Calcium in PDB 6ozk: Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After 68H Soak in CA2+

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 68H Soak in CA2+, PDB code: 6ozk 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) 35.54 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.823, 73.012, 155.229, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After 68H Soak in CA2+ (pdb code 6ozk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After 68H Soak in CA2+, PDB code: 6ozk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ozk

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Calcium 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 68H Soak in CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After 68H Soak in CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:58.2
occ:1.00
 OP1 C:U12 2.2 50.2 1.0
OD1 A:ASP240 2.3 62.9 1.0
OD2 A:ASP52 2.3 52.9 1.0
O A:HOH402 2.6 51.4 1.0
O C:HOH101 2.7 58.3 1.0
O A:HOH453 2.9 57.2 1.0
CG A:ASP52 3.1 54.8 1.0
OD1 A:ASP52 3.2 48.7 1.0
CG A:ASP240 3.4 62.2 1.0
P C:U12 3.5 50.2 1.0
NH2 A:ARG244 4.0 69.4 1.0
O5' C:U12 4.0 54.5 1.0
CB A:ASP240 4.0 47.2 1.0
OP2 C:U12 4.1 51.1 1.0
C5' C:U12 4.3 50.9 1.0
CA A:CA302 4.3 45.6 0.8
OD2 A:ASP240 4.4 70.9 1.0
OP2 C:A13 4.4 52.6 1.0
CB A:ASP52 4.5 49.5 1.0
OD2 A:ASP126 4.5 71.5 1.0
OG A:SER54 4.6 56.3 1.0
O3' C:A11 4.7 49.6 1.0
CA A:ASP240 4.7 39.3 1.0
O A:VAL53 4.8 47.5 1.0
CG A:ASP126 4.9 64.8 1.0
NZ A:LYS155 4.9 51.9 1.0

Calcium binding site 2 out of 4 in 6ozk

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Calcium 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 68H Soak in CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After 68H Soak in CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:45.6
occ:0.75
 OD1 A:ASP52 2.3 48.7 1.0
O C:HOH103 2.4 39.8 0.8
OD1 A:ASP126 2.6 73.6 1.0
O A:HOH405 2.6 42.0 0.8
O3' C:A11 2.7 49.6 1.0
OP1 C:U12 2.8 50.2 1.0
CG A:ASP126 3.1 64.8 1.0
P C:U12 3.4 50.2 1.0
CG A:ASP52 3.5 54.8 1.0
CB A:ASP126 3.5 50.7 1.0
O2' C:A11 3.8 53.3 1.0
C3' C:A11 3.9 41.2 1.0
O A:ASP126 3.9 58.5 1.0
OD2 A:ASP126 4.0 71.5 1.0
N A:VAL53 4.1 41.9 1.0
C5' C:U12 4.1 50.9 1.0
OD2 A:ASP52 4.1 52.9 1.0
O A:VAL53 4.2 47.5 1.0
O5' C:U12 4.2 54.5 1.0
C4' C:A11 4.3 39.2 1.0
OE2 A:GLU100 4.3 58.2 0.7
CA A:CA301 4.3 58.2 1.0
CA A:ASP52 4.4 43.6 1.0
OE1 A:GLU100 4.4 45.4 0.7
C2' C:A11 4.4 47.6 1.0
CB A:ASP52 4.5 49.5 1.0
OP2 C:U12 4.6 51.1 1.0
C A:ASP126 4.6 45.7 1.0
CA A:ASP126 4.7 43.0 1.0
CD A:GLU100 4.8 51.6 0.6
C A:ASP52 4.8 43.5 1.0
C A:VAL53 5.0 45.6 1.0
C5' C:A11 5.0 41.1 1.0
O A:HOH402 5.0 51.4 1.0

Calcium binding site 3 out of 4 in 6ozk

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Calcium 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 68H Soak in CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After 68H Soak in CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:52.5
occ:0.85
 OP1 D:U12 2.1 43.2 1.0
O B:HOH432 2.3 47.0 0.8
OD2 B:ASP52 2.3 52.6 0.9
OD1 B:ASP240 2.3 72.2 1.0
O B:HOH415 2.4 54.1 0.8
O D:HOH205 2.5 49.3 0.8
CG B:ASP52 3.2 53.3 1.0
OD1 B:ASP52 3.3 51.6 1.0
CG B:ASP240 3.4 67.8 1.0
P D:U12 3.4 54.2 1.0
O5' D:U12 4.0 58.0 1.0
CB B:ASP240 4.0 48.8 1.0
OP2 D:U12 4.1 53.7 1.0
CA B:CA302 4.1 50.1 0.8
C5' D:U12 4.3 55.0 1.0
OD2 B:ASP240 4.4 78.1 1.0
OD2 B:ASP126 4.4 77.0 1.0
OP2 D:A13 4.5 50.3 1.0
CB B:ASP52 4.6 45.2 1.0
O B:VAL53 4.6 49.5 1.0
O3' D:A11 4.6 52.7 1.0
CA B:ASP240 4.8 47.0 1.0
CG B:ASP126 4.8 65.7 0.8
OG B:SER54 4.9 54.8 1.0
NZ B:LYS155 5.0 65.5 1.0

Calcium binding site 4 out of 4 in 6ozk

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Calcium 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 68H Soak in CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Mus Musculus (Mm) Endonuclease V in Complex with A 23MER Rna Oligo Containing An Inosine After 68H Soak in CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:50.1
occ:0.80
 O B:HOH404 2.3 40.0 0.8
OD1 B:ASP52 2.3 51.6 1.0
O B:HOH435 2.4 54.9 0.8
OD1 B:ASP126 2.6 68.8 0.8
OP1 D:U12 2.7 43.2 1.0
O3' D:A11 2.8 52.7 1.0
CG B:ASP126 3.2 65.7 0.8
P D:U12 3.4 54.2 1.0
CG B:ASP52 3.5 53.3 1.0
CB B:ASP126 3.7 54.0 1.0
C3' D:A11 4.0 49.0 1.0
O B:VAL53 4.0 49.5 1.0
OD2 B:ASP126 4.0 77.0 1.0
N B:VAL53 4.0 41.4 1.0
OD2 B:ASP52 4.0 52.6 0.9
O2' D:A11 4.1 55.8 1.0
CA B:CA301 4.1 52.5 0.8
C5' D:U12 4.2 55.0 1.0
O B:ASP126 4.2 65.2 1.0
OE1 B:GLU100 4.3 48.4 0.7
O5' D:U12 4.3 58.0 1.0
OE2 B:GLU100 4.3 61.2 0.8
C4' D:A11 4.3 45.5 1.0
O B:HOH432 4.5 47.0 0.8
CA B:ASP52 4.5 45.3 1.0
OP2 D:U12 4.5 53.7 1.0
O B:HOH415 4.6 54.1 0.8
CB B:ASP52 4.6 45.2 1.0
C2' D:A11 4.6 55.3 1.0
CD B:GLU100 4.7 49.8 0.6
C B:ASP52 4.8 44.8 1.0
C B:VAL53 4.8 45.4 1.0
C B:ASP126 4.9 55.1 1.0
CA B:ASP126 4.9 50.4 1.0
CA B:VAL53 4.9 44.0 1.0
C5' D:A11 5.0 47.4 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: Sat Dec 12 07:24:42 2020

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