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Manganese in PDB 6ozo: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 30 Min Soak in 10 Mm MN2+, PDB code: 6ozo 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) 43.01 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.577, 72.422, 155.643, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.2

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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 30 Min Soak in 10 Mm MN2+ (pdb code 6ozo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 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 30 Min Soak in 10 Mm MN2+, PDB code: 6ozo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 6ozo

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Manganese binding site 1 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:37.6
occ:1.00
 OP1 C:U12 2.0 37.0 0.4
OP1 C:U12 2.0 39.7 0.6
OD1 A:ASP240 2.1 37.4 1.0
O C:HOH205 2.2 30.8 1.0
OD2 A:ASP52 2.2 45.2 1.0
O A:HOH429 2.4 32.3 1.0
OP3 C:U12 2.5 43.2 0.6
O C:HOH203 2.5 22.9 0.4
P C:U12 2.8 34.5 0.6
CG A:ASP52 3.1 40.9 1.0
OD1 A:ASP52 3.2 37.1 1.0
CG A:ASP240 3.3 50.7 1.0
P C:U12 3.4 37.4 0.4
O A:HOH448 3.7 23.8 0.6
MN C:MN101 3.7 36.3 1.0
CB A:ASP240 3.8 35.2 1.0
OP2 C:U12 3.9 33.2 0.6
OD2 A:ASP126 3.9 46.8 1.0
O5' C:U12 4.0 42.0 0.6
O5' C:U12 4.1 39.5 0.4
OP2 C:U12 4.2 33.4 0.4
C5' C:U12 4.2 39.9 0.4
MN C:MN102 4.3 36.8 0.6
OP2 C:A13 4.3 43.0 1.0
C5' C:U12 4.3 40.1 0.6
OD2 A:ASP240 4.3 51.0 1.0
O A:HOH494 4.3 38.1 1.0
CA A:ASP240 4.3 34.9 1.0
O A:VAL53 4.4 40.7 1.0
O3' C:A11 4.5 45.3 1.0
CB A:ASP52 4.5 35.4 1.0
OG A:SER54 4.5 42.2 1.0
O A:HOH407 4.7 29.4 1.0
CG A:ASP126 4.9 40.6 1.0

Manganese binding site 2 out of 12 in 6ozo

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Manganese binding site 2 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:61.8
occ:0.50
 OE1 A:GLN46 2.3 79.8 1.0
O A:HOH479 2.4 47.3 1.0
O A:HOH455 2.8 46.9 1.0
O A:HOH470 2.8 62.9 1.0
O A:LEU45 3.2 37.7 1.0
CD A:GLN46 3.2 70.8 1.0
O A:TYR72 3.8 43.9 1.0
NE2 A:GLN46 4.0 75.1 1.0
CG A:GLN46 4.2 52.2 1.0
C A:LEU45 4.2 34.9 1.0
N A:GLY44 4.5 34.5 1.0
CD A:PRO73 4.5 39.0 1.0
CA A:GLN46 4.7 28.4 1.0
N A:LEU45 4.8 26.9 1.0
C A:TYR72 4.8 40.6 1.0
O A:HOH486 4.9 61.6 1.0
N A:GLN46 4.9 28.2 1.0
C A:GLY44 5.0 29.1 1.0

