Magnesium in PDB 7tfh: Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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 the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End (pdb code 7tfh). 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 the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End, PDB code: 7tfh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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 the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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:46.7 occ:1.00 OG1 A:THR360 2.1 48.5 1.0 O3G A:AGS901 2.1 45.2 1.0 O1B A:AGS901 2.7 45.2 1.0 OD1 A:ASP424 3.1 64.8 1.0 CB A:THR360 3.3 48.5 1.0 PG A:AGS901 3.6 45.2 1.0 CG A:ASP424 3.8 64.8 1.0 PB A:AGS901 4.0 45.2 1.0 CG2 A:THR360 4.1 48.5 1.0 O3B A:AGS901 4.3 45.2 1.0 OE2 A:GLU425 4.3 65.5 1.0 CG2 A:ILE454 4.3 58.8 1.0 O2G A:AGS901 4.4 45.2 1.0 CA A:THR360 4.4 48.5 1.0 NH2 B:ARG128 4.4 47.6 1.0 CB A:ASP424 4.4 64.8 1.0 N A:THR360 4.4 48.5 1.0 OD2 A:ASP424 4.5 64.8 1.0 OE1 B:GLU132 4.6 45.6 1.0 O1A A:AGS901 4.8 45.2 1.0 S1G A:AGS901 4.8 45.2 1.0 O2B A:AGS901 4.8 45.2 1.0 CD A:GLU425 4.9 65.5 1.0 OE2 B:GLU132 4.9 45.6 1.0

Magnesium binding site 2 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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 the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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:35.2 occ:1.00 O2G B:AGS401 2.1 30.1 1.0 O1B B:AGS401 2.2 30.1 1.0 CG2 B:THR56 2.7 33.5 1.0 CB B:THR56 3.0 33.5 1.0 PG B:AGS401 3.6 30.1 1.0 PB B:AGS401 3.6 30.1 1.0 OD2 B:ASP114 3.9 43.2 1.0 OG1 B:THR56 3.9 33.5 1.0 NH1 C:ARG132 4.0 41.9 1.0 OD1 B:ASP114 4.0 43.2 1.0 O1A B:AGS401 4.0 30.1 1.0 OE2 C:GLU135 4.0 40.2 1.0 O3B B:AGS401 4.1 30.1 1.0 N B:THR56 4.2 33.5 1.0 CA B:THR56 4.2 33.5 1.0 NH2 C:ARG160 4.3 34.8 1.0 O3A B:AGS401 4.3 30.1 1.0 CG B:ASP114 4.4 43.2 1.0 O3G B:AGS401 4.5 30.1 1.0 OE1 C:GLU135 4.6 40.2 1.0 PA B:AGS401 4.6 30.1 1.0 S1G B:AGS401 4.7 30.1 1.0 O2B B:AGS401 4.7 30.1 1.0 CD C:GLU135 4.8 40.2 1.0 O2A B:AGS401 4.9 30.1 1.0

Magnesium binding site 3 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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 the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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:41.1 occ:1.00 O2G C:AGS401 2.1 53.9 1.0 CG2 C:THR60 2.5 35.4 1.0 CB C:THR60 2.8 35.4 1.0 O1B C:AGS401 2.9 53.9 1.0 PG C:AGS401 3.6 53.9 1.0 O3A C:AGS401 3.6 53.9 1.0 PB C:AGS401 3.7 53.9 1.0 OD1 C:ASP117 3.7 40.2 1.0 OG1 C:THR60 3.7 35.4 1.0 N C:THR60 4.0 35.4 1.0 NH2 D:ARG183 4.0 33.3 1.0 CA C:THR60 4.0 35.4 1.0 OD2 C:ASP117 4.0 40.2 1.0 OE1 D:GLU158 4.1 40.2 1.0 O3B C:AGS401 4.2 53.9 1.0 O3G C:AGS401 4.2 53.9 1.0 CG C:ASP117 4.3 40.2 1.0 OE2 D:GLU158 4.6 40.2 1.0 CD D:GLU158 4.8 40.2 1.0 PA C:AGS401 4.8 53.9 1.0 O2A C:AGS401 4.8 53.9 1.0 CD D:ARG155 4.9 41.3 1.0 S1G C:AGS401 4.9 53.9 1.0 CD1 C:LEU146 5.0 33.2 1.0

Magnesium binding site 4 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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 the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-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:34.0 occ:1.00 OG1 D:THR72 2.1 26.7 1.0 O3G D:AGS401 2.1 26.0 1.0 O2B D:AGS401 2.5 26.0 1.0 CB D:THR72 3.3 26.7 1.0 PG D:AGS401 3.6 26.0 1.0 OD2 D:ASP140 3.7 40.9 1.0 OD1 D:ASP140 3.8 40.9 1.0 PB D:AGS401 3.9 26.0 1.0 O2A D:AGS401 4.1 26.0 1.0 CG D:ASP140 4.1 40.9 1.0 CG2 D:THR72 4.2 26.7 1.0 OE1 E:GLU159 4.2 46.7 1.0 O3B D:AGS401 4.2 26.0 1.0 N D:THR72 4.2 26.7 1.0 CA D:THR72 4.3 26.7 1.0 O1B D:AGS401 4.4 26.0 1.0 OE2 E:GLU159 4.4 46.7 1.0 O2G D:AGS401 4.5 26.0 1.0 S1G D:AGS401 4.6 26.0 1.0 NH2 E:ARG155 4.7 47.5 1.0 CD E:GLU159 4.7 46.7 1.0 CG2 D:ILE169 4.8 33.2 1.0 NH2 E:ARG184 4.8 36.4 1.0 NH1 E:ARG156 5.0 50.4 1.0 O3A D:AGS401 5.0 26.0 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