Manganese in PDB 6ozm: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+
Protein crystallography data
The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+, PDB code: 6ozm
was solved by
N.L.Samara,
W.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.72 /
2.15
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.401,
72.322,
155.311,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.4 /
21.6
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+
(pdb code 6ozm). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the
Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+, PDB code: 6ozm:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
Manganese binding site 1 out
of 5 in 6ozm
Go back to
Manganese Binding Sites List in 6ozm
Manganese binding site 1 out
of 5 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn101
b:37.8
occ:1.00
|
OP1
|
C:U12
|
2.0
|
40.6
|
0.2
|
OP1
|
C:U12
|
2.1
|
39.3
|
0.8
|
OD1
|
A:ASP240
|
2.2
|
38.5
|
1.0
|
O
|
C:HOH212
|
2.2
|
35.9
|
1.0
|
OD2
|
A:ASP52
|
2.2
|
50.1
|
1.0
|
O
|
A:HOH429
|
2.3
|
37.9
|
1.0
|
OP3
|
C:U12
|
2.5
|
50.5
|
0.2
|
O
|
C:HOH205
|
2.5
|
26.0
|
0.8
|
P
|
C:U12
|
2.7
|
41.4
|
0.2
|
CG
|
A:ASP52
|
3.1
|
39.7
|
1.0
|
OD1
|
A:ASP52
|
3.2
|
35.7
|
1.0
|
CG
|
A:ASP240
|
3.2
|
46.0
|
1.0
|
P
|
C:U12
|
3.3
|
37.5
|
0.8
|
OP2
|
C:U12
|
3.6
|
37.5
|
0.2
|
O
|
C:HOH208
|
3.7
|
19.7
|
0.2
|
MN
|
C:MN102
|
3.8
|
35.0
|
0.9
|
CB
|
A:ASP240
|
3.8
|
31.8
|
1.0
|
O5'
|
C:U12
|
4.0
|
44.5
|
0.8
|
OP2
|
C:U12
|
4.0
|
36.3
|
0.8
|
O5'
|
C:U12
|
4.0
|
43.3
|
0.2
|
OD2
|
A:ASP126
|
4.1
|
38.2
|
1.0
|
O
|
A:HOH519
|
4.2
|
32.8
|
1.0
|
MN
|
C:MN103
|
4.2
|
28.1
|
0.2
|
OD2
|
A:ASP240
|
4.2
|
42.9
|
1.0
|
C5'
|
C:U12
|
4.3
|
43.8
|
0.8
|
OP2
|
C:A13
|
4.3
|
34.2
|
1.0
|
C5'
|
C:U12
|
4.4
|
43.6
|
0.2
|
CA
|
A:ASP240
|
4.4
|
33.7
|
1.0
|
O3'
|
C:A11
|
4.5
|
43.9
|
1.0
|
O
|
A:VAL53
|
4.5
|
42.0
|
1.0
|
CB
|
A:ASP52
|
4.5
|
32.7
|
1.0
|
OG
|
A:SER54
|
4.6
|
49.2
|
1.0
|
O
|
C:HOH211
|
4.6
|
10.6
|
0.2
|
CG
|
A:ASP126
|
4.8
|
34.0
|
1.0
|
O
|
A:HOH408
|
4.9
|
23.7
