.4
|
0.5
|
|
CB
|
A:ALA109
|
4.5
|
33.7
|
1.0
|
|
CA
|
A:LYS110
|
4.5
|
32.5
|
1.0
|
|
CB
|
A:ASP93
|
4.5
|
32.5
|
1.0
|
|
CB
|
A:LYS110
|
4.8
|
35.2
|
1.0
|
|
O
|
A:HOH456
|
5.0
|
34.1
|
1.0
|
|
Manganese binding site 6 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 6 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn304
b:34.6
occ:0.65
|
OP1
|
M:DA1
|
2.0
|
30.6
|
0.5
|
|
O
|
A:HOH457
|
2.1
|
29.1
|
0.6
|
|
O
|
A:HOH453
|
2.3
|
31.4
|
1.0
|
|
OD1
|
A:ASP93
|
2.3
|
32.8
|
1.0
|
|
O3'
|
P:DA4
|
2.4
|
35.5
|
0.5
|
|
OE1
|
A:GLN87
|
2.4
|
26.5
|
0.2
|
|
O3'
|
H:DA4
|
2.6
|
24.4
|
0.5
|
|
O
|
A:HOH454
|
2.6
|
49.5
|
1.0
|
|
OP1
|
H:DA5
|
2.9
|
25.0
|
0.5
|
|
C3'
|
P:DA4
|
3.1
|
35.5
|
0.5
|
|
CD
|
A:GLN87
|
3.2
|
28.0
|
0.2
|
|
NE2
|
A:GLN87
|
3.3
|
26.5
|
0.2
|
|
P
|
H:DA5
|
3.3
|
25.5
|
0.5
|
|
CG
|
A:ASP93
|
3.3
|
35.8
|
1.0
|
|
P
|
M:DA1
|
3.5
|
32.8
|
0.5
|
|
O
|
A:HOH458
|
3.7
|
26.7
|
0.6
|
|
C3'
|
H:DA4
|
3.7
|
24.6
|
0.5
|
|
OD2
|
A:ASP93
|
3.8
|
33.2
|
1.0
|
|
C4'
|
H:DA4
|
3.8
|
24.2
|
0.5
|
|
C5'
|
H:DA5
|
4.0
|
27.1
|
0.5
|
|
C5'
|
M:DA1
|
4.0
|
30.4
|
0.5
|
|
O
|
A:ARG88
|
4.1
|
26.9
|
0.6
|
|
O
|
A:ALA91
|
4.1
|
33.7
|
1.0
|
|
O5'
|
H:DA5
|
4.1
|
25.4
|
0.5
|
|
C4'
|
P:DA4
|
4.2
|
35.4
|
0.5
|
|
OD2
|
A:ASP108
|
4.2
|
53.2
|
1.0
|
|
O5'
|
M:DA1
|
4.2
|
30.2
|
0.5
|
|
OP3
|
M:DA1
|
4.2
|
33.5
|
0.5
|
|
MN
|
A:MN303
|
4.2
|
33.1
|
1.0
|
|
C2'
|
H:DA4
|
4.2
|
23.5
|
0.5
|
|
C2'
|
P:DA4
|
4.3
|
35.0
|
0.5
|
|
O
|
A:HOH452
|
4.3
|
30.1
|
1.0
|
|
O
|
A:HOH456
|
4.4
|
34.1
|
1.0
|
|
O
|
A:GLY92
|
4.4
|
30.1
|
1.0
|
|
OP2
|
M:DA1
|
4.5
|
31.7
|
0.5
|
|
CG
|
A:GLN87
|
4.6
|
29.6
|
0.2
|
|
OP2
|
H:DA5
|
4.6
|
27.4
|
0.5
|
|
C
|
A:GLY92
|
4.6
|
29.1
|
1.0
|
|
CB
|
A:ASP93
|
4.6
|
32.5
|
1.0
|
|
C5'
|
H:DA4
|
4.6
|
24.9
|
0.5
|
|
CA
|
A:ASP93
|
4.7
|
32.7
|
1.0
|
|
N
|
A:ASP93
|
4.8
|
29.9
|
1.0
|
|
C
|
A:ARG88
|
4.9
|
31.9
