Magnesium in PDB 8zp4: Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound

The binding sites of Magnesium atom in the Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound (pdb code 8zp4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound, PDB code: 8zp4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:46.2 occ:1.00 O3G A:AGS2001 2.2 60.1 1.0 NH2 D:ARG267 2.7 49.8 1.0 O2B A:AGS2001 2.9 60.1 1.0 OG1 A:THR486 3.1 52.8 1.0 O2A A:AGS2001 3.3 60.1 1.0 CB A:THR486 3.5 52.8 1.0 PG A:AGS2001 3.7 60.1 1.0 CZ D:ARG267 3.7 49.8 1.0 CG2 A:THR486 3.8 52.8 1.0 PB A:AGS2001 3.9 60.1 1.0 NH1 D:ARG267 4.0 49.8 1.0 O3A A:AGS2001 4.0 60.1 1.0 OD2 A:ASP566 4.0 47.5 1.0 O3B A:AGS2001 4.1 60.1 1.0 PA A:AGS2001 4.3 60.1 1.0 OE2 A:GLU567 4.4 50.9 1.0 OH D:TYR232 4.5 44.3 1.0 OD1 A:ASP566 4.5 47.5 1.0 CG A:ASP566 4.6 47.5 1.0 O2G A:AGS2001 4.6 60.1 1.0 S1G A:AGS2001 4.8 60.1 1.0 NE D:ARG267 4.9 49.8 1.0 NH1 A:ARG704 4.9 57.4 1.0 CA A:THR486 4.9 52.8 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:37.6 occ:1.00 O2G D:AGS2001 2.4 40.0 1.0 OG1 D:THR109 2.4 38.0 1.0 OE2 E:GLU154 3.0 46.5 1.0 OE1 E:GLU154 3.2 46.5 1.0 CD E:GLU154 3.5 46.5 1.0 OD1 D:ASP217 3.5 41.4 1.0 CG D:ASP217 3.6 41.4 1.0 O2B D:AGS2001 3.7 40.0 1.0 CB D:THR109 3.7 38.0 1.0 PG D:AGS2001 3.7 40.0 1.0 NZ E:LYS151 3.7 43.2 1.0 OD2 D:ASP217 4.0 41.4 1.0 CB D:ASP217 4.1 41.4 1.0 CG2 D:THR109 4.1 38.0 1.0 S1G D:AGS2001 4.3 40.0 1.0 O3G D:AGS2001 4.6 40.0 1.0 CE E:LYS151 4.6 43.2 1.0 CD E:LYS151 4.6 43.2 1.0 O3B D:AGS2001 4.6 40.0 1.0 PB D:AGS2001 4.7 40.0 1.0 CA D:THR109 4.9 38.0 1.0 CG E:GLU154 5.0 46.5 1.0 O3A D:AGS2001 5.0 40.0 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Origin Recognition Complex (ORC1 to 5) with ARS1 Dna Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg503 b:43.9 occ:1.00 O3G E:AGS502 2.5 45.4 1.0 CG2 E:THR44 2.6 39.7 1.0 OG1 E:THR44 3.0 39.7 1.0 CB E:THR44 3.2 39.7 1.0 O2A E:AGS502 3.6 45.4 1.0 OD2 E:ASP133 3.7 45.0 1.0 O2B E:AGS502 3.8 45.4 1.0 PG E:AGS502 3.9 45.4 1.0 O3B E:AGS502 3.9 45.4 1.0 PB E:AGS502 4.5 45.4 1.0 CA E:THR44 4.7 39.7 1.0 CG E:ASP133 4.7 45.0 1.0 PA E:AGS502 4.8 45.4 1.0 O2G E:AGS502 4.9 45.4 1.0 OD1 E:ASP133 5.0 45.0 1.0 S1G E:AGS502 5.0 45.4 1.0

W.H.Lam, D.Yu, Q.Zhang, Y.Lin, N.Li, J.Li, Y.Wu, Y.Zhang, N.Gao, B.K.Tye, Y.Zhai, S.Dang. Dna Bending Mediated By Orc Is Essential For Replication Licensing in Budding Yeast. Proc.Natl.Acad.Sci.Usa V. 122 77122 2025.
ISSN: ESSN 1091-6490
PubMed: 40184174
DOI: 10.1073/PNAS.2502277122