Magnesium 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:

Sodium

(Na)

5 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase, PDB code: 9c6l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg306 b:60.7 occ:1.00 O3P A:AMP301 2.0 67.0 1.0 O A:HOH405 2.3 51.0 1.0 O A:HOH402 2.4 35.7 1.0 P A:AMP301 3.4 74.3 1.0 H4' A:AMP301 3.5 62.0 1.0 NA A:NA304 3.7 38.2 1.0 NA A:NA305 4.0 44.1 1.0 O2P A:AMP301 4.1 65.0 1.0 O1P A:AMP301 4.1 59.7 1.0 HZ1 A:LYS73 4.2 61.1 1.0 O5' A:AMP301 4.4 65.1 1.0 C4' A:AMP301 4.5 51.5 1.0 HZ2 A:LYS73 4.8 61.1 1.0 NZ A:LYS73 4.9 50.8 1.0 HO3' A:AMP301 4.9 58.0 1.0 O A:GLY76 4.9 52.8 1.0 C5' A:AMP301 4.9 57.4 1.0

Magnesium binding site 2 out of 6 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:49.1 occ:1.00 O3P B:AMP301 2.0 56.1 1.0 P B:AMP301 3.4 40.4 1.0 HZ2 B:LYS253 3.5 70.5 1.0 HZ1 B:LYS253 3.6 70.5 1.0 O2P B:AMP301 3.9 31.5 1.0 NZ B:LYS253 3.9 58.6 1.0 O1P B:AMP301 4.2 46.0 1.0 HZ3 B:LYS253 4.3 70.5 1.0 O5' B:AMP301 4.4 55.2 1.0

Magnesium binding site 3 out of 6 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:66.0 occ:1.00 O3P C:AMP301 2.2 89.4 1.0 P C:AMP301 3.1 100.3 1.0 O1P C:AMP301 3.3 93.7 1.0 O2P C:AMP301 3.8 85.6 1.0 O5' C:AMP301 4.4 72.3 1.0 HZ2 C:LYS253 4.8 76.2 1.0 HZ1 C:LYS23 4.9 82.2 1.0 HZ3 C:LYS23 4.9 82.2 1.0 HZ1 C:LYS73 5.0 79.7 1.0

Magnesium binding site 4 out of 6 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:61.8 occ:1.00 O3P D:AMP301 2.0 87.8 1.0 P D:AMP301 3.0 77.1 1.0 O2P D:AMP301 3.3 82.5 1.0 O1P D:AMP301 3.9 48.8 1.0 HE3 D:LYS253 3.9 67.9 1.0 O5' D:AMP301 4.3 57.4 1.0 HZ3 D:LYS253 4.3 39.7 1.0 HZ2 D:LYS23 4.5 126.2 1.0 HD3 D:LYS23 4.6 121.0 1.0 HZ1 D:LYS253 4.6 39.7 1.0 HE3 D:LYS23 4.7 130.3 1.0 CE D:LYS253 4.7 56.5 1.0 NZ D:LYS253 4.8 33.0 1.0

Magnesium binding site 5 out of 6 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:44.5 occ:1.00 O3' E:AMP301 2.4 53.5 1.0 HB2 E:CYS78 2.7 67.2 1.0 HO3' E:AMP301 2.7 64.4 1.0 H4' E:AMP301 3.3 62.1 1.0 HO2' E:AMP301 3.4 60.3 1.0 NH1 E:ARG89 3.4 51.8 1.0 HB3 E:CYS78 3.5 67.2 1.0 CB E:CYS78 3.5 55.9 1.0 CZ E:ARG89 3.5 48.8 1.0 O2' E:AMP301 3.5 50.1 1.0 HH12 E:ARG89 3.5 62.3 1.0 C3' E:AMP301 3.6 46.4 1.0 HH11 E:ARG89 3.6 62.3 1.0 HD3 E:ARG89 3.7 67.5 1.0 NH2 E:ARG89 3.8 40.4 1.0 HG E:CYS78 3.9 37.2 1.0 NE E:ARG89 3.9 52.7 1.0 C4' E:AMP301 3.9 51.6 1.0 HH22 E:ARG89 3.9 48.7 1.0 C2' E:AMP301 4.1 43.9 1.0 H E:CYS78 4.1 47.3 1.0 HH21 E:ARG89 4.2 48.7 1.0 SG E:CYS78 4.3 31.8 1.0 HE E:ARG89 4.3 63.4 1.0 CD E:ARG89 4.4 56.0 1.0 O5' E:AMP301 4.4 66.5 1.0 O2P E:AMP301 4.5 58.6 1.0 H3' E:AMP301 4.5 55.9 1.0 MG E:MG303 4.6 55.5 1.0 CA E:CYS78 4.7 48.3 1.0 N E:CYS78 4.7 39.2 1.0 HG12 E:VAL20 4.7 61.5 1.0 C5' E:AMP301 4.8 60.1 1.0 HG11 E:VAL20 4.9 61.5 1.0 H2' E:AMP301 5.0 52.9 1.0 HD2 E:ARG89 5.0 67.5 1.0 H1' E:AMP301 5.0 54.8 1.0

Magnesium binding site 6 out of 6 in the Yasminevirus C12ORF29, A 5' to 3' Rna Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yasminevirus C12ORF29, A 5' to 3' Rna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:55.5 occ:1.00 O3P E:AMP301 2.0 77.5 1.0 P E:AMP301 3.3 75.6 1.0 O5' E:AMP301 3.6 66.5 1.0 HH22 E:ARG89 3.7 48.7 1.0 O2P E:AMP301 3.9 58.6 1.0 HZ2 E:LYS253 4.1 84.4 1.0 HZ3 E:LYS253 4.1 84.4 1.0 NH2 E:ARG89 4.2 40.4 1.0 HH21 E:ARG89 4.2 48.7 1.0 HZ1 E:LYS253 4.2 84.4 1.0 NZ E:LYS253 4.3 70.2 1.0 O1P E:AMP301 4.5 59.0 1.0 MG E:MG302 4.6 44.5 1.0 HG3 E:LYS23 4.7 71.5 1.0 HE3 E:LYS23 5.0 99.8 1.0 C5' E:AMP301 5.0 60.1 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.