|
0.6
|
|
CA
|
A:ARG88
|
4.9
|
34.4
|
0.6
|
|
C5'
|
P:DA4
|
4.9
|
37.4
|
0.5
|
|
O4'
|
H:DA4
|
5.0
|
22.1
|
0.5
|
|
Manganese binding site 7 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 7 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn301
b:29.6
occ:1.00
|
OP1
|
G:DA5
|
1.9
|
24.8
|
0.5
|
|
OP3
|
N:DA1
|
2.0
|
30.1
|
0.5
|
|
OD2
|
B:ASP93
|
2.0
|
25.5
|
1.0
|
|
O
|
B:ALA109
|
2.1
|
34.2
|
1.0
|
|
O
|
B:HOH466
|
2.2
|
24.0
|
1.0
|
|
OD1
|
B:ASP108
|
2.3
|
47.4
|
1.0
|
|
OP1
|
N:DA1
|
2.6
|
24.5
|
0.5
|
|
O
|
G:HOH104
|
2.8
|
23.1
|
0.5
|
|
P
|
N:DA1
|
2.8
|
27.9
|
0.5
|
|
CG
|
B:ASP108
|
3.0
|
47.4
|
1.0
|
|
CG
|
B:ASP93
|
3.1
|
25.9
|
1.0
|
|
OD2
|
B:ASP108
|
3.2
|
61.8
|
1.0
|
|
C
|
B:ALA109
|
3.2
|
27.0
|
1.0
|
|
P
|
G:DA5
|
3.3
|
24.6
|
0.5
|
|
N
|
B:ALA109
|
3.4
|
26.1
|
1.0
|
|
OD1
|
B:ASP93
|
3.4
|
25.8
|
1.0
|
|
CA
|
B:ALA109
|
3.9
|
27.4
|
1.0
|
|
O5'
|
N:DA1
|
3.9
|
26.4
|
0.5
|
|
OP2
|
G:DA5
|
3.9
|
26.7
|
0.5
|
|
OP2
|
N:DA1
|
4.0
|
28.5
|
0.5
|
|
O
|
G:HOH101
|
4.0
|
27.9
|
1.0
|
|
O5'
|
G:DA5
|
4.0
|
24.8
|
0.5
|
|
MN
|
B:MN302
|
4.1
|
37.9
|
0.8
|
|
C5'
|
G:DA5
|
4.1
|
23.4
|
0.5
|
|
C5'
|
N:DA1
|
4.1
|
24.1
|
0.5
|
|
C
|
B:ASP108
|
4.2
|
30.3
|
1.0
|
|
CB
|
B:ASP108
|
4.2
|
34.7
|
1.0
|
|
N
|
B:LYS110
|
4.3
|
28.1
|
1.0
|
|
OD1
|
B:ASP68
|
4.3
|
41.5
|
1.0
|
|
CA
|
B:ASP108
|
4.3
|
30.4
|
1.0
|
|
CB
|
B:ALA109
|
4.4
|
29.0
|
1.0
|
|
O3'
|
G:DA4
|
4.4
|
24.3
|
0.5
|
|
CB
|
B:ASP93
|
4.4
|
24.3
|
1.0
|
|
O
|
B:HOH467
|
4.5
|
42.6
|
1.0
|
|
CA
|
B:LYS110
|
4.5
|
28.9
|
1.0
|
|
CB
|
B:LYS110
|
4.9
|
28.5
|
1.0
|
|
Manganese binding site 8 out
of 8 in 3wvp
Go back to
Manganese Binding Sites List in 3wvp
Manganese binding site 8 out
of 8 in the Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Time-Resolved Crystal Structure of Hindiii with 60SEC Soaking within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn302
