Magnesium in PDB 7sgz: Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp

The binding sites of Magnesium atom in the Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp (pdb code 7sgz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp, PDB code: 7sgz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:54.6 occ:1.00 O3A A:AGS701 2.1 57.8 1.0 OE1 A:GLU187 2.2 65.8 1.0 O2B A:AGS701 2.4 57.8 1.0 PB A:AGS701 2.8 57.8 1.0 CB A:SER116 3.0 59.7 1.0 CD A:GLU187 3.3 65.8 1.0 PA A:AGS701 3.3 57.8 1.0 O1A A:AGS701 3.5 57.8 1.0 OG A:SER116 3.6 59.7 1.0 OE2 A:GLU187 3.8 65.8 1.0 O3B A:AGS701 3.9 57.8 1.0 O5' A:AGS701 3.9 57.8 1.0 O1B A:AGS701 3.9 57.8 1.0 CA A:SER116 4.3 59.7 1.0 O2G A:AGS701 4.3 57.8 1.0 N A:SER116 4.5 59.7 1.0 O2A A:AGS701 4.5 57.8 1.0 CG A:GLU187 4.6 65.8 1.0 N A:THR117 4.7 60.0 1.0 PG A:AGS701 4.7 57.8 1.0 C A:SER116 4.8 59.7 1.0

Magnesium binding site 2 out of 4 in the Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:47.7 occ:1.00 O2G B:AGS401 2.1 48.1 1.0 CG2 B:THR56 2.6 51.5 1.0 CB B:THR56 3.1 51.5 1.0 NH2 C:ARG160 3.2 49.6 1.0 OD1 B:ASP114 3.3 57.6 1.0 PG B:AGS401 3.6 48.1 1.0 O1B B:AGS401 3.6 48.1 1.0 OG1 B:THR56 3.8 51.5 1.0 OD2 B:ASP114 3.9 57.6 1.0 NH1 C:ARG132 4.0 57.7 1.0 O3G B:AGS401 4.0 48.1 1.0 CG B:ASP114 4.0 57.6 1.0 O1A B:AGS401 4.0 48.1 1.0 OE2 B:GLU115 4.4 59.0 1.0 CA B:THR56 4.4 51.5 1.0 CZ C:ARG160 4.4 49.6 1.0 N B:THR56 4.5 51.5 1.0 PB B:AGS401 4.6 48.1 1.0 O3B B:AGS401 4.6 48.1 1.0 S1G B:AGS401 4.7 48.1 1.0 PA B:AGS401 4.8 48.1 1.0 CG B:GLU115 4.9 59.0 1.0 O2A B:AGS401 4.9 48.1 1.0 CZ C:ARG132 4.9 57.7 1.0

Magnesium binding site 3 out of 4 in the Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:34.7 occ:1.00 O2G C:AGS401 2.1 35.3 1.0 CG2 C:THR60 2.7 37.6 1.0 OD2 C:ASP117 2.8 47.3 1.0 CB C:THR60 2.8 37.6 1.0 OD1 C:ASP117 3.0 47.3 1.0 CG C:ASP117 3.3 47.3 1.0 OG1 C:THR60 3.5 37.6 1.0 PG C:AGS401 3.6 35.3 1.0 O1B C:AGS401 3.8 35.3 1.0 OE1 D:GLU158 3.9 39.0 1.0 O3G C:AGS401 4.0 35.3 1.0 O3A C:AGS401 4.0 35.3 1.0 CA C:THR60 4.1 37.6 1.0 N C:THR60 4.3 37.6 1.0 PB C:AGS401 4.3 35.3 1.0 O3B C:AGS401 4.5 35.3 1.0 OE1 C:GLU118 4.7 49.8 1.0 NH1 D:ARG155 4.7 41.5 1.0 CD1 C:LEU146 4.7 41.9 1.0 CB C:ASP117 4.8 47.3 1.0 CD D:GLU158 4.8 39.0 1.0 S1G C:AGS401 4.8 35.3 1.0 OE2 D:GLU158 5.0 39.0 1.0 NH2 D:ARG183 5.0 35.3 1.0 O2A C:AGS401 5.0 35.3 1.0

Magnesium binding site 4 out of 4 in the Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Yeast RAD24-Rfc Loader Bound to Dna and the Closed 9- 1-1 Clamp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:35.6 occ:1.00 OG1 D:THR72 2.1 32.1 1.0 O2B D:AGS500 2.3 33.4 1.0 OE2 E:GLU159 2.6 53.1 1.0 O3G D:AGS500 2.6 33.4 1.0 OE1 E:GLU159 3.1 53.1 1.0 CD E:GLU159 3.2 53.1 1.0 CB D:THR72 3.4 32.1 1.0 PB D:AGS500 3.8 33.4 1.0 CG2 D:THR72 3.9 32.1 1.0 NH2 E:ARG184 3.9 43.6 1.0 PG D:AGS500 4.0 33.4 1.0 O2A D:AGS500 4.3 33.4 1.0 O3B D:AGS500 4.4 33.4 1.0 O1A D:AGS500 4.5 33.4 1.0 O3A D:AGS500 4.5 33.4 1.0 CA D:THR72 4.5 32.1 1.0 N D:THR72 4.6 32.1 1.0 OD2 D:ASP140 4.6 50.7 1.0 NH1 E:ARG184 4.6 43.6 1.0 OD1 D:ASP140 4.6 50.7 1.0 O2G D:AGS500 4.7 33.4 1.0 PA D:AGS500 4.7 33.4 1.0 O1B D:AGS500 4.7 33.4 1.0 CZ E:ARG184 4.7 43.6 1.0 CG E:GLU159 4.7 53.1 1.0 CG D:ASP140 4.8 50.7 1.0 NH1 E:ARG156 4.8 60.3 1.0

F.Zheng, R.E.Georgescu, N.Y.Yao, M.E.O'donnell, H.Li. Dna Is Loaded Through the 9-1-1 Dna Checkpoint Clamp in the Opposite Direction of the Pcna Clamp. Nat.Struct.Mol.Biol. V. 29 376 2022.
ISSN: ESSN 1545-9985
PubMed: 35314830
DOI: 10.1038/S41594-022-00742-6