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Magnesium in PDB 6ozs: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+

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 90 Min Soak in 10 Mm MG2+, PDB code: 6ozs 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) 36.25 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.086, 73.257, 155.704, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.6

Other elements in 6ozs:

The structure of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+ also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+ (pdb code 6ozs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+, PDB code: 6ozs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6ozs

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Magnesium binding site 1 out of 6 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 90 Min Soak in 10 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:55.1
occ:1.00
 OD1 A:ASP240 1.8 67.5 1.0
OP1 C:U318 1.9 0.6 1.0
O A:HOH411 2.0 56.1 1.0
OP3 C:U318 2.1 65.3 1.0
OD2 A:ASP52 2.2 58.6 1.0
O A:HOH414 2.4 56.2 1.0
P C:U318 2.5 66.5 1.0
CG A:ASP240 3.0 59.9 1.0
CG A:ASP52 3.1 57.5 1.0
OD1 A:ASP52 3.4 53.4 1.0
MG A:MG310 3.5 65.7 1.0
OP2 C:U318 3.6 63.7 1.0
O5' C:U318 3.6 69.2 1.0
MG C:MG401 3.7 71.4 0.9
CB A:ASP240 3.7 57.4 1.0
OD2 A:ASP126 3.8 56.4 1.0
C5' C:U318 3.9 78.4 1.0
OD2 A:ASP240 4.0 57.0 1.0
OP2 C:A319 4.1 78.4 1.0
O C:HOH503 4.2 65.3 1.0
O A:HOH425 4.2 72.7 1.0
O A:VAL53 4.3 56.3 1.0
CA A:ASP240 4.4 51.6 1.0
CB A:ASP52 4.5 56.4 1.0
OG A:SER54 4.6 74.5 1.0
O3' c:A304 4.7 58.6 1.0
O A:HOH402 4.7 55.0 1.0
O C:HOH501 4.9 75.2 1.0

Magnesium binding site 2 out of 6 in 6ozs

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Magnesium binding site 2 out of 6 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 90 Min Soak in 10 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:65.7
occ:1.00
 OP1 C:U318 1.9 0.6 1.0
O3' c:A304 2.0 58.6 1.0
O c:HOH402 2.1 46.0 1.0
O A:HOH402 2.2 55.0 1.0
OD1 A:ASP52 2.2 53.4 1.0
OD2 A:ASP126 2.3 56.4 1.0
P C:U318 3.0 66.5 1.0
CG A:ASP126 3.3 58.2 1.0
CG A:ASP52 3.3 57.5 1.0
C3' c:A304 3.3 50.4 1.0
O2' c:A304 3.4 58.1 1.0
OP2 C:U318 3.5 63.7 1.0
O5' C:U318 3.5 69.2 1.0
C5' C:U318 3.5 78.4 1.0
MG A:MG301 3.5 55.1 1.0
OD2 A:ASP52 3.8 58.6 1.0
C2' c:A304 3.8 51.5 1.0
CB A:ASP126 3.9 46.0 1.0
O A:VAL53 3.9 56.3 1.0
O A:HOH414 4.0 56.2 1.0
C4' c:A304 4.1 48.1 1.0
OD1 A:ASP126 4.2 70.2 1.0
OP3 C:U318 4.2 65.3 1.0
OE2 A:GLU100 4.2 62.3 0.7
N A:VAL53 4.4 57.0 1.0
O A:ASP126 4.4 57.4 1.0
O A:HOH411 4.4 56.1 1.0
OE1 A:GLU100 4.6 45.3 0.7
CB A:ASP52 4.6 56.4 1.0
NZ A:LYS155 4.6 52.7 1.0
CA A:ASP52 4.8 49.4 1.0
CD A:GLU100 4.9 54.2 0.6
C A:VAL53 4.9 57.0 1.0
C5' c:A304 4.9 48.8 1.0
C4' C:U318 5.0 75.2 1.0

Magnesium binding site 3 out of 6 in 6ozs

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Magnesium binding site 3 out of 6 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 90 Min Soak in 10 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:79.3
occ:1.00
 OD1 B:ASP240 1.8 0.5 1.0
OP1 D:U318 1.9 0.2 1.0
OP3 D:U318 2.2 87.2 1.0
OD2 B:ASP52 2.3 73.7 0.9
P D:U318 2.5 97.8 1.0
O B:HOH404 2.8 64.3 1.0
CG B:ASP240 3.0 79.5 1.0
CG B:ASP52 3.2 72.5 1.0
OD1 B:ASP52 3.4 74.2 1.0
O D:HOH501 3.6 70.8 1.0
OP2 D:U318 3.6 92.6 1.0
O5' D:U318 3.6 96.8 1.0
CB B:ASP240 3.8 73.2 1.0
OD2 B:ASP126 3.8 77.7 0.8
C5' D:U318 4.0 0.3 1.0
OD2 B:ASP240 4.0 73.6 1.0
O B:VAL53 4.1 86.6 1.0
MG D:MG401 4.1 91.9 0.9
MG B:MG304 4.2 81.4 1.0
OP2 D:A319 4.3 90.2 1.0
CA B:ASP240 4.4 76.4 1.0
O B:HOH401 4.4 68.4 1.0
OG B:SER54 4.5 89.5 1.0
CB B:ASP52 4.6 73.2 1.0
O3' d:A304 4.7 81.5 1.0
C B:VAL53 4.9 82.7 1.0
OP1 D:A319 4.9 0.0 1.0
NE B:ARG244 5.0 77.1 0.8

