Magnesium in PDB 6d9k: Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair

Protein crystallography data

The structure of Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair, PDB code: 6d9k was solved by Y.Liu, D.Esyunina, I.Olovnikov, M.Teplova, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.54 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.119, 119.130, 118.134, 90.00, 95.60, 90.00
R / Rfree (%) 19.5 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair (pdb code 6d9k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair, PDB code: 6d9k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6d9k

Go back to Magnesium Binding Sites List in 6d9k
Magnesium binding site 1 out of 2 in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:35.4
occ:1.00
OP1 C:A3 2.0 39.3 1.0
OP3 C:U1 2.0 35.8 1.0
O C:HOH205 2.1 33.6 1.0
O A:HOH970 2.1 34.4 1.0
OXT A:LEU777 2.3 40.7 1.0
O A:LEU777 2.3 36.6 1.0
C A:LEU777 2.7 41.5 1.0
P C:U1 3.2 32.6 1.0
P C:A3 3.3 34.7 1.0
OP1 C:U1 3.4 31.4 1.0
O3' C:U2 3.8 33.3 1.0
NZ A:LYS506 3.9 34.1 1.0
O5' C:U1 4.1 37.1 1.0
OE1 A:GLN478 4.1 36.0 1.0
C5' C:U1 4.1 35.0 1.0
NH2 A:ARG731 4.1 42.9 1.0
NE2 A:GLN478 4.1 34.4 1.0
OP2 C:U1 4.2 33.1 1.0
CA A:LEU777 4.2 37.0 1.0
OP2 C:A3 4.2 30.1 1.0
O A:HOH923 4.2 38.8 1.0
O5' C:A3 4.3 33.5 1.0
NE A:ARG731 4.4 48.2 1.0
O C:HOH211 4.4 49.5 1.0
CD A:GLN478 4.6 34.2 1.0
O A:HOH961 4.6 43.4 1.0
CZ A:ARG731 4.7 45.9 1.0
CB A:LEU777 4.7 36.0 1.0
CE A:LYS506 5.0 31.6 1.0

Magnesium binding site 2 out of 2 in 6d9k

Go back to Magnesium Binding Sites List in 6d9k
Magnesium binding site 2 out of 2 in the Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Rsago Complex with Guide Rna and Target Dna Containing A-G Non-Canonical Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg101

b:37.1
occ:1.00
OP1 H:A3 1.9 38.8 1.0
O H:HOH204 1.9 32.9 1.0
OP3 H:U1 2.0 35.4 1.0
O F:HOH955 2.1 32.6 1.0
O F:LEU777 2.2 45.0 1.0
OXT F:LEU777 2.3 48.0 1.0
C F:LEU777 2.6 49.1 1.0
P H:U1 3.2 35.6 1.0
P H:A3 3.3 39.5 1.0
OP1 H:U1 3.5 36.8 1.0
O3' H:U2 3.7 40.0 1.0
NZ F:LYS506 4.0 42.5 1.0
O5' H:U1 4.1 38.3 1.0
NH2 F:ARG731 4.1 48.8 1.0
C5' H:U1 4.1 37.8 1.0
CA F:LEU777 4.1 41.6 1.0
OE1 F:GLN478 4.1 38.9 1.0
NE2 F:GLN478 4.2 34.2 1.0
O5' H:A3 4.2 40.6 1.0
OP2 H:U1 4.3 38.6 1.0
OP2 H:A3 4.3 36.1 1.0
NE F:ARG731 4.3 54.5 1.0
O F:HOH921 4.4 44.7 1.0
CD F:GLN478 4.6 36.7 1.0
O F:HOH952 4.6 49.4 1.0
CB F:LEU777 4.7 39.5 1.0
CZ F:ARG731 4.7 50.1 1.0
CE F:LYS506 4.9 39.4 1.0

Reference:

Y.Liu, D.Esyunina, I.Olovnikov, M.Teplova, A.Kulbachinskiy, A.A.Aravin, D.J.Patel. Accommodation of Helical Imperfections in Rhodobacter Sphaeroides Argonaute Ternary Complexes with Guide Rna and Target Dna. Cell Rep V. 24 453 2018.
ISSN: ESSN 2211-1247
PubMed: 29996105
DOI: 10.1016/J.CELREP.2018.06.021
Page generated: Mon Dec 14 22:34:25 2020

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