Manganese binding site 3 out of 12 in 6ozo

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Manganese binding site 3 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:43.1
occ:0.95
 OD1 B:ASP240 2.1 50.1 1.0
OP1 D:U12 2.1 45.3 0.6
OP1 D:U12 2.2 45.8 0.4
OD2 B:ASP52 2.2 53.2 1.0
O D:HOH207 2.3 33.1 0.9
O B:HOH422 2.3 35.8 0.9
OP3 D:U12 2.4 59.2 0.6
O D:HOH206 2.5 33.9 0.4
P D:U12 2.9 46.8 0.6
CG B:ASP52 3.2 41.7 1.0
CG B:ASP240 3.2 48.5 1.0
OD1 B:ASP52 3.4 33.5 1.0
P D:U12 3.5 46.1 0.4
O D:HOH201 3.5 30.0 0.6
CB B:ASP240 3.8 41.1 1.0
MN B:MN302 3.9 38.8 0.9
OP2 D:U12 4.0 45.6 0.6
OD2 B:ASP126 4.0 47.3 1.0
O5' D:U12 4.0 49.9 0.6
O5' D:U12 4.2 49.0 0.4
OP2 D:U12 4.2 44.8 0.4
OD2 B:ASP240 4.2 48.8 1.0
C5' D:U12 4.3 48.5 0.6
C5' D:U12 4.3 48.8 0.4
OP2 D:A13 4.3 47.8 1.0
MN D:MN101 4.3 57.3 0.6
CA B:ASP240 4.4 41.5 1.0
OG B:SER54 4.4 52.2 1.0
O B:VAL53 4.5 40.7 1.0
CB B:ASP52 4.6 32.4 1.0
O B:HOH401 4.6 30.1 0.9
O3' D:A11 4.7 53.5 1.0

Manganese binding site 4 out of 12 in 6ozo

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Manganese binding site 4 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:38.8
occ:0.90
 OD1 B:ASP52 2.1 33.5 1.0
O B:HOH431 2.1 38.5 0.9
OD2 B:ASP126 2.2 47.3 1.0
O B:HOH401 2.3 30.1 0.9
O3' D:A11 2.3 53.5 1.0
OP1 D:U12 2.4 45.3 0.6
OP1 D:U12 2.4 45.8 0.4
P D:U12 3.0 46.1 0.4
CG B:ASP126 3.2 49.1 1.0
CG B:ASP52 3.3 41.7 1.0
C3' D:A11 3.5 50.8 1.0
P D:U12 3.6 46.8 0.6
O2' D:A11 3.6 60.7 1.0
CB B:ASP126 3.6 34.5 1.0
OD2 B:ASP52 3.9 53.2 1.0
MN B:MN301 3.9 43.1 0.9
O5' D:U12 4.0 49.0 0.4
O D:HOH207 4.0 33.1 0.9
C5' D:U12 4.0 48.5 0.6
C5' D:U12 4.0 48.8 0.4
OP2 D:U12 4.0 45.6 0.6
C4' D:A11 4.1 43.5 1.0
O5' D:U12 4.1 49.9 0.6
O B:VAL53 4.1 40.7 1.0
C2' D:A11 4.1 59.5 1.0
OP2 D:U12 4.1 44.8 0.4
O B:ASP126 4.2 51.5 1.0
OE2 B:GLU100 4.2 53.8 1.0
OE1 B:GLU100 4.2 48.2 1.0
OD1 B:ASP126 4.3 53.6 1.0
N B:VAL53 4.4 38.0 1.0
CB B:ASP52 4.5 32.4 1.0
CD B:GLU100 4.7 54.2 1.0
CA B:ASP52 4.7 33.6 1.0
OP3 D:U12 4.7 59.2 0.6
C5' D:A11 4.8 42.5 1.0
O B:HOH422 4.8 35.8 0.9
CA B:ASP126 4.9 32.7 1.0
NZ B:LYS155 4.9 54.3 1.0
C B:ASP126 4.9 41.6 1.0

Manganese binding site 5 out of 12 in 6ozo

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Manganese binding site 5 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:49.9
occ:0.30
 MN B:MN303 0.0 49.9 0.3
NE2 B:GLN46 2.6 49.8 0.5
MN B:MN303 2.7 78.4 0.4
OE1 B:GLN46 2.7 46.5 0.5
O B:HOH408 2.8 66.5 1.0
O B:TYR72 2.8 47.6 1.0
O B:HOH426 2.8 53.8 1.0
CD B:GLN46 2.9 45.8 0.5
O B:LEU45 3.5 34.8 1.0
CD B:PRO73 3.7 42.8 1.0
C B:TYR72 3.8 46.7 1.0
CG B:GLN46 4.2 40.8 0.5
N B:PRO73 4.2 47.1 1.0
CG B:GLN46 4.4 40.2 0.5
CA B:GLN46 4.4 34.0 0.5
CA B:GLN46 4.4 34.0 0.5
C B:LEU45 4.5 36.0 1.0
O B:HOH449 4.7 56.1 1.0
CB B:GLN46 4.7 37.5 0.5
CB B:GLN46 4.7 37.5 0.5
NE2 B:GLN46 4.7 54.0 0.5
N B:GLN46 5.0 31.8 1.0

