Magnesium in PDB 8fs8: Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound Dna)

The binding sites of Magnesium atom in the Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound Dna) (pdb code 8fs8). 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound Dna), PDB code: 8fs8:
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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound Dna) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:89.8 occ:1.00 OG A:SER116 2.4 77.4 1.0 CB A:SER116 2.4 81.0 1.0 OE1 A:GLU187 2.7 81.8 1.0 OE2 A:GLU187 2.8 83.0 1.0 O2B A:AGS501 2.9 84.9 1.0 CD A:GLU187 3.1 79.1 1.0 O3A A:AGS501 3.1 85.0 1.0 PB A:AGS501 3.6 75.4 1.0 CA A:SER116 4.0 80.2 1.0 O2G A:AGS501 4.2 88.8 1.0 O3B A:AGS501 4.4 84.0 1.0 PA A:AGS501 4.4 92.1 1.0 NZ A:LYS120 4.5 95.0 1.0 CG A:GLU187 4.6 73.7 1.0 OE2 B:GLU132 4.6 94.7 1.0 N A:SER116 4.7 80.0 1.0 O1A A:AGS501 4.7 92.3 1.0 C A:SER116 4.7 84.0 1.0 O5' A:AGS501 4.8 84.5 1.0 O1B A:AGS501 4.9 83.6 1.0 PG A:AGS501 4.9 88.9 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound Dna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:79.9 occ:1.00 O2G B:AGS401 2.1 84.7 1.0 OG1 B:THR56 2.2 78.2 1.0 O1B B:AGS401 3.0 82.8 1.0 CB B:THR56 3.1 79.0 1.0 O1A B:AGS401 3.4 85.5 1.0 PG B:AGS401 3.6 78.6 1.0 OD2 B:ASP114 3.7 67.6 1.0 NH2 C:ARG160 3.7 75.5 1.0 CG2 B:THR56 3.7 87.6 1.0 NH2 C:ARG132 4.0 78.4 1.0 PB B:AGS401 4.0 83.9 1.0 OE2 B:GLU115 4.1 90.5 1.0 PA B:AGS401 4.3 80.9 1.0 O3A B:AGS401 4.3 82.8 1.0 O3B B:AGS401 4.3 87.0 1.0 CA B:THR56 4.4 76.3 1.0 O3G B:AGS401 4.5 82.7 1.0 CG B:ASP114 4.5 65.3 1.0 OD1 B:ASP114 4.5 66.3 1.0 N B:THR56 4.6 82.7 1.0 S1G B:AGS401 4.6 79.3 1.0 CZ C:ARG132 4.6 81.3 1.0 NH2 B:ARG203 4.6 79.6 1.0 O2A B:AGS401 4.7 85.1 1.0 NE C:ARG132 4.8 76.0 1.0 CZ C:ARG160 5.0 73.8 1.0 NH1 B:ARG203 5.0 78.7 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound Dna) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:36.5 occ:1.00 O2G C:AGS401 2.0 63.7 1.0 OG1 C:THR60 2.0 64.0 1.0 O1B C:AGS401 2.9 56.2 1.0 O3A C:AGS401 3.0 63.1 1.0 CB C:THR60 3.1 53.5 1.0 OD2 C:ASP117 3.2 75.9 1.0 PB C:AGS401 3.4 57.1 1.0 PG C:AGS401 3.5 61.6 1.0 OD1 C:ASP117 3.9 76.3 1.0 CG C:ASP117 3.9 69.4 1.0 O3B C:AGS401 3.9 56.6 1.0 O2A C:AGS401 3.9 49.3 1.0 PA C:AGS401 3.9 40.2 1.0 CG2 C:THR60 4.0 43.1 1.0 N C:THR60 4.2 42.8 1.0 NH2 D:ARG183 4.2 52.6 1.0 CA C:THR60 4.2 47.3 1.0 O1A C:AGS401 4.3 50.9 1.0 O3G C:AGS401 4.4 68.2 1.0 S1G C:AGS401 4.6 51.8 1.0 O2B C:AGS401 4.8 67.5 1.0 CZ D:ARG155 4.9 70.6 1.0 NE D:ARG155 5.0 71.8 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound 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 5- Nt Gapped Dna (9-1-1 Encircling Fully Bound Dna) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:60.5 occ:1.00 O2B D:AGS401 2.3 46.1 1.0 OG1 D:THR72 2.4 57.2 1.0 S1G D:AGS401 2.7 73.9 1.0 O3G D:AGS401 3.0 57.7 1.0 OD2 D:ASP140 3.3 72.3 1.0 PG D:AGS401 3.4 70.2 1.0 CB D:THR72 3.5 45.8 1.0 PB D:AGS401 3.6 54.2 1.0 OE1 E:GLU159 3.9 87.9 1.0 O3B D:AGS401 4.0 64.6 1.0 OD1 D:ASP140 4.0 81.0 1.0 O2A D:AGS401 4.0 55.5 1.0 CG D:ASP140 4.1 72.7 1.0 O3A D:AGS401 4.1 44.6 1.0 NH2 E:ARG184 4.4 72.7 1.0 OE2 E:GLU159 4.4 87.4 1.0 CG2 D:THR72 4.4 38.2 1.0 NH1 E:ARG156 4.5 98.5 1.0 N D:THR72 4.5 24.2 1.0 PA D:AGS401 4.5 27.9 1.0 CD E:GLU159 4.6 90.7 1.0 CA D:THR72 4.6 20.2 1.0 O1A D:AGS401 4.7 50.7 1.0 NH1 E:ARG184 4.8 77.5 1.0 O2G D:AGS401 4.8 33.1 1.0 O1B D:AGS401 4.8 52.1 1.0 OE2 D:GLU141 4.9 90.2 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