Atomistry » Manganese » PDB 6oe2-6q9f » 6ozm
Atomistry »
  Manganese »
    PDB 6oe2-6q9f »
      6ozm »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy