Magnesium in PDB 7tfl: Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Dna

The binding sites of Magnesium atom in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Dna (pdb code 7tfl). 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 Dna, PDB code: 7tfl:
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 Dna


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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:71.9 occ:1.00 CB A:ASP424 2.6 79.0 1.0 O3G A:AGS901 2.6 79.1 1.0 OG1 A:THR360 2.7 81.2 1.0 CG A:ASP424 2.7 79.0 1.0 OD2 A:ASP424 3.2 79.0 1.0 OD1 A:ASP424 3.3 79.0 1.0 OE2 A:GLU425 3.4 81.5 1.0 O1B A:AGS901 3.7 79.1 1.0 CA A:ASP424 3.7 79.0 1.0 CG2 A:ILE454 3.7 77.5 1.0 CB A:THR360 4.0 81.2 1.0 N A:GLU425 4.0 81.5 1.0 PG A:AGS901 4.1 79.1 1.0 CD A:GLU425 4.1 81.5 1.0 CB A:ILE454 4.2 77.5 1.0 CG A:GLU425 4.3 81.5 1.0 C A:ASP424 4.3 79.0 1.0 O1A A:AGS901 4.4 79.1 1.0 O2G A:AGS901 4.4 79.1 1.0 NH2 B:ARG129 4.4 65.4 1.0 CG2 A:THR360 4.4 81.2 1.0 PB A:AGS901 4.8 79.1 1.0 O3B A:AGS901 4.8 79.1 1.0 O A:ILE454 4.8 77.5 1.0 N A:ASP424 4.9 79.0 1.0

Magnesium binding site 2 out of 4 in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Dna


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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:53.0 occ:1.00 O3G B:AGS401 2.1 58.7 1.0 O2G B:AGS401 2.1 58.7 1.0 CG2 B:THR56 2.6 58.8 1.0 PG B:AGS401 2.6 58.7 1.0 OE2 B:GLU115 2.7 66.3 1.0 CB B:THR56 3.2 58.8 1.0 O1B B:AGS401 3.2 58.7 1.0 OD1 B:ASP114 3.4 65.9 1.0 O1A B:AGS401 3.5 58.7 1.0 NH2 C:ARG160 3.6 63.0 1.0 O3B B:AGS401 3.7 58.7 1.0 CD B:GLU115 3.7 66.3 1.0 OD2 B:ASP114 3.9 65.9 1.0 PB B:AGS401 3.9 58.7 1.0 S1G B:AGS401 4.0 58.7 1.0 CG B:ASP114 4.0 65.9 1.0 N B:THR56 4.1 58.8 1.0 OE1 B:GLU115 4.2 66.3 1.0 OG1 B:THR56 4.2 58.8 1.0 PA B:AGS401 4.3 58.7 1.0 CA B:THR56 4.3 58.8 1.0 O2A B:AGS401 4.4 58.7 1.0 O3A B:AGS401 4.5 58.7 1.0 O B:ALA143 4.8 61.9 1.0 CZ C:ARG160 4.8 63.0 1.0 NH1 C:ARG132 4.9 71.2 1.0 CG B:GLU115 4.9 66.3 1.0 CB B:LYS55 4.9 58.8 1.0 CB B:ALA143 5.0 61.9 1.0 C B:LYS55 5.0 58.8 1.0

Magnesium binding site 3 out of 4 in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Dna


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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:61.5 occ:1.00 O3G C:AGS401 2.1 59.3 1.0 O2G C:AGS401 2.2 59.3 1.0 PG C:AGS401 2.6 59.3 1.0 CG2 C:THR60 3.3 54.7 1.0 O1B C:AGS401 3.5 59.3 1.0 O3A C:AGS401 3.6 59.3 1.0 O3B C:AGS401 3.6 59.3 1.0 OD2 C:ASP117 3.7 70.0 1.0 NH1 D:ARG155 3.7 64.3 1.0 CB C:THR60 3.7 54.7 1.0 OE1 D:GLU158 3.7 64.7 1.0 PB C:AGS401 3.7 59.3 1.0 NH2 D:ARG183 3.9 63.0 1.0 OD1 C:ASP117 4.0 70.0 1.0 CD D:ARG155 4.1 64.3 1.0 S1G C:AGS401 4.2 59.3 1.0 CG C:ASP117 4.3 70.0 1.0 CZ D:ARG155 4.5 64.3 1.0 NE D:ARG155 4.6 64.3 1.0 N C:THR60 4.6 54.7 1.0 OG1 C:THR60 4.6 54.7 1.0 CD D:GLU158 4.7 64.7 1.0 NH1 D:ARG183 4.8 63.0 1.0 CE C:LYS59 4.8 56.5 1.0 CA C:THR60 4.8 54.7 1.0 CZ D:ARG183 4.8 63.0 1.0 PA C:AGS401 4.9 59.3 1.0 OE2 D:GLU158 5.0 64.7 1.0 NH1 C:ARG206 5.0 63.8 1.0

Magnesium binding site 4 out of 4 in the Atomic Model of S. Cerevisiae Clamp Loader Rfc Bound to Dna


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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:69.4 occ:1.00 O3G D:AGS500 2.1 59.6 1.0 OG1 D:THR72 2.2 51.9 1.0 O2B D:AGS500 2.5 59.6 1.0 OE2 E:GLU159 2.5 85.8 1.0 OE1 E:GLU159 2.9 85.8 1.0 CD E:GLU159 3.0 85.8 1.0 CB D:THR72 3.1 51.9 1.0 PG D:AGS500 3.6 59.6 1.0 O2A D:AGS500 3.6 59.6 1.0 CG2 D:THR72 3.6 51.9 1.0 NH1 E:ARG156 3.8 88.0 1.0 PB D:AGS500 3.9 59.6 1.0 O3B D:AGS500 4.1 59.6 1.0 CG E:GLU159 4.3 85.8 1.0 OD1 D:ASP140 4.4 78.2 1.0 CZ E:ARG156 4.4 88.0 1.0 CA D:THR72 4.4 51.9 1.0 NH2 E:ARG184 4.4 78.8 1.0 NH2 E:ARG156 4.5 88.0 1.0 PA D:AGS500 4.6 59.6 1.0 O2G D:AGS500 4.6 59.6 1.0 S1G D:AGS500 4.6 59.6 1.0 N D:THR72 4.6 51.9 1.0 O1A D:AGS500 4.7 59.6 1.0 O3A D:AGS500 4.8 59.6 1.0 OD2 D:ASP140 4.8 78.2 1.0 O1B D:AGS500 4.9 59.6 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