b:37.9
occ:0.84
|
OP1
|
N:DA1
|
1.9
|
24.5
|
0.5
|
|
OD1
|
B:ASP93
|
2.3
|
25.8
|
1.0
|
|
O
|
B:HOH469
|
2.3
|
25.9
|
0.6
|
|
O
|
O:HOH104
|
2.3
|
29.9
|
1.0
|
|
O3'
|
O:DA4
|
2.4
|
20.3
|
0.5
|
|
O3'
|
G:DA4
|
2.5
|
24.3
|
0.5
|
|
O
|
B:HOH467
|
2.6
|
42.6
|
1.0
|
|
OP1
|
G:DA5
|
2.7
|
24.8
|
0.5
|
|
OE1
|
B:GLN87
|
2.7
|
28.0
|
0.3
|
|
NE2
|
B:GLN87
|
3.2
|
27.4
|
0.3
|
|
P
|
G:DA5
|
3.2
|
24.6
|
0.5
|
|
C3'
|
O:DA4
|
3.2
|
20.7
|
0.5
|
|
P
|
N:DA1
|
3.3
|
27.9
|
0.5
|
|
CD
|
B:GLN87
|
3.3
|
28.9
|
0.3
|
|
CG
|
B:ASP93
|
3.3
|
25.9
|
1.0
|
|
C3'
|
G:DA4
|
3.7
|
26.2
|
0.5
|
|
O
|
B:HOH470
|
3.8
|
13.4
|
0.6
|
|
OD2
|
B:ASP93
|
3.8
|
25.5
|
1.0
|
|
C4'
|
G:DA4
|
3.9
|
28.2
|
0.5
|
|
O5'
|
N:DA1
|
4.0
|
26.4
|
0.5
|
|
C5'
|
N:DA1
|
4.0
|
24.1
|
0.5
|
|
C5'
|
G:DA5
|
4.0
|
23.4
|
0.5
|
|
O5'
|
G:DA5
|
4.1
|
24.8
|
0.5
|
|
MN
|
B:MN301
|
4.1
|
29.6
|
1.0
|
|
OP2
|
N:DA1
|
4.1
|
28.5
|
0.5
|
|
C2'
|
G:DA4
|
4.2
|
26.9
|
0.5
|
|
O
|
B:ALA91
|
4.2
|
31.7
|
1.0
|
|
C4'
|
O:DA4
|
4.2
|
22.2
|
0.5
|
|
O
|
B:ARG88
|
4.3
|
17.5
|
0.6
|
|
OP3
|
N:DA1
|
4.3
|
30.1
|
0.5
|
|
O
|
B:HOH413
|
4.3
|
30.0
|
1.0
|
|
C2'
|
O:DA4
|
4.3
|
20.6
|
0.5
|
|
OD2
|
B:ASP108
|
4.3
|
61.8
|
1.0
|
|
O
|
B:GLY92
|
4.4
|
30.6
|
1.0
|
|
O
|
B:HOH466
|
4.4
|
24.0
|
1.0
|
|
OP2
|
G:DA5
|
4.5
|
26.7
|
0.5
|
|
C
|
B:GLY92
|
4.6
|
27.2
|
1.0
|
|
CB
|
B:ASP93
|
4.6
|
24.3
|
1.0
|
|
CA
|
B:ASP93
|
4.6
|
26.3
|
1.0
|
|
C5'
|
G:DA4
|
4.7
|
27.7
|
0.5
|
|
N
|
B:ASP93
|
4.7
|
23.2
|
1.0
|
|
CG
|
B:GLN87
|
4.8
|
30.2
|
0.3
|
|
CA
|
B:ARG88
|
5.0
|
24.5
|
0.6
|
|
C
|
B:ARG88
|
5.0
|
22.3
|
0.6
|
|
Reference:
T.Kawamura,
T.Kobayashi,
N.Watanabe.
Analysis of the Hindiii-Catalyzed Reaction By Time-Resolved Crystallography Acta Crystallogr.,Sect.D V. 71 256 2015.
ISSN: ISSN 0907-4449
PubMed: 25664735
DOI: 10.1107/S1399004714025188
Page generated: Sat Oct 5 18:29:20 2024
|
