Manganese in PDB 6ozl: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in 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 2 Min Soak in MN2+, PDB code: 6ozl
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)
|
35.82 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.621,
72.519,
155.764,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.6 /
21.7
|
Other elements in 6ozl:
The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in MN2+ also contains other interesting chemical elements:
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 2 Min Soak in MN2+
(pdb code 6ozl). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 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 2 Min Soak in MN2+, PDB code: 6ozl:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6ozl
Go back to
Manganese Binding Sites List in 6ozl
Manganese binding site 1 out
of 4 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in 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 2 Min Soak in MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn301
b:39.6
occ:1.00
|
OD1
|
A:ASP240
|
2.0
|
50.5
|
1.0
|
OP1
|
C:U12
|
2.1
|
33.8
|
1.0
|
O
|
C:HOH205
|
2.2
|
39.7
|
1.0
|
O
|
A:HOH420
|
2.3
|
35.4
|
1.0
|
OD2
|
A:ASP52
|
2.3
|
40.9
|
1.0
|
O
|
C:HOH201
|
2.5
|
36.2
|
1.0
|
CG
|
A:ASP240
|
3.0
|
54.4
|
1.0
|
CG
|
A:ASP52
|
3.1
|
45.2
|
1.0
|
OD1
|
A:ASP52
|
3.3
|
36.1
|
1.0
|
P
|
C:U12
|
3.4
|
36.5
|
1.0
|
CB
|
A:ASP240
|
3.8
|
34.3
|
1.0
|
MN
|
A:MN302
|
4.0
|
42.1
|
1.0
|
OD2
|
A:ASP240
|
4.0
|
49.1
|
1.0
|
O5'
|
C:U12
|
4.1
|
45.6
|
1.0
|
OP2
|
C:U12
|
4.1
|
29.7
|
1.0
|
O
|
A:HOH472
|
4.2
|
42.5
|
1.0
|
OP2
|
C:A13
|
4.3
|
43.2
|
1.0
|
OD2
|
A:ASP126
|
4.4
|
45.0
|
1.0
|
C5'
|
C:U12
|
4.4
|
43.2
|
1.0
|
CA
|
A:ASP240
|
4.4
|
36.8
|
1.0
|
O
|
A:VAL53
|
4.5
|
41.5
|
1.0
|
CB
|
A:ASP52
|
4.5
|
39.9
|
1.0
|
O3'
|
C:A11
|
4.6
|
43.0
|
1.0
|
OG
|
A:SER54
|
4.6
|
52.1
|
1.0
|
CG
|
A:ASP126
|
4.8
|
42.4
|
1.0
|
O
|
A:HOH415
|
4.9
|
37.5
|
1.0
|
NZ
|
A:LYS155
|
4.9
|
45.7
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6ozl
Go back to
Manganese Binding Sites List in 6ozl
Manganese binding site 2 out
of 4 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in 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 2 Min Soak in MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn302
b:42.1
occ:1.00
|
OD1
|
A:ASP52
|
2.1
|
36.1
|
1.0
|
OD2
|
A:ASP126
|
2.1
|
45.0
|
1.0
|
O
|
A:HOH415
|
2.3
|
37.5
|
1.0
|
O3'
|
C:A11
|
2.4
|
43.0
|
1.0
|
OP1
|
C:U12
|
2.5
|
33.8
|
1.0
|
O
|
A:HOH411
|
2.5
|
39.9
|
1.0
|
P
|
C:U12
|
3.0
|
36.5
|
1.0
|
CG
|
A:ASP126
|
3.1
|
42.4
|
1.0
|
CG
|
A:ASP52
|
3.3
|
45.2
|
1.0
|
CB
|
A:ASP126
|
3.5
|
33.4
|
1.0
|
C3'
|
C:A11
|
3.6
|
31.9
|
1.0
|
O2'
|
C:A11
|
3.9
|
39.4
|
1.0
|
OD2
|
A:ASP52
|
3.9
|
40.9
|
1.0
|
MN
|
A:MN301
|
4.0
|
39.6
|
1.0
|
C4'
|
C:A11
|
4.0
|
33.1
|
1.0
|
O
|
A:VAL53
|
4.0
|
41.5
|
1.0
|
O5'
|
C:U12
|
4.0
|
45.6
|
1.0
|
OP2
|
C:U12
|
4.1
|
29.7
|
1.0
|
C5'
|
C:U12
|
4.1
|
43.2
|
1.0
|
O
|
A:ASP126
|
4.2
|
49.5
|
1.0
|
OD1
|
A:ASP126
|
4.2
|
49.1
|
1.0
|
N
|
A:VAL53
|
4.2
|
35.7
|
1.0
|
O
|
C:HOH205
|
4.3
|
39.7
|
1.0
|
OE1
|
A:GLU100
|
4.3
|
55.8
|
1.0
|
C2'
|
C:A11
|
4.3
|
33.3
|
1.0
|
OE2
|
A:GLU100
|
4.4
|
68.7
|
1.0
|
CB
|
A:ASP52
|
4.5
|
39.9
|
1.0
|
CA
|
A:ASP52
|
4.5
|
33.1
|
1.0
|
C5'
|
C:A11
|
4.6
|
37.7
|
1.0
|
O
|
A:HOH420
|
4.7
|
35.4
|
1.0
|
C
|
A:ASP126
|
4.8
|
44.8
|
1.0
|
CA
|
A:ASP126
|
4.8
|
36.5
|
1.0
|
CD
|
A:GLU100
|
4.8
|
66.2
|
1.0
|
NZ
|
A:LYS155
|
4.9
|
45.7
|
1.0
|
C
|
A:ASP52
|
4.9
|
33.9
|
1.0
|
C
|
A:VAL53
|
4.9
|
36.1
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6ozl
Go back to
Manganese Binding Sites List in 6ozl
Manganese binding site 3 out
of 4 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in 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 2 Min Soak in MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn301
b:43.4
occ:1.00
|
OD1
|
B:ASP240
|
2.1
|
48.2
|
1.0
|
OP1
|
D:U12
|
2.2
|
44.7
|
1.0
|
OD2
|
B:ASP52
|
2.2
|
47.4
|
1.0
|
O
|
D:HOH206
|
2.3
|
42.4
|
1.0
|
O
|
B:HOH412
|
2.3
|
36.3
|
1.0
|
O
|
D:HOH207
|
2.5
|
45.7
|
1.0
|
CG
|
B:ASP52
|
3.1
|
39.2
|
1.0
|
CG
|
B:ASP240
|
3.2
|
40.4
|
1.0
|
OD1
|
B:ASP52
|
3.3
|
35.3
|
1.0
|
P
|
D:U12
|
3.5
|
45.8
|
1.0
|
CB
|
B:ASP240
|
3.8
|
33.5
|
1.0
|
MN
|
B:MN302
|
4.0
|
42.4
|
1.0
|
OD2
|
B:ASP126
|
4.0
|
48.7
|
1.0
|
O5'
|
D:U12
|
4.1
|
49.0
|
1.0
|
OD2
|
B:ASP240
|
4.2
|
47.2
|
1.0
|
OP2
|
D:U12
|
4.2
|
46.0
|
1.0
|
O
|
B:HOH441
|
4.2
|
57.4
|
1.0
|
C5'
|
D:U12
|
4.4
|
46.7
|
1.0
|
CA
|
B:ASP240
|
4.4
|
37.3
|
1.0
|
O
|
B:VAL53
|
4.4
|
34.2
|
1.0
|
OP2
|
D:A13
|
4.4
|
47.1
|
1.0
|
CB
|
B:ASP52
|
4.5
|
35.0
|
1.0
|
OG
|
B:SER54
|
4.6
|
55.4
|
1.0
|
O3'
|
D:A11
|
4.7
|
46.1
|
1.0
|
O
|
B:HOH401
|
4.7
|
36.8
|
1.0
|
CG
|
B:ASP126
|
5.0
|
49.7
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6ozl
Go back to
Manganese Binding Sites List in 6ozl
Manganese binding site 4 out
of 4 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 2 Min Soak in 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 2 Min Soak in MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn302
b:42.4
occ:1.00
|
OD2
|
B:ASP126
|
2.1
|
48.7
|
1.0
|
OD1
|
B:ASP52
|
2.1
|
35.3
|
1.0
|
O
|
B:HOH401
|
2.3
|
36.8
|
1.0
|
O
|
B:HOH406
|
2.4
|
39.0
|
1.0
|
O3'
|
D:A11
|
2.6
|
46.1
|
1.0
|
OP1
|
D:U12
|
2.6
|
44.7
|
1.0
|
CG
|
B:ASP126
|
3.1
|
49.7
|
1.0
|
P
|
D:U12
|
3.2
|
45.8
|
1.0
|
CG
|
B:ASP52
|
3.3
|
39.2
|
1.0
|
CB
|
B:ASP126
|
3.5
|
37.7
|
1.0
|
C3'
|
D:A11
|
3.8
|
44.1
|
1.0
|
OD2
|
B:ASP52
|
4.0
|
47.4
|
1.0
|
MN
|
B:MN301
|
4.0
|
43.4
|
1.0
|
O2'
|
D:A11
|
4.0
|
45.9
|
1.0
|
O
|
B:VAL53
|
4.1
|
34.2
|
1.0
|
OE2
|
B:GLU100
|
4.1
|
67.3
|
1.0
|
O
|
D:HOH206
|
4.2
|
42.4
|
1.0
|
C5'
|
D:U12
|
4.2
|
46.7
|
1.0
|
O
|
B:ASP126
|
4.2
|
53.6
|
1.0
|
C4'
|
D:A11
|
4.2
|
44.2
|
1.0
|
OE1
|
B:GLU100
|
4.2
|
67.5
|
1.0
|
O5'
|
D:U12
|
4.2
|
49.0
|
1.0
|
OD1
|
B:ASP126
|
4.2
|
51.1
|
1.0
|
N
|
B:VAL53
|
4.2
|
36.9
|
1.0
|
OP2
|
D:U12
|
4.2
|
46.0
|
1.0
|
CB
|
B:ASP52
|
4.5
|
35.0
|
1.0
|
C2'
|
D:A11
|
4.5
|
47.3
|
1.0
|
CA
|
B:ASP52
|
4.6
|
34.6
|
1.0
|
CD
|
B:GLU100
|
4.6
|
69.6
|
1.0
|
O
|
B:HOH412
|
4.8
|
36.3
|
1.0
|
C5'
|
D:A11
|
4.8
|
43.1
|
1.0
|
CA
|
B:ASP126
|
4.8
|
35.7
|
1.0
|
C
|
B:ASP126
|
4.8
|
47.0
|
1.0
|
C
|
B:ASP52
|
5.0
|
31.2
|
1.0
|
C
|
B:VAL53
|
5.0
|
35.5
|
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
|