Magnesium in PDB 7tjk: S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain

The binding sites of Magnesium atom in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain (pdb code 7tjk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain, PDB code: 7tjk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:56.0 occ:1.00 OG1 A:THR486 2.1 52.7 1.0 O2G A:ATP1001 2.1 53.9 1.0 O A:HOH1101 2.1 55.0 1.0 O A:HOH1117 2.1 56.8 1.0 O A:HOH1111 2.2 58.2 1.0 O1B A:ATP1001 2.5 53.9 1.0 CB A:THR486 3.3 52.7 1.0 PG A:ATP1001 3.5 53.9 1.0 PB A:ATP1001 3.5 53.9 1.0 O3B A:ATP1001 3.7 53.9 1.0 OD2 A:ASP566 3.7 57.7 1.0 NH2 D:ARG267 3.8 52.1 1.0 O1A A:ATP1001 3.9 53.9 1.0 OD1 A:ASP566 4.0 57.7 1.0 OE2 A:GLU567 4.0 59.8 1.0 CG2 A:THR486 4.1 52.7 1.0 O A:HOH1119 4.1 58.6 1.0 O3A A:ATP1001 4.2 53.9 1.0 O3G A:ATP1001 4.2 53.9 1.0 CG A:ASP566 4.3 57.7 1.0 N A:THR486 4.3 52.7 1.0 CA A:THR486 4.4 52.7 1.0 NH2 A:ARG704 4.4 54.4 1.0 PA A:ATP1001 4.5 53.9 1.0 O1G A:ATP1001 4.5 53.9 1.0 O2A A:ATP1001 4.8 53.9 1.0 O2B A:ATP1001 4.9 53.9 1.0 CD A:GLU567 5.0 59.8 1.0

Magnesium binding site 2 out of 4 in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:51.1 occ:1.00 OG1 D:THR109 2.1 50.0 1.0 O2G D:ATP1001 2.1 51.3 1.0 O D:HOH1132 2.3 52.6 1.0 O E:HOH1112 2.3 53.2 1.0 O E:HOH1107 2.4 50.9 1.0 O1B D:ATP1001 2.6 51.3 1.0 CB D:THR109 3.3 50.0 1.0 PG D:ATP1001 3.3 51.3 1.0 O3B D:ATP1001 3.4 51.3 1.0 PB D:ATP1001 3.5 51.3 1.0 NZ E:LYS151 3.8 51.5 1.0 O D:HOH1110 3.8 53.2 1.0 O D:HOH1101 4.0 53.4 1.0 OE2 E:GLU154 4.1 55.1 1.0 O D:HOH1140 4.1 55.4 1.0 CG2 D:THR109 4.2 50.0 1.0 N D:THR109 4.2 50.0 1.0 O1G D:ATP1001 4.3 51.3 1.0 OD1 D:ASP217 4.3 55.4 1.0 O3G D:ATP1001 4.3 51.3 1.0 CA D:THR109 4.3 50.0 1.0 CE E:LYS151 4.4 51.5 1.0 OE1 E:GLU154 4.5 55.1 1.0 O3A D:ATP1001 4.5 51.3 1.0 CG D:ASP217 4.6 55.4 1.0 CD E:GLU154 4.7 55.1 1.0 O1A D:ATP1001 4.7 51.3 1.0 O2B D:ATP1001 4.7 51.3 1.0 O2A D:ATP1001 4.9 51.3 1.0 OD2 D:ASP217 4.9 55.4 1.0 PA D:ATP1001 4.9 51.3 1.0

Magnesium binding site 3 out of 4 in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1002 b:52.1 occ:1.00 O3G E:ATP1001 2.1 52.4 1.0 O E:HOH1105 2.1 54.9 1.0 OG1 E:THR44 2.2 48.0 1.0 O E:HOH1125 2.2 53.5 1.0 O E:HOH1104 2.3 55.2 1.0 O2B E:ATP1001 2.8 52.4 1.0 PG E:ATP1001 3.4 52.4 1.0 CB E:THR44 3.4 48.0 1.0 O3B E:ATP1001 3.6 52.4 1.0 OD1 E:ASP133 3.6 53.0 1.0 PB E:ATP1001 3.8 52.4 1.0 O E:HOH1114 3.9 53.9 1.0 O1G E:ATP1001 4.0 52.4 1.0 CG2 E:THR44 4.1 48.0 1.0 CG E:ASP133 4.2 53.0 1.0 OD2 E:ASP133 4.3 53.0 1.0 O1A E:ATP1001 4.3 52.4 1.0 CA E:THR44 4.5 48.0 1.0 N E:THR44 4.5 48.0 1.0 O2G E:ATP1001 4.5 52.4 1.0 O3A E:ATP1001 4.6 52.4 1.0 PA E:ATP1001 4.9 52.4 1.0 O1B E:ATP1001 5.0 52.4 1.0

Magnesium binding site 4 out of 4 in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 2) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg1002 b:74.4 occ:1.00 O2B I:ATP1001 2.1 73.9 1.0 OG1 I:THR115 2.1 78.3 1.0 O3G I:ATP1001 2.2 73.9 1.0 O I:HOH1101 2.3 74.4 1.0 O I:HOH1104 2.8 79.9 1.0 CB I:THR115 3.0 78.3 1.0 PB I:ATP1001 3.4 73.9 1.0 PG I:ATP1001 3.5 73.9 1.0 O3B I:ATP1001 3.7 73.9 1.0 OE2 I:GLU224 3.7 86.8 1.0 OD2 I:ASP223 3.9 88.2 1.0 CG2 I:THR115 3.9 78.3 1.0 O1A I:ATP1001 3.9 73.9 1.0 NH2 A:ARG616 4.0 65.2 1.0 O1G I:ATP1001 4.0 73.9 1.0 N I:THR115 4.1 78.3 1.0 CA I:THR115 4.1 78.3 1.0 OD1 I:ASP223 4.2 88.2 1.0 O3A I:ATP1001 4.3 73.9 1.0 O1B I:ATP1001 4.5 73.9 1.0 CG I:ASP223 4.5 88.2 1.0 PA I:ATP1001 4.5 73.9 1.0 O2G I:ATP1001 4.6 73.9 1.0 O2A I:ATP1001 4.8 73.9 1.0 CD I:GLU224 4.9 86.8 1.0

J.M.Schmidt, R.Yang, A.Kumar, O.Hunker, J.Seebacher, F.Bleichert. A Mechanism of Origin Licensing Control Through Autoinhibition of S. Cerevisiae Orc·Dna·CDC6. Nat Commun V. 13 1059 2022.
ISSN: ESSN 2041-1723
PubMed: 35217664
DOI: 10.1038/S41467-022-28695-W