Magnesium in PDB 7tjj: S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 1) 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 1) with Docked ORC6 N-Terminal Domain (pdb code 7tjj). 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 1) with Docked ORC6 N-Terminal Domain, PDB code: 7tjj:
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 1) 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 1) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:55.8 occ:1.00 O A:HOH1124 2.1 56.4 1.0 O A:HOH1115 2.1 53.2 1.0 O2G A:ATP1001 2.2 55.5 1.0 O A:HOH1102 2.2 56.0 1.0 OG1 A:THR486 2.2 52.0 1.0 O2B A:ATP1001 2.4 55.5 1.0 CB A:THR486 3.4 52.0 1.0 PG A:ATP1001 3.4 55.5 1.0 PB A:ATP1001 3.5 55.5 1.0 O3B A:ATP1001 3.6 55.5 1.0 OD2 A:ASP566 3.6 56.4 1.0 OE2 A:GLU567 3.8 59.5 1.0 NH2 D:ARG267 3.8 51.8 1.0 OD1 A:ASP566 3.9 56.4 1.0 O3G A:ATP1001 4.1 55.5 1.0 O1A A:ATP1001 4.1 55.5 1.0 CG A:ASP566 4.2 56.4 1.0 CG2 A:THR486 4.2 52.0 1.0 O3A A:ATP1001 4.2 55.5 1.0 N A:THR486 4.3 52.0 1.0 CA A:THR486 4.4 52.0 1.0 O1G A:ATP1001 4.5 55.5 1.0 NH2 A:ARG704 4.6 55.6 1.0 O A:HOH1125 4.6 58.9 1.0 PA A:ATP1001 4.7 55.5 1.0 O1B A:ATP1001 4.7 55.5 1.0 CD A:GLU567 4.8 59.5 1.0 CE A:LYS485 5.0 51.5 1.0 CZ D:ARG267 5.0 51.8 1.0

Magnesium binding site 2 out of 4 in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 1) 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 1) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:48.8 occ:1.00 OG1 D:THR109 2.1 48.8 1.0 O3G D:ATP1001 2.1 49.2 1.0 O D:HOH1131 2.1 52.3 1.0 O1B D:ATP1001 2.2 49.2 1.0 O D:HOH1118 2.5 51.9 1.0 O E:HOH1117 2.5 52.6 1.0 PB D:ATP1001 3.4 49.2 1.0 PG D:ATP1001 3.4 49.2 1.0 CB D:THR109 3.4 48.8 1.0 O3B D:ATP1001 3.6 49.2 1.0 O D:HOH1132 3.8 54.1 1.0 O D:HOH1116 4.0 57.5 1.0 O2G D:ATP1001 4.1 49.2 1.0 N D:THR109 4.1 48.8 1.0 O D:HOH1138 4.2 53.2 1.0 O3A D:ATP1001 4.2 49.2 1.0 NZ E:LYS151 4.3 49.6 1.0 OD1 D:ASP217 4.3 55.4 1.0 CG2 D:THR109 4.3 48.8 1.0 CA D:THR109 4.3 48.8 1.0 OE1 E:GLU154 4.4 55.8 1.0 O1G D:ATP1001 4.5 49.2 1.0 O2A D:ATP1001 4.5 49.2 1.0 O2B D:ATP1001 4.6 49.2 1.0 OE2 E:GLU154 4.6 55.8 1.0 CG D:ASP217 4.8 55.4 1.0 O E:HOH1107 4.8 56.5 1.0 PA D:ATP1001 4.9 49.2 1.0 CE E:LYS151 4.9 49.6 1.0 CB D:LYS108 5.0 45.3 1.0 CD E:GLU154 5.0 55.8 1.0

Magnesium binding site 3 out of 4 in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 1) 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 1) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1002 b:48.0 occ:1.00 OG1 E:THR44 2.1 44.2 1.0 O E:HOH1110 2.1 50.6 1.0 O3G E:ATP1001 2.2 49.3 1.0 O E:HOH1129 2.2 52.2 1.0 O E:HOH1102 2.4 53.0 1.0 O2B E:ATP1001 2.4 49.3 1.0 CB E:THR44 3.3 44.2 1.0 PG E:ATP1001 3.3 49.3 1.0 O3B E:ATP1001 3.5 49.3 1.0 PB E:ATP1001 3.6 49.3 1.0 O1G E:ATP1001 3.8 49.3 1.0 OD1 E:ASP133 4.0 50.0 1.0 O E:HOH1123 4.0 55.1 1.0 O E:HOH1119 4.1 53.9 1.0 CG2 E:THR44 4.1 44.2 1.0 OD2 E:ASP133 4.1 50.0 1.0 O1A E:ATP1001 4.2 49.3 1.0 N E:THR44 4.3 44.2 1.0 CG E:ASP133 4.4 50.0 1.0 CA E:THR44 4.4 44.2 1.0 O3A E:ATP1001 4.4 49.3 1.0 O2G E:ATP1001 4.5 49.3 1.0 O1B E:ATP1001 4.7 49.3 1.0 PA E:ATP1001 4.7 49.3 1.0 O2A E:ATP1001 4.9 49.3 1.0

Magnesium binding site 4 out of 4 in the S. Cerevisiae Orc Bound to 84 Bp ARS1 Dna and CDC6 (State 1) 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 1) with Docked ORC6 N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg1002 b:73.9 occ:1.00 O3G I:ATP1001 2.0 73.8 1.0 OG1 I:THR115 2.1 76.4 1.0 O I:HOH1102 2.1 75.2 1.0 O I:HOH1105 2.1 76.3 1.0 O I:HOH1104 2.3 73.8 1.0 O2B I:ATP1001 2.5 73.8 1.0 CB I:THR115 3.2 76.4 1.0 PG I:ATP1001 3.4 73.8 1.0 NH2 A:ARG616 3.5 64.5 1.0 PB I:ATP1001 3.7 73.8 1.0 OD2 I:ASP223 3.7 83.6 1.0 O3B I:ATP1001 3.8 73.8 1.0 CG2 I:THR115 3.9 76.4 1.0 OD1 I:ASP223 3.9 83.6 1.0 O2A I:ATP1001 4.0 73.8 1.0 O1G I:ATP1001 4.0 73.8 1.0 CG I:ASP223 4.2 83.6 1.0 O3A I:ATP1001 4.3 73.8 1.0 OE2 I:GLU224 4.3 83.3 1.0 CA I:THR115 4.4 76.4 1.0 O2G I:ATP1001 4.5 73.8 1.0 N I:THR115 4.5 76.4 1.0 NH2 I:ARG332 4.6 69.6 1.0 PA I:ATP1001 4.6 73.8 1.0 CZ A:ARG616 4.7 64.5 1.0 O I:HOH1103 4.8 80.1 1.0 CD I:GLU224 4.9 83.3 1.0 O1A I:ATP1001 4.9 73.8 1.0 O1B I:ATP1001 4.9 73.8 1.0 OH A:TYR580 4.9 64.1 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