Magnesium in PDB 8fs4: Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 2 (Open 9-1-1 Ring and Flexibly 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 2 (Open 9-1-1 Ring and Flexibly Bound Chamber Dna) (pdb code 8fs4). 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 2 (Open 9-1-1 Ring and Flexibly Bound Chamber Dna), PDB code: 8fs4:
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 2 (Open 9-1-1 Ring and Flexibly 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 2 (Open 9-1-1 Ring and Flexibly Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:66.1 occ:1.00 O3A A:AGS601 2.2 69.8 1.0 OG A:SER116 2.4 83.7 1.0 O2B A:AGS601 2.6 69.0 1.0 PB A:AGS601 3.0 67.7 1.0 PA A:AGS601 3.4 66.8 1.0 O1A A:AGS601 3.5 74.0 1.0 CB A:SER116 3.7 82.7 1.0 O2G A:AGS601 3.7 66.3 1.0 OE1 A:GLU187 3.9 92.5 1.0 O1B A:AGS601 4.0 58.0 1.0 O3B A:AGS601 4.1 73.5 1.0 O5' A:AGS601 4.2 63.2 1.0 NH2 A:ARG312 4.4 59.3 1.0 CG A:GLU187 4.5 93.6 1.0 O2A A:AGS601 4.6 75.2 1.0 CD A:GLU187 4.6 94.7 1.0 PG A:AGS601 4.6 61.3 1.0 N A:SER116 4.7 76.8 1.0 NH2 B:ARG157 4.8 60.8 1.0 CA A:SER116 4.8 77.7 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 2 (Open 9-1-1 Ring and Flexibly 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 2 (Open 9-1-1 Ring and Flexibly Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:52.3 occ:1.00 O2G B:AGS401 2.4 42.4 1.0 OG1 B:THR56 2.6 53.0 1.0 O1B B:AGS401 2.7 44.7 1.0 O3G B:AGS401 3.0 37.8 1.0 PG B:AGS401 3.2 36.3 1.0 CB B:THR56 3.5 50.8 1.0 OD2 B:ASP114 3.7 64.3 1.0 OD1 B:ASP114 3.8 60.0 1.0 PB B:AGS401 3.9 54.2 1.0 OE2 B:GLU115 4.0 56.7 1.0 O3B B:AGS401 4.0 48.5 1.0 NH2 C:ARG131 4.1 53.1 1.0 CG B:ASP114 4.1 61.7 1.0 O1A B:AGS401 4.3 43.7 1.0 CG2 B:THR56 4.4 49.1 1.0 N B:THR56 4.6 44.9 1.0 CA B:THR56 4.6 44.4 1.0 OE2 C:GLU135 4.8 55.6 1.0 O3A B:AGS401 4.8 46.3 1.0 NH2 C:ARG160 4.9 39.6 1.0 S1G B:AGS401 4.9 47.5 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 2 (Open 9-1-1 Ring and Flexibly 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 2 (Open 9-1-1 Ring and Flexibly Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:32.3 occ:1.00 O2G C:AGS401 1.8 59.5 1.0 OG1 C:THR60 2.1 48.4 1.0 OD2 C:ASP117 3.1 51.3 1.0 O1B C:AGS401 3.2 62.5 1.0 CB C:THR60 3.3 34.3 1.0 PG C:AGS401 3.4 48.5 1.0 OD1 C:ASP117 3.5 36.4 1.0 O3A C:AGS401 3.6 49.5 1.0 CG C:ASP117 3.7 42.2 1.0 PB C:AGS401 3.8 27.0 1.0 OE2 C:GLU118 4.0 48.9 1.0 CG2 C:THR60 4.1 37.9 1.0 O3G C:AGS401 4.1 58.2 1.0 O3B C:AGS401 4.1 53.4 1.0 CA C:THR60 4.4 19.7 1.0 N C:THR60 4.5 27.2 1.0 OE1 D:GLU158 4.5 46.8 1.0 NH2 D:ARG183 4.5 51.0 1.0 NH1 D:ARG183 4.5 38.0 1.0 S1G C:AGS401 4.5 32.8 1.0 O2A C:AGS401 4.7 62.1 1.0 PA C:AGS401 4.8 26.4 1.0 CD D:ARG155 4.8 41.8 1.0 NH1 D:ARG155 4.9 44.6 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 2 (Open 9-1-1 Ring and Flexibly 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 2 (Open 9-1-1 Ring and Flexibly Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:47.7 occ:1.00 O2B D:AGS401 1.9 55.7 1.0 O3G D:AGS401 1.9 63.5 1.0 OG1 D:THR72 2.2 47.7 1.0 PG D:AGS401 3.2 41.7 1.0 PB D:AGS401 3.3 36.0 1.0 CB D:THR72 3.4 44.8 1.0 NH2 E:ARG184 3.7 60.2 1.0 O3B D:AGS401 3.7 58.0 1.0 OD2 D:ASP140 3.7 51.1 1.0 O3A D:AGS401 3.8 56.1 1.0 S1G D:AGS401 3.9 73.4 1.0 CG2 D:THR72 4.1 37.4 1.0 OD1 D:ASP140 4.2 50.9 1.0 CG D:ASP140 4.4 49.5 1.0 O2A D:AGS401 4.4 60.4 1.0 OE1 E:GLU159 4.4 59.7 1.0 O1B D:AGS401 4.4 48.8 1.0 O2G D:AGS401 4.4 43.2 1.0 N D:THR72 4.5 23.9 1.0 CA D:THR72 4.5 35.1 1.0 PA D:AGS401 4.6 26.5 1.0 NH2 E:ARG155 4.6 54.1 1.0 OE2 D:GLU141 4.8 41.4 1.0 NH1 E:ARG156 4.8 60.7 1.0 O1A D:AGS401 4.9 61.7 1.0 CZ E:ARG184 4.9 51.7 1.0 CD E:ARG156 4.9 53.5 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