Magnesium in PDB 7tfk: Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End

The binding sites of Magnesium atom in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End (pdb code 7tfk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End, PDB code: 7tfk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:63.5 occ:1.00 OD2 A:ASP424 2.1 67.9 1.0 O3G A:AGS901 2.1 64.8 1.0 OG1 A:THR360 2.2 64.0 1.0 O1B A:AGS901 3.1 64.8 1.0 CG A:ASP424 3.2 67.9 1.0 PG A:AGS901 3.3 64.8 1.0 CB A:THR360 3.4 64.0 1.0 O2G A:AGS901 3.5 64.8 1.0 CG2 A:ILE454 3.9 60.3 1.0 O1A A:AGS901 3.9 64.8 1.0 CB A:ASP424 3.9 67.9 1.0 CG2 A:THR360 4.1 64.0 1.0 PB A:AGS901 4.2 64.8 1.0 OD1 A:ASP424 4.2 67.9 1.0 O3B A:AGS901 4.2 64.8 1.0 OE2 A:GLU425 4.4 70.7 1.0 CA A:THR360 4.5 64.0 1.0 N A:THR360 4.6 64.0 1.0 CB A:ILE454 4.7 60.3 1.0 O3A A:AGS901 4.8 64.8 1.0 S1G A:AGS901 4.8 64.8 1.0 PA A:AGS901 4.8 64.8 1.0 NH2 B:ARG128 4.9 60.9 1.0

Magnesium binding site 2 out of 4 in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:54.5 occ:1.00 O1B B:AGS401 2.1 57.5 1.0 O2G B:AGS401 2.1 57.5 1.0 O1A B:AGS401 2.1 57.5 1.0 O3A B:AGS401 2.5 57.5 1.0 PB B:AGS401 2.7 57.5 1.0 PA B:AGS401 2.8 57.5 1.0 PG B:AGS401 3.1 57.5 1.0 OG1 B:THR56 3.1 55.1 1.0 CB B:THR56 3.2 55.1 1.0 O3B B:AGS401 3.3 57.5 1.0 O2A B:AGS401 3.7 57.5 1.0 S1G B:AGS401 3.8 57.5 1.0 O5' B:AGS401 4.0 57.5 1.0 O2B B:AGS401 4.1 57.5 1.0 CG2 B:THR56 4.1 55.1 1.0 NH1 C:ARG132 4.2 65.2 1.0 N B:THR56 4.2 55.1 1.0 CA B:THR56 4.4 55.1 1.0 NH2 C:ARG160 4.4 57.5 1.0 O3G B:AGS401 4.5 57.5 1.0 NH1 C:ARG160 4.6 57.5 1.0 OE2 B:GLU115 4.7 65.2 1.0 OE1 B:GLU115 4.9 65.2 1.0 C5' B:AGS401 5.0 57.5 1.0 CZ C:ARG160 5.0 57.5 1.0

Magnesium binding site 3 out of 4 in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:56.3 occ:1.00 O3G C:AGS401 2.2 54.2 1.0 O2G C:AGS401 2.2 54.2 1.0 O1B C:AGS401 2.4 54.2 1.0 PG C:AGS401 2.5 54.2 1.0 PB C:AGS401 3.0 54.2 1.0 O3B C:AGS401 3.0 54.2 1.0 CG2 C:THR60 3.2 49.6 1.0 O3A C:AGS401 3.2 54.2 1.0 CB C:THR60 3.6 49.6 1.0 OD1 C:ASP117 3.9 61.7 1.0 CE C:LYS59 3.9 50.6 1.0 N C:THR60 4.0 49.6 1.0 NH2 D:ARG183 4.2 52.5 1.0 NH1 D:ARG155 4.2 52.5 1.0 CD D:ARG155 4.3 52.5 1.0 NH2 D:ARG154 4.3 50.2 1.0 S1G C:AGS401 4.4 54.2 1.0 OD2 C:ASP117 4.4 61.7 1.0 O2B C:AGS401 4.5 54.2 1.0 CA C:THR60 4.5 49.6 1.0 CG C:ASP117 4.5 61.7 1.0 PA C:AGS401 4.5 54.2 1.0 NZ C:LYS59 4.6 50.6 1.0 CB C:LYS59 4.6 50.6 1.0 CZ D:ARG155 4.6 52.5 1.0 NE D:ARG155 4.7 52.5 1.0 OG1 C:THR60 4.8 49.6 1.0 NH2 C:ARG206 4.8 53.3 1.0 O1A C:AGS401 4.8 54.2 1.0 OE1 D:GLU158 4.9 56.0 1.0 O2A C:AGS401 5.0 54.2 1.0 CD1 C:LEU146 5.0 52.0 1.0

Magnesium binding site 4 out of 4 in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'- Recessed End within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:53.0 occ:1.00 O3G D:AGS401 2.1 45.3 1.0 OG1 D:THR72 2.2 40.3 1.0 O2B D:AGS401 2.9 45.3 1.0 OE1 E:GLU159 3.1 77.0 1.0 CB D:THR72 3.3 40.3 1.0 OD1 D:ASP140 3.4 64.2 1.0 OE2 E:GLU159 3.5 77.0 1.0 OD2 D:ASP140 3.6 64.2 1.0 CD E:GLU159 3.6 77.0 1.0 PG D:AGS401 3.7 45.3 1.0 CG D:ASP140 3.9 64.2 1.0 CG2 D:THR72 3.9 40.3 1.0 O2A D:AGS401 4.2 45.3 1.0 NH2 E:ARG184 4.2 65.4 1.0 PB D:AGS401 4.3 45.3 1.0 O3B D:AGS401 4.4 45.3 1.0 O2G D:AGS401 4.5 45.3 1.0 CA D:THR72 4.6 40.3 1.0 S1G D:AGS401 4.7 45.3 1.0 N D:THR72 4.8 40.3 1.0 NH1 E:ARG156 4.9 81.0 1.0

F.Zheng, R.Georgescu, N.Y.Yao, H.Li, M.E.O'donnell. Cryo-Em Structures Reveal That Rfc Recognizes Both the 3'- and 5'-Dna Ends to Load Pcna Onto Gaps For Dna Repair. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35829698
DOI: 10.7554/ELIFE.77469