|
0.9
|
|
Manganese binding site 2 out
of 5 in 6ozm
Go back to
Manganese Binding Sites List in 6ozm
Manganese binding site 2 out
of 5 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn102
b:35.0
occ:0.95
|
OD2
|
A:ASP126
|
2.1
|
38.2
|
1.0
|
OD1
|
A:ASP52
|
2.1
|
35.7
|
1.0
|
OP1
|
C:U12
|
2.2
|
39.3
|
0.8
|
O3'
|
C:A11
|
2.3
|
43.9
|
1.0
|
O
|
A:HOH422
|
2.4
|
29.6
|
0.9
|
O
|
A:HOH408
|
2.4
|
23.7
|
0.9
|
OP1
|
C:U12
|
2.4
|
40.6
|
0.2
|
P
|
C:U12
|
2.9
|
37.5
|
0.8
|
CG
|
A:ASP126
|
3.1
|
34.0
|
1.0
|
CG
|
A:ASP52
|
3.3
|
39.7
|
1.0
|
P
|
C:U12
|
3.5
|
41.4
|
0.2
|
C3'
|
C:A11
|
3.5
|
30.7
|
1.0
|
CB
|
A:ASP126
|
3.6
|
26.3
|
1.0
|
O2'
|
C:A11
|
3.6
|
50.2
|
1.0
|
MN
|
C:MN101
|
3.8
|
37.8
|
1.0
|
OP2
|
C:U12
|
3.9
|
37.5
|
0.2
|
O5'
|
C:U12
|
3.9
|
44.5
|
0.8
|
C5'
|
C:U12
|
3.9
|
43.8
|
0.8
|
C5'
|
C:U12
|
4.0
|
43.6
|
0.2
|
OD2
|
A:ASP52
|
4.0
|
50.1
|
1.0
|
C4'
|
C:A11
|
4.0
|
30.8
|
1.0
|
O5'
|
C:U12
|
4.0
|
43.3
|
0.2
|
O
|
A:VAL53
|
4.0
|
42.0
|
1.0
|
O
|
C:HOH212
|
4.1
|
35.9
|
1.0
|
OP2
|
C:U12
|
4.1
|
36.3
|
0.8
|
O
|
A:ASP126
|
4.1
|
46.5
|
1.0
|
C2'
|
C:A11
|
4.1
|
40.8
|
1.0
|
N
|
A:VAL53
|
4.2
|
32.3
|
1.0
|
OD1
|
A:ASP126
|
4.2
|
39.5
|
0.9
|
OE1
|
A:GLU100
|
4.4
|
42.4
|
1.0
|
OE2
|
A:GLU100
|
4.4
|
46.4
|
1.0
|
CB
|
A:ASP52
|
4.5
|
32.7
|
1.0
|
CA
|
A:ASP52
|
4.5
|
31.1
|
1.0
|
OP3
|
C:U12
|
4.7
|
50.5
|
0.2
|
C5'
|
C:A11
|
4.7
|
35.8
|
1.0
|
O
|
A:HOH429
|
4.8
|
37.9
|
1.0
|
C
|
A:ASP126
|
4.8
|
35.0
|
1.0
|
CA
|
A:ASP126
|
4.8
|
30.1
|
1.0
|
CD
|
A:GLU100
|
4.9
|
49.1
|
1.0
|
C
|
A:VAL53
|
4.9
|
37.2
|
1.0
|
C
|
A:ASP52
|
5.0
|
30.2
|
1.0
|
|
Manganese binding site 3 out
of 5 in 6ozm
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Manganese Binding Sites List in 6ozm
Manganese binding site 3 out
of 5 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn103
b:28.1
occ:0.25
|
O
|
C:HOH205
|
1.9
|
26.0
|
0.8
|
O
|
C:HOH207
|
2.0
|
24.6
|
0.2
|
O
|
C:HOH211
|
2.0
|
10.6
|
0.2
|
OP2
|
C:A13
|
2.0
|
34.2
|
1.0
|
OP3
|
C:U12
|
2.1
|
50.5
|
0.2
|
O
|
C:HOH208
|
2.2
|
19.7
|
0.2
|
O
