Magnesium in PDB 8fs3: Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 1 (Open 9-1-1 and Shoulder Bound Dna Only)

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 1 (Open 9-1-1 and Shoulder Bound Dna Only) (pdb code 8fs3). 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 1 (Open 9-1-1 and Shoulder Bound Dna Only), PDB code: 8fs3:
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 1 (Open 9-1-1 and Shoulder Bound Dna Only)


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 1 (Open 9-1-1 and Shoulder Bound Dna Only) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:50.1 occ:1.00 O3A A:AGS602 1.9 62.8 1.0 OG A:SER116 2.0 74.3 1.0 CB A:SER116 2.4 74.2 1.0 PA A:AGS602 3.0 62.5 1.0 PB A:AGS602 3.1 69.0 1.0 O2B A:AGS602 3.1 71.4 1.0 O1A A:AGS602 3.2 73.1 1.0 O5' A:AGS602 3.4 57.2 1.0 CA A:SER116 3.8 64.4 1.0 N A:SER116 4.0 66.5 1.0 O3B A:AGS602 4.0 65.1 1.0 OE1 A:GLU187 4.0 73.4 1.0 O1B A:AGS602 4.2 57.6 1.0 O2A A:AGS602 4.3 66.7 1.0 O2G A:AGS602 4.4 67.3 1.0 CD A:GLU187 4.4 73.7 1.0 C A:SER116 4.6 65.0 1.0 N A:THR117 4.8 67.2 1.0 OE2 A:GLU187 4.8 78.3 1.0 C5' A:AGS602 4.8 56.3 1.0 CG A:GLU187 4.9 70.7 1.0 PG A:AGS602 4.9 69.5 1.0 NH2 A:ARG312 4.9 54.8 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 1 (Open 9-1-1 and Shoulder Bound Dna Only)


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 1 (Open 9-1-1 and Shoulder Bound Dna Only) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:45.4 occ:1.00 OG1 B:THR56 2.0 58.4 1.0 O2G B:AGS401 2.0 46.4 1.0 O1B B:AGS401 2.5 31.4 1.0 CB B:THR56 3.2 50.3 1.0 PG B:AGS401 3.5 33.6 1.0 O1A B:AGS401 3.6 44.6 1.0 OD1 B:ASP114 3.7 58.2 1.0 PB B:AGS401 3.7 42.5 1.0 CG2 B:THR56 3.7 42.1 1.0 NH2 C:ARG160 4.1 41.5 1.0 NH2 C:ARG132 4.1 51.8 1.0 O3B B:AGS401 4.1 52.0 1.0 O3A B:AGS401 4.2 50.4 1.0 OE2 B:GLU115 4.3 56.6 1.0 CA B:THR56 4.4 37.0 1.0 O3G B:AGS401 4.4 43.0 1.0 PA B:AGS401 4.4 35.3 1.0 N B:THR56 4.5 39.9 1.0 CG B:ASP114 4.5 54.9 1.0 S1G B:AGS401 4.6 37.9 1.0 NE C:ARG132 4.6 52.4 1.0 OD2 B:ASP114 4.7 58.8 1.0 CZ C:ARG132 4.8 54.2 1.0 O2A B:AGS401 5.0 51.0 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 1 (Open 9-1-1 and Shoulder Bound Dna Only)


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 1 (Open 9-1-1 and Shoulder Bound Dna Only) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:46.9 occ:1.00 O2G C:AGS402 1.9 49.2 1.0 OG1 C:THR60 2.2 35.6 1.0 O1B C:AGS402 2.5 49.8 1.0 OD1 C:ASP117 3.1 35.5 1.0 PG C:AGS402 3.4 30.8 1.0 CB C:THR60 3.5 25.0 1.0 OD2 C:ASP117 3.6 42.4 1.0 PB C:AGS402 3.6 26.9 1.0 CG C:ASP117 3.7 41.3 1.0 NH2 D:ARG183 3.9 42.2 1.0 O3A C:AGS402 3.9 48.3 1.0 OE2 C:GLU118 4.0 47.7 1.0 O3B C:AGS402 4.1 41.3 1.0 O3G C:AGS402 4.1 49.4 1.0 CG2 C:THR60 4.2 35.5 1.0 OE1 D:GLU158 4.3 47.7 1.0 N C:THR60 4.5 38.2 1.0 CA C:THR60 4.5 19.5 1.0 NH2 D:ARG154 4.6 15.3 1.0 CD D:ARG155 4.8 43.5 1.0 S1G C:AGS402 4.8 39.6 1.0 CD C:GLU118 4.9 44.3 1.0 O2A C:AGS402 5.0 50.1 1.0 O2B C:AGS402 5.0 40.0 1.0 CG C:GLU118 5.0 44.1 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 1 (Open 9-1-1 and Shoulder Bound Dna Only)


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 1 (Open 9-1-1 and Shoulder Bound Dna Only) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:34.7 occ:1.00 O3G D:AGS401 2.0 69.9 1.0 OG1 D:THR72 2.4 40.0 1.0 O2B D:AGS401 2.4 61.7 1.0 OE1 E:GLU159 3.4 55.6 1.0 PG D:AGS401 3.5 46.1 1.0 CB D:THR72 3.6 33.9 1.0 PB D:AGS401 3.7 33.2 1.0 OD2 D:ASP140 3.8 48.5 1.0 O3A D:AGS401 3.9 59.4 1.0 OD1 D:ASP140 4.1 48.8 1.0 O3B D:AGS401 4.1 67.3 1.0 CG D:ASP140 4.3 45.4 1.0 OE2 D:GLU141 4.3 44.6 1.0 CG2 D:THR72 4.4 32.9 1.0 CD E:GLU159 4.5 56.7 1.0 O2G D:AGS401 4.5 42.3 1.0 S1G D:AGS401 4.5 70.1 1.0 N D:THR72 4.6 28.4 1.0 NH1 E:ARG156 4.6 51.4 1.0 CA D:THR72 4.6 32.4 1.0 NH1 E:ARG184 4.7 37.9 1.0 NH2 E:ARG155 4.8 37.9 1.0 O2A D:AGS401 4.8 59.5 1.0 OE2 E:GLU159 4.8 51.1 1.0 NH2 E:ARG184 4.8 56.8 1.0 O1B D:AGS401 4.9 59.3 1.0 PA D:AGS401 5.0 17.0 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