Sodium in PDB 9c6l: Yasminevirus C12ORF29, A 5' to 3' Rna Ligase

The structure of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase, PDB code: 9c6l was solved by Y.Hu, V.A.Lopez, V.S.Tagliabracci, D.R.Tomchick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.897, 84.221, 115.24, 90, 106.88, 90
R / Rfree (%)	23.2 / 27.5

The structure of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase (pdb code 9c6l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase, PDB code: 9c6l:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:39.8 occ:1.00 NA A:NA303 3.3 41.2 1.0 O2P A:AMP301 3.4 65.0 1.0 HZ1 A:LYS253 3.5 88.0 1.0 HD3 A:LYS23 4.1 94.4 1.0 HE3 A:LYS253 4.1 71.8 1.0 O1P A:AMP301 4.2 59.7 1.0 HZ2 A:LYS253 4.2 88.0 1.0 NZ A:LYS253 4.2 73.2 1.0 P A:AMP301 4.4 74.3 1.0 HD2 A:LYS23 4.4 94.4 1.0 HE3 A:LYS23 4.4 103.8 1.0 O A:HOH402 4.5 35.7 1.0 CD A:LYS23 4.6 78.5 1.0 CE A:LYS253 4.7 59.7 1.0 HZ2 A:LYS23 4.9 114.2 1.0 HZ3 A:LYS253 4.9 88.0 1.0 HE2 A:LYS253 5.0 71.8 1.0

Sodium binding site 2 out of 5 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:41.2 occ:1.00 O A:HOH402 3.2 35.7 1.0 NA A:NA302 3.3 39.8 1.0

Sodium binding site 3 out of 5 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:38.2 occ:1.00 HA A:ASP75 2.7 52.0 1.0 H A:GLY76 2.8 43.2 1.0 OE2 A:GLU174 2.9 46.6 1.0 O A:THR74 3.1 35.7 1.0 HZ3 A:LYS73 3.1 61.1 1.0 H1' A:AMP301 3.1 45.7 1.0 O A:HOH405 3.1 51.0 1.0 HZ2 A:LYS73 3.2 61.1 1.0 OE1 A:GLU240 3.3 44.0 1.0 HZ1 A:LYS73 3.3 61.1 1.0 NZ A:LYS73 3.4 50.8 1.0 N A:GLY76 3.6 35.8 1.0 CA A:ASP75 3.6 43.2 1.0 H4' A:AMP301 3.7 62.0 1.0 OD1 A:ASP75 3.7 39.6 1.0 H8 A:AMP301 3.7 51.7 1.0 MG A:MG306 3.7 60.7 1.0 O A:GLY76 3.8 52.8 1.0 OE2 A:GLU240 3.8 48.2 1.0 O4' A:AMP301 3.8 42.4 1.0 CD A:GLU240 3.9 40.9 1.0 C1' A:AMP301 3.9 37.9 1.0 CD A:GLU174 4.0 42.4 1.0 O3P A:AMP301 4.0 67.0 1.0 C A:THR74 4.1 33.7 1.0 C A:ASP75 4.1 35.9 1.0 C4' A:AMP301 4.3 51.5 1.0 N A:ASP75 4.3 32.8 1.0 C8 A:AMP301 4.5 42.9 1.0 CG A:ASP75 4.5 37.2 1.0 C A:GLY76 4.5 38.1 1.0 CB A:ASP75 4.5 34.1 1.0 HG2 A:LYS73 4.6 43.3 1.0 HG2 A:GLU174 4.6 43.4 1.0 OE1 A:GLU174 4.6 35.9 1.0 CA A:GLY76 4.6 39.0 1.0 N9 A:AMP301 4.7 41.6 1.0 HB2 A:ASP75 4.7 41.1 1.0 CG A:GLU174 4.9 36.0 1.0 CE A:LYS73 4.9 45.8 1.0 HO3' A:AMP301 5.0 58.0 1.0

Sodium binding site 4 out of 5 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:44.1 occ:1.00 HA A:THR77 2.7 47.0 1.0 H A:CYS78 3.2 50.5 1.0 O A:GLY76 3.4 52.8 1.0 CA A:THR77 3.7 39.0 1.0 O A:HOH405 3.9 51.0 1.0 N A:CYS78 3.9 41.9 1.0 MG A:MG306 4.0 60.7 1.0 OG1 A:THR77 4.3 58.5 1.0 C A:GLY76 4.3 38.1 1.0 HB A:THR77 4.3 43.6 1.0 C A:THR77 4.4 43.0 1.0 CB A:THR77 4.4 37.1 1.0 N A:THR77 4.5 42.0 1.0 HB2 A:CYS78 4.6 47.5 1.0 HO3' A:AMP301 4.7 58.0 1.0 HB3 A:CYS78 4.8 47.5 1.0 HG1 A:THR77 4.9 70.3 1.0

Sodium binding site 5 out of 5 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:44.8 occ:1.00 O C:HOH407 2.4 51.5 1.0 OD1 C:ASP75 2.6 52.2 1.0 O C:GLY76 3.2 28.8 1.0 H C:GLY76 3.3 33.1 1.0 HA C:ASP75 3.3 34.5 1.0 N C:GLY76 3.7 28.3 1.0 HG2 C:GLN181 3.7 55.2 1.0 CG C:ASP75 3.8 37.9 1.0 OE2 C:GLU240 3.9 49.2 1.0 CA C:ASP75 4.0 28.9 1.0 C C:GLY76 4.1 31.3 1.0 C C:ASP75 4.2 29.1 1.0 OE1 C:GLU240 4.4 43.1 1.0 CA C:GLY76 4.4 28.6 1.0 OE1 C:GLN181 4.4 36.5 1.0 CB C:ASP75 4.5 34.5 1.0 CD C:GLN181 4.5 46.6 1.0 CG C:GLN181 4.5 45.9 1.0 OE2 C:GLU174 4.6 31.1 1.0 CD C:GLU240 4.6 48.9 1.0 HA2 C:GLY76 4.7 33.4 1.0 OD2 C:ASP75 4.7 31.2 1.0 O3P C:AMP301 4.8 89.4 1.0 HB2 C:ASP75 4.8 41.5 1.0 O C:THR74 4.9 42.4 1.0 HG3 C:GLN181 4.9 55.2 1.0

Y.Hu, V.A.Lopez, H.Xu, B.Song, K.A.Servage, M.Sakurai, B.T.Jones, J.T.Mendell, T.Wang, J.Wu, A.M.Lambowitz, D.R.Tomchick, K.Pawlowski, V.S.Tagliabracci. Biochemical and Structural Insights Into A 5' to 3' Rna Ligase Reveal A Potential Role in Trna Ligation To Be Published.