Magnesium in PDB 6ty9: In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State

The binding sites of Magnesium atom in the In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State (pdb code 6ty9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State, PDB code: 6ty9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:38.0 occ:1.00 O1A M:GTP2 2.1 52.1 1.0 OD1 A:ASP680 2.5 29.7 1.0 OD2 A:ASP680 2.9 29.7 1.0 CG A:ASP680 3.0 29.7 1.0 OD1 A:ASP681 3.3 25.7 1.0 PA M:GTP2 3.4 52.1 1.0 CG A:ASP681 3.8 25.7 1.0 O3A M:GTP2 3.9 52.1 1.0 MG A:MG1302 3.9 40.6 1.0 O3' M:A1 4.1 59.0 1.0 O A:ASP680 4.2 29.7 1.0 OD2 A:ASP681 4.2 25.7 1.0 C A:ASP680 4.2 29.7 1.0 O5' M:GTP2 4.2 52.1 1.0 N A:ASP681 4.3 25.7 1.0 CB A:ASP680 4.4 29.7 1.0 O2A M:GTP2 4.5 52.1 1.0 CA A:ASP681 4.5 25.7 1.0 CB A:ASP681 4.5 25.7 1.0 C5' M:GTP2 4.7 52.1 1.0 CA A:ASP680 4.8 29.7 1.0

Magnesium binding site 2 out of 3 in the In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:40.6 occ:1.00 OD2 A:ASP680 2.0 29.7 1.0 O A:VAL548 2.2 27.8 1.0 O3A M:GTP2 2.6 52.1 1.0 CG A:ASP680 3.2 29.7 1.0 PB M:GTP2 3.4 52.1 1.0 O3B M:GTP2 3.4 52.1 1.0 C A:VAL548 3.4 27.8 1.0 N A:GLY550 3.7 28.8 1.0 O2B M:GTP2 3.7 52.1 1.0 PA M:GTP2 3.9 52.1 1.0 MG A:MG1301 3.9 38.0 1.0 O1A M:GTP2 4.0 52.1 1.0 CB A:ASP680 4.1 29.7 1.0 N A:MET551 4.1 25.8 1.0 OD1 A:ASP680 4.1 29.7 1.0 O1G M:GTP2 4.2 52.1 1.0 PG M:GTP2 4.3 52.1 1.0 N A:ALA549 4.3 26.5 1.0 CA A:VAL548 4.4 27.8 1.0 CA A:ALA549 4.4 26.5 1.0 CA A:GLY550 4.4 28.8 1.0 C A:ALA549 4.4 26.5 1.0 N A:VAL548 4.4 27.8 1.0 C5' M:GTP2 4.5 52.1 1.0 O2G M:GTP2 4.6 52.1 1.0 CB A:VAL548 4.6 27.8 1.0 CB A:MET551 4.7 25.8 1.0 C A:GLY550 4.8 28.8 1.0 O A:ASP680 4.8 29.7 1.0 O5' M:GTP2 4.8 52.1 1.0 O1B M:GTP2 4.8 52.1 1.0

Magnesium binding site 3 out of 3 in the In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of In Situ Structure of Bmcpv Rna Dependent Rna Polymerase at Initiation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:20.9 occ:1.00 OD1 A:ASP681 2.7 25.7 1.0 CG A:ASP681 3.7 25.7 1.0 O A:ILE546 3.8 24.1 1.0 CB A:ASP547 4.2 29.7 1.0 OD2 A:ASP681 4.3 25.7 1.0 O A:ILE682 4.4 21.5 1.0 C A:ILE546 4.5 24.1 1.0 CA A:ASP547 4.5 29.7 1.0 O A:SER545 4.6 21.5 1.0 CB A:ASP681 4.6 25.7 1.0 CA A:ASP681 4.6 25.7 1.0 O A:VAL721 4.7 18.4 1.0 N A:ILE682 4.7 21.5 1.0 C A:SER545 4.8 21.5 1.0 N A:ASP547 4.8 29.7 1.0 CB A:SER545 5.0 21.5 1.0

Y.Cui, Y.Zhang, K.Zhou, J.Sun, Z.H.Zhou. Conservative Transcription in Three Steps Visualized in A Double-Stranded Rna Virus. Nat.Struct.Mol.Biol. V. 26 1023 2019.
ISSN: ESSN 1545-9985
PubMed: 31695188
DOI: 10.1038/S41594-019-0320-0