Magnesium in PDB 6sjd: ZC3H12B-Ribonuclease Domain Bound to Rna

The structure of ZC3H12B-Ribonuclease Domain Bound to Rna, PDB code: 6sjd was solved by E.Morgunova, G.Bourenkov, J.Taipale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.95 / 3.29
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.237, 114.237, 165.268, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27.9

The structure of ZC3H12B-Ribonuclease Domain Bound to Rna also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Magnesium atom in the ZC3H12B-Ribonuclease Domain Bound to Rna (pdb code 6sjd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the ZC3H12B-Ribonuclease Domain Bound to Rna, PDB code: 6sjd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the ZC3H12B-Ribonuclease Domain Bound to Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of ZC3H12B-Ribonuclease Domain Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:52.5 occ:1.00 O B:HOH1104 2.3 33.8 1.0 O B:HOH1106 2.5 92.8 1.0 O D:HOH211 2.7 35.3 1.0 OD1 B:ASP280 2.8 80.2 1.0 O B:HOH1105 3.0 52.3 1.0 CG B:ASP280 3.6 84.0 1.0 OD2 B:ASP280 3.7 82.4 1.0 OD1 B:ASP279 3.9 0.9 1.0 HG B:SER197 3.9 92.8 1.0 OG B:SER197 4.3 77.3 1.0 OP2 D:A16 4.4 0.9 1.0 HE1 B:TYR278 4.6 0.4 1.0 HB2 B:SER197 4.6 75.6 1.0 OD2 B:ASP195 4.7 63.5 1.0 OD2 B:ASP298 4.8 95.9 1.0 CG B:ASP279 4.8 0.8 1.0 OP1 D:A16 4.9 0.3 1.0 H B:ASP280 4.9 0.5 1.0 OD2 B:ASP279 4.9 0.4 1.0

Magnesium binding site 2 out of 2 in the ZC3H12B-Ribonuclease Domain Bound to Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of ZC3H12B-Ribonuclease Domain Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:0.8 occ:1.00 O A:HOH1102 2.3 24.7 1.0 O A:HOH1105 2.8 35.4 1.0 OD2 A:ASP280 2.9 72.0 1.0 OD2 A:ASP298 3.1 0.5 1.0 O A:HOH1107 3.1 45.8 1.0 OD1 A:ASP280 3.1 73.2 1.0 CG A:ASP280 3.4 78.2 1.0 HE1 A:TYR278 4.0 0.9 1.0 CG A:ASP298 4.3 99.5 1.0 O A:HOH1106 4.3 72.2 1.0 HE1 A:TYR300 4.4 81.3 1.0 OD2 A:ASP195 4.6 53.0 1.0 HB2 A:ASP298 4.6 1.0 1.0 CE1 A:TYR278 4.7 0.7 1.0 OH A:TYR278 4.7 0.8 1.0 CB A:ASP280 4.9 77.5 1.0 CB A:ASP298 4.9 87.4 1.0 HD1 A:TYR300 5.0 85.4 1.0

A.Jolma, J.Zhang, E.Mondragon, E.Morgunova, T.Kivioja, K.U.Laverty, Y.Yin, F.Zhu, G.Bourenkov, Q.Morris, T.R.Hughes, L.J.Maher 3Rd, J.Taipale. Binding Specificities of Human Rna-Binding Proteins Toward Structured and Linear Rna Sequences. Genome Res. V. 30 962 2020.
ISSN: ISSN 1088-9051
PubMed: 32703884
DOI: 10.1101/GR.258848.119