Atomistry » Magnesium » PDB 5erv-5f35 » 5ew7
Atomistry »
  Magnesium »
    PDB 5erv-5f35 »
      5ew7 »

Magnesium in PDB 5ew7: Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+

Protein crystallography data

The structure of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+, PDB code: 5ew7 was solved by D.R.Tomchick, D.W.Dodd, K.T.Gagnon, D.R.Corey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.20 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.134, 47.659, 59.495, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 25.8

Other elements in 5ew7:

The structure of Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+ also contains other interesting chemical elements:

Potassium (K) 4 atoms
Barium (Ba) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+ (pdb code 5ew7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+, PDB code: 5ew7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ew7

Go back to Magnesium Binding Sites List in 5ew7
Magnesium binding site 1 out of 4 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+


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 C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:47.0
occ:1.00
OP2 A:C13 2.2 27.5 1.0
H3' A:G12 2.7 26.3 1.0
H5 A:C13 2.8 19.4 1.0
O5' A:G12 3.5 24.3 1.0
P A:C13 3.5 27.3 1.0
O A:HOH217 3.6 34.0 1.0
C5 A:C13 3.6 16.1 1.0
C3' A:G12 3.6 21.9 1.0
H6 A:C13 3.7 19.5 1.0
H8 A:G12 3.7 21.4 1.0
OP2 A:G12 3.9 24.1 1.0
C8 A:G12 3.9 17.8 1.0
O3' A:G12 4.0 23.4 1.0
C6 A:C13 4.1 16.2 1.0
O5' A:C13 4.1 22.2 1.0
P A:G12 4.2 24.3 1.0
N7 A:G12 4.2 17.2 1.0
H2' A:G12 4.3 24.5 1.0
C5' A:G12 4.4 24.2 1.0
N9 A:G12 4.4 18.2 1.0
H5'' A:G12 4.5 29.0 1.0
C4' A:G12 4.5 22.4 1.0
C2' A:G12 4.5 20.4 1.0
H41 A:C13 4.6 20.3 1.0
O A:HOH211 4.6 23.4 1.0
OP1 A:G12 4.6 25.5 1.0
O A:HOH238 4.7 33.8 1.0
OP1 A:C13 4.7 28.7 1.0
C4 A:C13 4.8 16.4 1.0
C5 A:G12 4.9 16.5 1.0
C1' A:G12 4.9 19.2 1.0
O4' A:G12 4.9 20.4 1.0

Magnesium binding site 2 out of 4 in 5ew7

Go back to Magnesium Binding Sites List in 5ew7
Magnesium binding site 2 out of 4 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+


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 C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:40.0
occ:1.00
O A:HOH210 2.1 26.2 1.0
O A:HOH243 2.1 36.8 1.0
N7 A:G17 3.9 17.2 1.0
O A:HOH233 4.0 27.1 1.0
O B:HOH253 4.1 36.3 1.0
C8 A:G17 4.5 16.7 1.0
N7 A:G18 4.6 17.2 1.0
C5 A:G17 4.6 17.6 1.0
H8 A:G17 4.6 20.1 1.0
H41 A:C19 4.7 24.8 1.0
O B:HOH214 4.7 10.5 1.0
O6 A:G17 4.8 18.3 1.0
C6 A:G17 5.0 18.2 1.0

Magnesium binding site 3 out of 4 in 5ew7

Go back to Magnesium Binding Sites List in 5ew7
Magnesium binding site 3 out of 4 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+


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 C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:45.9
occ:1.00
O3' A:C2 2.1 48.2 1.0
H5' A:C3 2.5 49.1 1.0
P A:C3 3.2 45.4 1.0
O5' A:C3 3.3 39.5 1.0
C5' A:C3 3.3 40.9 1.0
H6 A:C3 3.6 50.3 1.0
O4' A:C3 3.7 43.1 1.0
H5'' A:C3 4.0 49.1 1.0
C4' A:C3 4.1 41.1 1.0
OP1 A:C3 4.1 45.6 1.0
OP2 A:C3 4.4 42.2 1.0
C6 A:C3 4.4 41.9 1.0
H4' A:C3 4.5 49.4 1.0
C1' A:C3 4.9 43.2 1.0

Magnesium binding site 4 out of 4 in 5ew7

Go back to Magnesium Binding Sites List in 5ew7
Magnesium binding site 4 out of 4 in the Crystal Structure of C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+


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 C9ORF72 Antisense Ccccgg Repeat Rna Associated with Lou Gehrig'S Disease and Frontotemporal Dementia, Crystallized with BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg105

b:49.6
occ:1.00
OP1 B:C14 2.1 22.8 1.0
O3' B:C13 2.9 17.1 1.0
P B:C14 3.1 22.4 1.0
H5' B:C14 3.7 22.2 1.0
H5'' B:C14 3.7 22.2 1.0
C5' B:C14 4.0 18.5 1.0
O5' B:C14 4.0 18.3 1.0
OP2 B:C14 4.3 22.0 1.0
C3' B:C13 4.3 17.3 1.0
H4' B:C13 4.4 21.8 1.0
H5'' B:C13 4.4 21.9 1.0
C4' B:C13 4.8 18.1 1.0
O2' B:C13 4.8 18.7 1.0
H3' B:C13 4.8 20.7 1.0

Reference:

D.W.Dodd, D.R.Tomchick, D.R.Corey, K.T.Gagnon. Pathogenic C9ORF72 Antisense Repeat Rna Forms A Double Helix with Tandem C:C Mismatches. Biochemistry V. 55 1283 2016.
ISSN: ISSN 0006-2960
PubMed: 26878348
DOI: 10.1021/ACS.BIOCHEM.6B00136
Page generated: Mon Dec 14 20:16:33 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy