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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

Go back to 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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