Magnesium in PDB 8fs5: Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 3 (Open 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 3 (Open 9-1-1 and Stably Bound Chamber Dna) (pdb code 8fs5). 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 3 (Open 9-1-1 and Stably Bound Chamber Dna), PDB code: 8fs5:
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 3 (Open 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 3 (Open 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:52.3 occ:1.00 OE2 A:GLU187 2.1 72.3 1.0 O3A A:AGS601 2.3 71.5 1.0 OG A:SER116 2.7 59.7 1.0 O2B A:AGS601 2.8 81.5 1.0 PB A:AGS601 3.1 71.5 1.0 O2G A:AGS601 3.2 70.0 1.0 CD A:GLU187 3.3 77.3 1.0 PA A:AGS601 3.5 69.4 1.0 O3B A:AGS601 3.8 72.4 1.0 CB A:SER116 3.9 60.4 1.0 O1A A:AGS601 3.9 87.5 1.0 O5' A:AGS601 3.9 57.5 1.0 OE1 A:GLU187 4.0 73.3 1.0 PG A:AGS601 4.2 63.9 1.0 NH2 A:ARG312 4.3 51.1 1.0 CG A:GLU187 4.3 73.3 1.0 O1B A:AGS601 4.3 41.5 1.0 NH2 B:ARG157 4.6 70.7 1.0 O2A A:AGS601 4.7 72.5 1.0 NH1 A:ARG312 4.8 59.9 1.0 N A:SER116 5.0 63.5 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 3 (Open 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 3 (Open 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:58.4 occ:1.00 O2G B:AGS401 2.1 62.4 1.0 OG1 B:THR56 2.1 61.4 1.0 CB B:THR56 3.0 56.6 1.0 O1B B:AGS401 3.0 52.4 1.0 O1A B:AGS401 3.5 66.1 1.0 PG B:AGS401 3.5 54.6 1.0 CG2 B:THR56 3.6 57.6 1.0 OD2 B:ASP114 3.7 75.2 1.0 OE2 C:GLU135 3.7 75.3 1.0 PB B:AGS401 4.0 46.7 1.0 NH2 C:ARG160 4.2 51.9 1.0 O3A B:AGS401 4.3 55.1 1.0 O3B B:AGS401 4.3 66.1 1.0 CA B:THR56 4.3 53.5 1.0 OE1 C:GLU135 4.3 68.7 1.0 S1G B:AGS401 4.3 51.3 1.0 PA B:AGS401 4.3 27.8 1.0 CD C:GLU135 4.4 74.3 1.0 OE2 B:GLU115 4.4 63.2 1.0 N B:THR56 4.5 59.8 1.0 CG B:ASP114 4.5 68.8 1.0 OD1 B:ASP114 4.6 67.8 1.0 O3G B:AGS401 4.6 60.9 1.0 O2A B:AGS401 4.7 62.3 1.0 NH2 C:ARG131 4.8 54.4 1.0 CD C:ARG132 5.0 55.1 1.0 NH2 B:ARG16 5.0 69.3 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 3 (Open 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 3 (Open 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:66.2 occ:1.00 O2G C:AGS401 2.1 75.5 1.0 OG1 C:THR60 2.3 55.7 1.0 OD2 C:ASP117 3.2 57.4 1.0 CB C:THR60 3.4 51.9 1.0 O1B C:AGS401 3.5 76.1 1.0 PG C:AGS401 3.6 47.2 1.0 O3A C:AGS401 3.7 74.3 1.0 OD1 C:ASP117 3.7 69.9 1.0 CG C:ASP117 3.8 58.8 1.0 OE2 C:GLU118 3.9 60.4 1.0 PB C:AGS401 4.0 25.7 1.0 CG2 C:THR60 4.1 59.0 1.0 O3G C:AGS401 4.3 78.1 1.0 NH2 D:ARG183 4.3 54.8 1.0 O3B C:AGS401 4.3 70.5 1.0 NH1 D:ARG183 4.3 45.1 1.0 OE1 D:GLU158 4.4 60.7 1.0 O2A C:AGS401 4.5 83.6 1.0 CA C:THR60 4.5 44.8 1.0 N C:THR60 4.6 51.1 1.0 CD D:ARG155 4.6 51.3 1.0 PA C:AGS401 4.7 55.6 1.0 NH1 D:ARG155 4.7 54.0 1.0 S1G C:AGS401 4.8 57.6 1.0 CZ D:ARG183 4.8 41.9 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 3 (Open 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 3 (Open 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:59.3 occ:1.00 OG1 D:THR72 2.1 57.8 1.0 O3G D:AGS401 2.1 86.4 1.0 O2B D:AGS401 2.2 73.4 1.0 PG D:AGS401 3.3 58.0 1.0 CB D:THR72 3.3 38.9 1.0 NH2 E:ARG184 3.5 56.9 1.0 PB D:AGS401 3.5 51.1 1.0 OD2 D:ASP140 3.5 58.6 1.0 S1G D:AGS401 3.7 95.0 1.0 O3B D:AGS401 3.9 68.8 1.0 CG2 D:THR72 4.0 40.4 1.0 O3A D:AGS401 4.0 79.1 1.0 OE1 E:GLU159 4.1 72.1 1.0 OD1 D:ASP140 4.2 62.5 1.0 CG D:ASP140 4.3 57.9 1.0 OE1 D:GLU141 4.4 61.9 1.0 O2A D:AGS401 4.4 75.0 1.0 CD E:ARG156 4.5 61.9 1.0 NH2 E:ARG155 4.5 50.2 1.0 CA D:THR72 4.5 38.9 1.0 N D:THR72 4.6 45.1 1.0 O2G D:AGS401 4.6 54.9 1.0 PA D:AGS401 4.7 51.3 1.0 O1B D:AGS401 4.7 55.8 1.0 CZ E:ARG184 4.7 55.6 1.0 O1A D:AGS401 4.9 72.9 1.0 CD E:GLU159 5.0 75.5 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