Manganese binding site 6 out of 12 in 6ozo

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Manganese binding site 6 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 6 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:78.4
occ:0.40
 MN B:MN303 0.0 78.4 0.4
OE1 B:GLN46 2.3 46.5 0.5
MN B:MN303 2.7 49.9 0.3
O B:HOH408 3.0 66.5 1.0
CD B:GLN46 3.4 45.8 0.5
O B:TYR72 3.5 47.6 1.0
NE2 B:GLN46 3.9 49.8 0.5
OE2 B:GLU74 3.9 70.0 1.0
NE2 B:GLN46 4.1 54.0 0.5
OE1 B:GLU74 4.2 58.6 1.0
CD B:GLU74 4.5 61.4 1.0
C B:TYR72 4.6 46.7 1.0
CD B:PRO73 4.7 42.8 1.0
CG B:GLN46 4.7 40.8 0.5
CB B:GLN46 4.9 37.5 0.5
CB B:GLN46 4.9 37.5 0.5
CG B:GLN46 5.0 40.2 0.5

Manganese binding site 7 out of 12 in 6ozo

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Manganese binding site 7 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 7 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn101

b:36.3
occ:1.00
 OD2 A:ASP126 2.1 46.8 1.0
OD1 A:ASP52 2.1 37.1 1.0
O3' C:A11 2.2 45.3 1.0
O A:HOH407 2.3 29.4 1.0
OP1 C:U12 2.4 39.7 0.6
O A:HOH415 2.4 32.2 1.0
OP1 C:U12 2.4 37.0 0.4
P C:U12 2.8 37.4 0.4
CG A:ASP126 3.1 40.6 1.0
CG A:ASP52 3.3 40.9 1.0
C3' C:A11 3.4 32.2 1.0
O2' C:A11 3.4 56.4 1.0
P C:U12 3.5 34.5 0.6
CB A:ASP126 3.7 29.6 1.0
MN A:MN301 3.7 37.6 1.0
O5' C:U12 3.8 39.5 0.4
C5' C:U12 3.9 39.9 0.4
OP2 C:U12 3.9 33.2 0.6
OD2 A:ASP52 3.9 45.2 1.0
C2' C:A11 3.9 43.7 1.0
O C:HOH205 3.9 30.8 1.0
C5' C:U12 4.0 40.1 0.6
C4' C:A11 4.0 33.6 1.0
OP2 C:U12 4.0 33.4 0.4
O A:VAL53 4.1 40.7 1.0
O5' C:U12 4.1 42.0 0.6
O A:ASP126 4.2 46.7 1.0
OD1 A:ASP126 4.2 45.9 1.0
N A:VAL53 4.3 27.4 1.0
OE1 A:GLU100 4.5 40.3 1.0
CB A:ASP52 4.5 35.4 1.0
OE2 A:GLU100 4.6 57.1 1.0
OP3 C:U12 4.6 43.2 0.6
CA A:ASP52 4.7 32.8 1.0
C5' C:A11 4.8 35.1 1.0
O A:HOH429 4.9 32.3 1.0
NZ A:LYS155 4.9 39.7 1.0
C A:ASP126 4.9 34.6 1.0
CA A:ASP126 4.9 33.3 1.0
C A:VAL53 5.0 34.4 1.0
CD A:GLU100 5.0 57.1 1.0

Manganese binding site 8 out of 12 in 6ozo

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Manganese binding site 8 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 8 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn102

b:36.8
occ:0.60
 O C:HOH203 1.9 22.9 0.4
OP2 C:A13 2.1 43.0 1.0
O A:HOH448 2.2 23.8 0.6
O C:HOH210 2.2 25.5 0.6
OP3 C:U12 2.3 43.2 0.6
O C:HOH216 2.3 42.8 0.6
O C:HOH215 2.3 28.7 0.6
P C:A13 3.5 43.8 1.0
P C:U12 3.5 34.5 0.6
O5' C:U12 3.8 42.0 0.6
O5' C:A13 4.0 51.4 1.0
O C:HOH201 4.2 39.8 1.0
O A:HOH429 4.2 32.3 1.0
OP2 C:U12 4.3 33.2 0.6
MN A:MN301 4.3 37.6 1.0
N7 C:A13 4.3 35.9 1.0
O5' C:U12 4.3 39.5 0.4
C3' C:U12 4.3 41.3 0.4
C8 C:A13 4.3 39.7 1.0
C3' C:U12 4.4 41.6 0.6
OD1 A:ASP240 4.4 37.4 1.0
O3' C:U12 4.4 42.7 0.4
OP2 C:U12 4.4 33.4 0.4
O3' C:U12 4.4 42.4 0.6
OP1 C:U12 4.5 37.0 0.4
OP1 C:U12 4.5 39.7 0.6
OP1 C:A13 4.5 47.5 1.0
P C:U12 4.6 37.4 0.4
C5' C:U12 4.7 39.9 0.4
C5' C:U12 4.7 40.1 0.6
NE A:ARG244 4.9 58.4 1.0
CD A:ARG244 5.0 61.9 1.0

Manganese binding site 9 out of 12 in 6ozo

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Manganese binding site 9 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 9 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn103

b:98.2
occ:1.00
 O C:HOH214 2.6 41.3 1.0
O C:HOH208 3.5 45.4 1.0
O4 C:U18 3.7 38.9 1.0
C4 C:U18 4.2 38.3 1.0
C5 C:U18 4.3 38.9 1.0
O6 C:G19 4.4 54.0 1.0
N7 C:G19 4.5 51.6 1.0

Manganese binding site 10 out of 12 in 6ozo

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Manganese binding site 10 out of 12 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 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 10 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 30 Min Soak in 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:57.3
occ:0.60
 O D:HOH206 2.0 33.9 0.4
O D:HOH205 2.0 63.7 0.6
O D:HOH211 2.0 42.4 0.6
O D:HOH201 2.2 30.0 0.6
OP2 D:A13 2.2 47.8 1.0
OP3 D:U12 2.3 59.2 0.6
P D:U12 3.5 46.8 0.6
P D:A13 3.6 52.4 1.0
O5' D:U12 3.7 49.9 0.6
O5' D:U12 4.0 49.0 0.4
N7 D:A13 4.0 54.2 1.0
OP2 D:U12 4.1 45.6 0.6
C3' D:U12 4.2 48.5 0.6
OP2 D:U12 4.2 44.8 0.4
C3' D:U12 4.2 48.8 0.4
O5' D:A13 4.2 57.2 1.0
C8 D:A13 4.2 57.6 1.0
MN B:MN301 4.3 43.1 0.9
P D:U12 4.4 46.1 0.4
O3' D:U12 4.4 50.5 0.6
O3' D:U12 4.4 50.7 0.4
O B:HOH422 4.4 35.8 0.9
OP1 D:U12 4.5 45.8 0.4
OP1 D:U12 4.5 45.3 0.6
C5' D:U12 4.5 48.5 0.6
C5' D:U12 4.6 48.8 0.4
OD1 B:ASP240 4.7 50.1 1.0
OP1 D:A13 4.7 54.2 1.0
C6 D:U12 4.9 50.2 1.0
C4' D:U12 4.9 50.0 0.6
C4' D:U12 5.0 50.1 0.4

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: Tue Dec 15 04:58:41 2020

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