|
C:HOH216
|
2.2
|
30.2
|
0.3
|
P
|
C:A13
|
3.5
|
39.8
|
1.0
|
P
|
C:U12
|
3.5
|
41.4
|
0.2
|
O
|
C:HOH202
|
3.7
|
39.5
|
1.0
|
O5'
|
C:U12
|
3.9
|
43.3
|
0.2
|
O5'
|
C:U12
|
4.0
|
44.5
|
0.8
|
O5'
|
C:A13
|
4.0
|
43.5
|
1.0
|
N7
|
C:A13
|
4.1
|
39.0
|
1.0
|
OP2
|
C:U12
|
4.1
|
37.5
|
0.2
|
C3'
|
C:U12
|
4.2
|
41.9
|
0.8
|
OP2
|
C:U12
|
4.2
|
36.3
|
0.8
|
C3'
|
C:U12
|
4.2
|
41.8
|
0.2
|
C8
|
C:A13
|
4.2
|
43.5
|
1.0
|
MN
|
C:MN101
|
4.2
|
37.8
|
1.0
|
O3'
|
C:U12
|
4.3
|
41.1
|
0.2
|
O3'
|
C:U12
|
4.3
|
40.4
|
0.8
|
O
|
A:HOH429
|
4.3
|
37.9
|
1.0
|
P
|
C:U12
|
4.4
|
37.5
|
0.8
|
OP1
|
C:U12
|
4.5
|
40.6
|
0.2
|
OD1
|
A:ASP240
|
4.5
|
38.5
|
1.0
|
OP1
|
C:A13
|
4.6
|
45.5
|
1.0
|
OP1
|
C:U12
|
4.7
|
39.3
|
0.8
|
C5'
|
C:U12
|
4.7
|
43.8
|
0.8
|
C5'
|
C:U12
|
4.7
|
43.6
|
0.2
|
NE
|
A:ARG244
|
4.9
|
64.3
|
1.0
|
|
Manganese binding site 4 out
of 5 in 6ozm
Go back to
Manganese Binding Sites List in 6ozm
Manganese binding site 4 out
of 5 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn101
b:41.6
occ:1.00
|
OP1
|
D:U12
|
2.0
|
42.5
|
0.8
|
OD1
|
B:ASP240
|
2.1
|
37.2
|
1.0
|
OP1
|
D:U12
|
2.1
|
43.2
|
0.2
|
O
|
D:HOH205
|
2.2
|
35.2
|
1.0
|
OD2
|
B:ASP52
|
2.2
|
50.4
|
1.0
|
OP3
|
D:U12
|
2.3
|
54.7
|
0.2
|
O
|
B:HOH446
|
2.3
|
37.0
|
1.0
|
O
|
D:HOH201
|
2.5
|
39.3
|
0.8
|
P
|
D:U12
|
2.7
|
41.5
|
0.2
|
CG
|
B:ASP52
|
3.1
|
41.3
|
1.0
|
CG
|
B:ASP240
|
3.2
|
43.3
|
1.0
|
P
|
D:U12
|
3.3
|
43.1
|
0.8
|
OD1
|
B:ASP52
|
3.3
|
37.5
|
1.0
|
OP2
|
D:U12
|
3.8
|
39.8
|
0.2
|
CB
|
B:ASP240
|
3.8
|
34.7
|
1.0
|
MN
|
D:MN102
|
3.8
|
35.6
|
0.9
|
O5'
|
D:U12
|
3.9
|
47.0
|
0.8
|
OP2
|
D:U12
|
3.9
|
37.4
|
0.8
|
O5'
|
D:U12
|
3.9
|
45.6
|
0.2
|
OD2
|
B:ASP126
|
3.9
|
43.5
|
1.0
|
OD2
|
B:ASP240
|
4.1
|
41.1
|
1.0
|
C5'
|
D:U12
|
4.2
|
47.6
|
0.2
|
C5'
|
D:U12
|
4.3
|
47.8
|
0.8
|
O
|
B:VAL53
|
4.4
|
39.1
|
1.0
|
OP2
|
D:A13
|
4.4
|
47.5
|
1.0
|
O
|
B:HOH472
|
4.4
|
44.7
|
1.0
|
CA
|
B:ASP240
|
4.5
|
41.1
|
1.0
|
O3'
|
D:A11
|
4.5
|
48.7
|
1.0
|
CB
|
B:ASP52
|
4.5
|
33.8
|
1.0
|
O
|
B:HOH408
|
4.6
|
31.4
|
0.9
|
OG
|
B:SER54
|
4.8
|
55.1
|
1.0
|
CG
|
B:ASP126
|
4.9
|
47.1
|
1.0
|
NZ
|
B:LYS155
|
5.0
|
58.1
|
1.0
|
|
Manganese binding site 5 out
of 5 in 6ozm
Go back to
Manganese Binding Sites List in 6ozm
Manganese binding site 5 out
of 5 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 10 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn102
b:35.6
occ:0.90
|
OD1
|
B:ASP52
|
2.1
|
37.5
|
1.0
|
OD2
|
B:ASP126
|
2.1
|
43.5
|
1.0
|
O
|
B:HOH408
|
2.2
|
31.4
|
0.9
|
OP1
|
D:U12
|
2.2
|
42.5
|
0.8
|
O3'
|
D:A11
|
2.4
|
48.7
|
1.0
|
O
|
B:HOH416
|
2.4
|
32.9
|
0.9
|
OP1
|
D:U12
|
2.4
|
43.2
|
0.2
|
P
|
D:U12
|
2.9
|
43.1
|
0.8
|
CG
|
B:ASP126
|
3.1
|
47.1
|
1.0
|
CG
|
B:ASP52
|
3.2
|
41.3
|
1.0
|
CB
|
B:ASP126
|
3.6
|
36.1
|
1.0
|
P
|
D:U12
|
3.6
|
41.5
|
0.2
|
C3'
|
D:A11
|
3.6
|
46.7
|
1.0
|
O2'
|
D:A11
|
3.8
|
53.6
|
1.0
|
MN
|
D:MN101
|
3.8
|
41.6
|
1.0
|
OD2
|
B:ASP52
|
3.8
|
50.4
|
1.0
|
O
|
D:HOH205
|
3.9
|
35.2
|
1.0
|
O5'
|
D:U12
|
4.0
|
47.0
|
0.8
|
C5'
|
D:U12
|
4.0
|
47.6
|
0.2
|
OP2
|
D:U12
|
4.0
|
39.8
|
0.2
|
C5'
|
D:U12
|
4.0
|
47.8
|
0.8
|
C4'
|
D:A11
|
4.1
|
44.1
|
1.0
|
O
|
B:VAL53
|
4.1
|
39.1
|
1.0
|
OP2
|
D:U12
|
4.1
|
37.4
|
0.8
|
O
|
B:ASP126
|
4.1
|
52.2
|
1.0
|
OD1
|
B:ASP126
|
4.2
|
48.4
|
1.0
|
OE1
|
B:GLU100
|
4.2
|
53.5
|
1.0
|
O5'
|
D:U12
|
4.3
|
45.6
|
0.2
|
OE2
|
B:GLU100
|
4.3
|
58.9
|
1.0
|
N
|
B:VAL53
|
4.3
|
35.2
|
1.0
|
C2'
|
D:A11
|
4.3
|
51.5
|
1.0
|
CB
|
B:ASP52
|
4.4
|
33.8
|
1.0
|
CA
|
B:ASP52
|
4.6
|
30.6
|
1.0
|
OP3
|
D:U12
|
4.7
|
54.7
|
0.2
|
CD
|
B:GLU100
|
4.7
|
57.7
|
1.0
|
C5'
|
D:A11
|
4.7
|
45.0
|
1.0
|
O
|
B:HOH446
|
4.8
|
37.0
|
1.0
|
CA
|
B:ASP126
|
4.8
|
32.5
|
1.0
|
C
|
B:ASP126
|
4.9
|
41.8
|
1.0
|
NZ
|
B:LYS155
|
4.9
|
58.1
|
1.0
|
|
Reference:
J.Wu,
N.L.Samara,
I.Kuraoka,
W.Yang.
Evolution of Inosine-Specific Endonuclease V From Bacterial Dnase to Eukaryotic Rnase. Mol.Cell V. 76 44 2019.
ISSN: ISSN 1097-2765
PubMed: 31444105
DOI: 10.1016/J.MOLCEL.2019.06.046
Page generated: Sun Oct 6 05:47:26 2024
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