Magnesium in PDB 8fs7: Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna)

The binding sites of Magnesium atom in the Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna) (pdb code 8fs7). 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 S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna), PDB code: 8fs7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:42.0 occ:1.00 OG A:SER116 2.3 44.1 1.0 O3A A:AGS602 2.4 48.6 1.0 O2B A:AGS602 2.5 60.1 1.0 CB A:SER116 2.8 37.0 1.0 PB A:AGS602 3.1 49.1 1.0 O2G A:AGS602 3.3 54.0 1.0 OE1 A:GLU187 3.6 48.7 1.0 CD A:GLU187 3.6 52.5 1.0 PA A:AGS602 3.8 37.6 1.0 OE2 A:GLU187 3.9 54.1 1.0 O1A A:AGS602 4.0 50.0 1.0 O3B A:AGS602 4.0 55.7 1.0 CG A:GLU187 4.0 51.5 1.0 O1B A:AGS602 4.2 34.9 1.0 CA A:SER116 4.2 32.9 1.0 O5' A:AGS602 4.3 50.3 1.0 PG A:AGS602 4.3 48.0 1.0 NH2 A:ARG312 4.5 35.0 1.0 N A:SER116 4.6 46.2 1.0 OE2 B:GLU132 4.7 62.2 1.0 NH1 A:ARG312 4.8 40.2 1.0 O2A A:AGS602 4.9 58.3 1.0

Magnesium binding site 2 out of 4 in the Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:42.7 occ:1.00 O2G B:AGS401 2.1 58.5 1.0 OG1 B:THR56 2.1 51.1 1.0 O1B B:AGS401 2.8 53.2 1.0 CB B:THR56 3.0 46.7 1.0 OE2 C:GLU135 3.3 55.0 1.0 PG B:AGS401 3.6 47.7 1.0 O1A B:AGS401 3.6 57.3 1.0 CG2 B:THR56 3.7 40.7 1.0 OE1 C:GLU135 3.8 52.5 1.0 OD1 B:ASP114 3.8 46.5 1.0 PB B:AGS401 3.9 39.1 1.0 CD C:GLU135 3.9 54.1 1.0 OE2 B:GLU115 4.2 46.8 1.0 O3A B:AGS401 4.2 56.7 1.0 O3B B:AGS401 4.2 59.1 1.0 CA B:THR56 4.3 36.4 1.0 NH2 C:ARG160 4.3 37.3 1.0 OD2 B:ASP114 4.4 44.2 1.0 PA B:AGS401 4.4 44.3 1.0 CG B:ASP114 4.4 43.9 1.0 S1G B:AGS401 4.4 53.8 1.0 N B:THR56 4.4 37.7 1.0 NH1 C:ARG132 4.5 48.0 1.0 O3G B:AGS401 4.6 59.2 1.0 O2A B:AGS401 4.9 59.5 1.0

Magnesium binding site 3 out of 4 in the Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:46.8 occ:1.00 O2G C:AGS402 2.1 59.9 1.0 OG1 C:THR60 2.1 47.1 1.0 O1B C:AGS402 3.0 55.7 1.0 CB C:THR60 3.3 40.2 1.0 OD1 C:ASP117 3.4 43.5 1.0 PG C:AGS402 3.6 39.0 1.0 O3A C:AGS402 3.8 62.7 1.0 OD2 C:ASP117 3.8 44.1 1.0 PB C:AGS402 3.8 29.3 1.0 NH2 D:ARG183 3.9 43.7 1.0 CG2 C:THR60 3.9 38.0 1.0 OE1 C:GLU118 3.9 47.5 1.0 CG C:ASP117 4.0 46.0 1.0 OE1 D:GLU158 4.0 45.6 1.0 O3B C:AGS402 4.2 47.3 1.0 CA C:THR60 4.5 27.5 1.0 O3G C:AGS402 4.5 62.5 1.0 N C:THR60 4.5 31.9 1.0 S1G C:AGS402 4.6 40.6 1.0 NH2 D:ARG154 4.6 29.2 1.0 O2A C:AGS402 4.6 57.1 1.0 CD D:ARG155 4.7 40.7 1.0 PA C:AGS402 4.8 35.6 1.0 CZ D:ARG183 4.8 34.4 1.0 CD D:GLU158 4.9 48.7 1.0 CD C:GLU118 4.9 53.0 1.0 OE2 D:GLU158 5.0 54.1 1.0 NH1 D:ARG183 5.0 38.2 1.0

Magnesium binding site 4 out of 4 in the Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 5 (Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:39.9 occ:1.00 O3G D:AGS401 2.1 57.9 1.0 O2B D:AGS401 2.1 54.2 1.0 OG1 D:THR72 2.2 40.2 1.0 PG D:AGS401 3.3 44.2 1.0 CB D:THR72 3.4 27.3 1.0 PB D:AGS401 3.5 36.2 1.0 NH2 E:ARG184 3.6 56.4 1.0 S1G D:AGS401 3.7 79.7 1.0 OE1 E:GLU159 3.8 70.9 1.0 OD2 D:ASP140 3.8 48.1 1.0 O3B D:AGS401 3.9 54.4 1.0 OD1 D:ASP140 4.1 59.1 1.0 OE2 E:GLU159 4.1 66.4 1.0 CG2 D:THR72 4.1 25.4 1.0 O3A D:AGS401 4.2 60.4 1.0 O2A D:AGS401 4.3 56.5 1.0 CG D:ASP140 4.4 50.2 1.0 CD E:GLU159 4.4 65.0 1.0 OE1 D:GLU141 4.5 51.2 1.0 N D:THR72 4.5 15.2 1.0 CA D:THR72 4.5 18.6 1.0 O2G D:AGS401 4.6 37.0 1.0 O1B D:AGS401 4.6 47.7 1.0 PA D:AGS401 4.7 33.9 1.0 NH2 E:ARG155 4.8 55.3 1.0 NH1 E:ARG156 4.9 62.9 1.0 CZ E:ARG184 4.9 47.0 1.0 O1A D:AGS401 4.9 50.4 1.0

F.Zheng, R.E.Georgescu, N.Y.Yao, M.E.O'donnell, H.Li. Structures of 9-1-1 Dna Checkpoint Clamp Loading at Gaps From Start to Finish and Ramification to Biology. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 37205533
DOI: 10.1101/2023.05.03.539266