Magnesium in PDB 6wy2: Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg

The structure of Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg, PDB code: 6wy2 was solved by B.Sekula, M.Ruszkowski, S.Mao, P.Haruehanroengra, J.Sheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.05 / 1.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.740, 30.425, 58.511, 90.00, 106.49, 90.00
R / Rfree (%)	18.7 / 21.8

The structure of Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg (pdb code 6wy2). 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 Rna-10MER: Ccgg(N4-Methyl-C)Gccgg, PDB code: 6wy2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg


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 Rna-10MER: Ccgg(N4-Methyl-C)Gccgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:30.3 occ:1.00 O A:HOH220 2.0 28.4 1.0 O A:HOH207 2.0 26.4 1.0 O A:HOH237 2.1 32.5 1.0 O A:HOH232 2.1 28.4 1.0 O A:HOH206 2.1 27.4 1.0 O A:HOH234 2.1 30.2 1.0 O A:HOH210 3.9 27.8 1.0 O A:HOH215 3.9 32.1 1.0 O A:HOH236 3.9 26.0 1.0 N7 A:G3 4.1 23.2 1.0 O6 A:G4 4.3 30.5 1.0 O A:HOH223 4.3 32.7 1.0 O6 A:G3 4.4 25.4 1.0 N7 A:G4 4.4 25.9 1.0 O A:HOH233 4.6 32.5 1.0 C5 A:G3 4.8 23.8 1.0 C41 A:B8T5 4.9 30.4 1.0 C6 A:G3 4.9 26.0 1.0 C8 A:G3 5.0 23.0 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg


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 Rna-10MER: Ccgg(N4-Methyl-C)Gccgg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:45.0 occ:1.00 O B:HOH229 2.1 44.7 1.0 O B:HOH214 2.1 41.8 1.0 O B:HOH213 2.1 43.9 1.0 O B:HOH218 2.1 44.1 1.0 O B:HOH209 3.9 42.5 1.0 O B:HOH204 4.2 48.9 1.0 O C:HOH214 4.3 33.9 1.0 O6 B:G10 4.5 38.5 1.0 O6 B:G9 4.6 32.7 1.0 N4 B:C8 4.6 28.0 1.0 C5 B:C8 4.7 34.4 1.0 O B:HOH211 4.7 37.2 1.0 N7 B:G9 4.8 36.6 1.0 N4 C:C1 4.9 34.0 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg


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 Rna-10MER: Ccgg(N4-Methyl-C)Gccgg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:35.8 occ:1.00 O B:HOH205 2.0 33.2 1.0 O B:HOH232 2.1 36.7 1.0 O B:HOH227 2.1 34.7 1.0 O B:HOH207 2.1 35.1 1.0 O B:HOH235 2.1 35.8 1.0 O B:HOH230 2.1 36.7 1.0 O B:HOH206 3.7 32.4 1.0 N7 B:G3 3.9 29.2 1.0 O B:HOH216 4.0 41.1 1.0 O C:HOH209 4.0 35.4 1.0 O B:HOH223 4.1 33.6 1.0 O B:HOH233 4.1 40.6 1.0 O C:HOH224 4.2 44.2 1.0 O6 B:G3 4.3 31.4 1.0 O C:HOH227 4.3 31.9 1.0 O6 B:G4 4.4 33.5 1.0 C5 B:G3 4.6 29.2 1.0 N7 B:G4 4.7 31.4 1.0 C6 B:G3 4.8 30.8 1.0 C8 B:G3 4.8 29.2 1.0 O B:HOH231 4.8 42.3 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg


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 Rna-10MER: Ccgg(N4-Methyl-C)Gccgg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:30.1 occ:1.00 O C:HOH208 2.0 30.1 1.0 O C:HOH225 2.1 31.0 1.0 O C:HOH210 2.1 26.9 1.0 O C:HOH228 2.1 29.7 1.0 O C:HOH226 2.1 30.4 1.0 O C:HOH217 2.1 28.5 1.0 O B:HOH219 3.7 23.8 1.0 O C:HOH205 3.9 27.9 1.0 O B:HOH233 4.0 40.6 1.0 O C:HOH227 4.1 31.9 1.0 O C:HOH220 4.1 41.3 1.0 N7 C:G3 4.2 28.5 1.0 O6 C:G4 4.3 26.3 1.0 O C:HOH206 4.3 26.4 1.0 O6 C:G3 4.3 27.4 1.0 N7 C:G4 4.4 27.8 1.0 C41 C:B8T5 4.8 29.8 1.0 C5 C:G3 4.8 27.2 1.0 C6 C:G3 4.9 28.1 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg


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 Rna-10MER: Ccgg(N4-Methyl-C)Gccgg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:50.4 occ:1.00 O D:HOH216 2.1 50.5 1.0 O D:HOH210 2.1 48.8 1.0 O D:HOH211 2.1 50.8 1.0 O D:HOH207 2.1 50.4 1.0 O D:HOH218 2.1 49.2 1.0 O D:HOH204 3.7 44.4 1.0 O E:HOH213 3.8 41.4 1.0 O D:HOH205 3.9 44.5 1.0 O D:HOH217 4.0 38.2 1.0 O E:HOH217 4.0 42.6 1.0 N7 D:G3 4.3 35.4 1.0 O D:HOH213 4.5 38.4 1.0 O6 D:G4 4.5 44.6 1.0 N7 D:G4 4.6 43.9 1.0 O6 D:G3 4.7 37.5 1.0 C41 D:B8T5 4.8 47.4 1.0 O E:HOH219 4.9 41.6 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Rna-10MER: Ccgg(N4-Methyl-C)Gccgg


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 Rna-10MER: Ccgg(N4-Methyl-C)Gccgg within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:44.0 occ:1.00 O E:HOH204 2.1 43.7 1.0 O E:HOH209 2.1 44.5 1.0 O E:HOH216 2.1 45.9 1.0 O E:HOH220 2.1 42.0 1.0 O E:HOH218 2.1 45.1 1.0 O E:HOH207 2.1 41.4 1.0 O E:HOH217 3.8 42.6 1.0 O E:HOH205 3.8 36.0 1.0 O D:HOH209 4.0 41.0 1.0 O E:HOH203 4.1 44.3 1.0 N7 E:G3 4.2 56.1 1.0 O E:HOH206 4.2 53.7 1.0 O D:HOH217 4.3 38.2 1.0 O6 E:G3 4.4 53.5 1.0 N7 E:G4 4.5 49.2 1.0 O E:HOH219 4.5 41.6 1.0 O6 E:G4 4.6 46.6 1.0 C41 E:B8T5 4.8 43.9 1.0 C5 E:G3 4.8 57.4 1.0 C6 E:G3 4.9 56.5 1.0

S.Mao, B.Sekula, M.Ruszkowski, S.V.Ranganathan, P.Haruehanroengra, Y.Wu, F.Shen, J.Sheng. Base Pairing, Structural and Functional Insights Into N4-Methylcytidine (M4C) and N4,N4-Dimethylcytidine (M42C) Modified Rna. Nucleic Acids Res. V. 48 10087 2020.
ISSN: ESSN 1362-4962
PubMed: 32941619
DOI: 10.1093/NAR/GKAA737