Magnesium binding site 4 out of 6 in 6ozs

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Magnesium binding site 4 out of 6 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 90 Min Soak in 10 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:81.4
occ:1.00
 O B:HOH401 2.0 68.4 1.0
O3' d:A304 2.1 81.5 1.0
OD1 B:ASP52 2.3 74.2 1.0
OD2 B:ASP126 2.4 77.7 0.8
OP1 D:U318 2.5 0.2 1.0
CG B:ASP126 3.1 74.1 0.8
O2' d:A304 3.1 84.2 1.0
C3' d:A304 3.3 86.9 1.0
CG B:ASP52 3.5 72.5 1.0
P D:U318 3.6 97.8 1.0
CB B:ASP126 3.6 61.4 1.0
C2' d:A304 3.7 88.5 1.0
OE1 B:GLU100 3.8 65.0 0.7
O B:ASP126 3.9 76.2 1.0
OP2 D:U318 3.9 92.6 1.0
C4' d:A304 3.9 87.2 1.0
OD1 B:ASP126 3.9 82.1 1.0
C5' D:U318 4.1 0.3 1.0
O5' D:U318 4.1 96.8 1.0
OD2 B:ASP52 4.1 73.7 0.9
O B:VAL53 4.1 86.6 1.0
MG B:MG301 4.2 79.3 1.0
OE2 B:GLU100 4.2 81.1 0.8
N B:VAL53 4.4 76.3 1.0
CD B:GLU100 4.5 74.0 0.6
CB B:ASP52 4.6 73.2 1.0
C B:ASP126 4.7 66.7 1.0
CA B:ASP126 4.8 61.0 1.0
C5' d:A304 4.8 89.2 1.0
O B:HOH404 4.8 64.3 1.0
CA B:ASP52 4.8 67.8 1.0
OP3 D:U318 4.8 87.2 1.0
C1' d:A304 5.0 90.7 1.0
NZ B:LYS155 5.0 80.5 1.0

Magnesium binding site 5 out of 6 in 6ozs

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Magnesium binding site 5 out of 6 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 90 Min Soak in 10 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:71.4
occ:0.95
 O C:HOH503 2.1 65.3 1.0
O C:HOH501 2.1 75.2 1.0
O C:HOH502 2.1 90.2 1.0
OP2 C:A319 2.1 78.4 1.0
OP3 C:U318 2.1 65.3 1.0
P C:U318 3.5 66.5 1.0
P C:A319 3.6 80.7 1.0
MG A:MG301 3.7 55.1 1.0
OD1 A:ASP240 3.7 67.5 1.0
O5' C:U318 3.9 69.2 1.0
OP2 C:U318 4.1 63.7 1.0
O A:HOH411 4.1 56.1 1.0
O5' C:A319 4.4 79.2 1.0
O A:HOH425 4.4 72.7 1.0
NE A:ARG244 4.4 70.0 1.0
OP1 C:U318 4.4 0.6 1.0
CD A:ARG244 4.5 65.8 1.0
OD2 A:ASP240 4.5 57.0 1.0
C3' C:U318 4.5 74.0 1.0
OP1 C:A319 4.5 82.5 1.0
CG A:ASP240 4.5 59.9 1.0
O3' C:U318 4.5 76.4 1.0
C5' C:U318 4.7 78.4 1.0
N7 C:A319 4.8 84.2 1.0
O A:HOH414 4.8 56.2 1.0
C8 C:A319 4.9 85.7 1.0

Magnesium binding site 6 out of 6 in 6ozs

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Magnesium binding site 6 out of 6 in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After A 90 Min Soak in 10 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 90 Min Soak in 10 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:91.9
occ:0.90
 O D:HOH501 2.0 70.8 1.0
OP3 D:U318 2.2 87.2 1.0
OP2 D:A319 2.4 90.2 1.0
P D:U318 3.4 97.8 1.0
O5' D:U318 3.7 96.8 1.0
OP2 D:U318 3.9 92.6 1.0
P D:A319 3.9 0.6 1.0
MG B:MG301 4.1 79.3 1.0
OD1 B:ASP240 4.3 0.5 1.0
C3' D:U318 4.4 96.5 1.0
N7 D:A319 4.4 0.8 1.0
OP1 D:U318 4.6 0.2 1.0
O5' D:A319 4.7 99.9 1.0
O3' D:U318 4.7 95.9 1.0
C8 D:A319 4.7 0.1 1.0
C5' D:U318 4.7 0.3 1.0
NE B:ARG244 4.8 77.1 0.8
C6 D:U318 4.8 95.4 1.0
OP1 D:A319 4.8 0.0 1.0
O B:HOH404 4.9 64.3 1.0
CD B:ARG244 5.0 80.0 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: Tue Oct 1 13:43:27 2024

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