Magnesium in PDB 8fs6: Structure of S. Cerevisiae RAD24-Rfc Loading the 9-1-1 Clamp Onto A 10-Nt Gapped Dna in Step 4 (Partially 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 4 (Partially Closed 9-1-1 and Stably Bound Chamber Dna) (pdb code 8fs6). 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 4 (Partially Closed 9-1-1 and Stably Bound Chamber Dna), PDB code: 8fs6:
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 4 (Partially 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 4 (Partially Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:61.2 occ:1.00 OE2 A:GLU187 2.1 88.8 1.0 O3A A:AGS601 2.1 76.2 1.0 OG A:SER116 2.4 73.9 1.0 O2B A:AGS601 2.8 77.1 1.0 PB A:AGS601 3.0 75.4 1.0 CD A:GLU187 3.2 90.5 1.0 O2G A:AGS601 3.3 77.2 1.0 PA A:AGS601 3.4 66.8 1.0 OE1 A:GLU187 3.5 87.8 1.0 CB A:SER116 3.6 68.3 1.0 O5' A:AGS601 3.7 62.4 1.0 O3B A:AGS601 3.8 74.5 1.0 O1A A:AGS601 3.8 87.1 1.0 PG A:AGS601 4.2 73.9 1.0 O1B A:AGS601 4.2 60.0 1.0 NH2 A:ARG312 4.3 59.4 1.0 CG A:GLU187 4.5 89.8 1.0 O2A A:AGS601 4.6 70.2 1.0 NH1 A:ARG312 4.7 70.7 1.0 NH2 B:ARG157 4.7 70.6 1.0 CA A:SER116 4.8 65.1 1.0 OE1 B:GLU132 4.8 83.4 1.0 N A:SER116 5.0 74.6 1.0 CZ A:ARG312 5.0 58.0 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 4 (Partially 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 4 (Partially Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:60.1 occ:1.00 OG1 C:THR60 2.0 66.3 1.0 O2G C:AGS401 2.1 57.5 1.0 CB C:THR60 3.1 56.0 1.0 OD2 C:ASP117 3.2 61.9 1.0 CG2 C:THR60 3.5 58.0 1.0 PG C:AGS401 3.6 59.0 1.0 O1B C:AGS401 3.7 65.3 1.0 NH2 D:ARG183 3.7 59.5 1.0 O3A C:AGS401 3.7 50.0 1.0 OE1 C:GLU118 3.9 64.7 1.0 OD1 C:ASP117 4.0 71.8 1.0 CG C:ASP117 4.0 68.6 1.0 PB C:AGS401 4.1 27.2 1.0 O3B C:AGS401 4.3 56.5 1.0 CA C:THR60 4.4 52.6 1.0 OE1 D:GLU158 4.4 69.5 1.0 O3G C:AGS401 4.5 66.6 1.0 CD D:ARG155 4.5 61.0 1.0 NH1 D:ARG155 4.6 66.1 1.0 O2A C:AGS401 4.6 68.2 1.0 S1G C:AGS401 4.6 51.5 1.0 N C:THR60 4.6 61.0 1.0 PA C:AGS401 4.7 33.4 1.0 NH2 D:ARG154 4.8 49.5 1.0 CZ D:ARG183 4.8 60.3 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 4 (Partially 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 4 (Partially Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:56.3 occ:1.00 O2G B:AGS500 2.5 66.8 1.0 OE1 C:GLU135 2.6 70.3 1.0 NH2 C:ARG160 2.8 60.1 1.0 OG1 B:THR56 2.8 62.7 1.0 O1A B:AGS500 3.1 56.3 1.0 OE2 C:GLU135 3.1 75.6 1.0 CD C:GLU135 3.2 68.7 1.0 CB B:THR56 3.5 57.2 1.0 CG2 B:THR56 3.8 60.4 1.0 O1B B:AGS500 3.9 54.1 1.0 PG B:AGS500 4.0 68.4 1.0 CZ C:ARG160 4.0 63.0 1.0 NE C:ARG132 4.1 65.7 1.0 O3A B:AGS500 4.2 55.3 1.0 CD C:ARG132 4.2 65.5 1.0 PA B:AGS500 4.3 37.2 1.0 CZ C:ARG132 4.5 71.9 1.0 NH1 B:ARG203 4.5 66.7 1.0 OD2 B:ASP114 4.5 78.7 1.0 PB B:AGS500 4.5 44.4 1.0 O3B B:AGS500 4.6 60.6 1.0 O3G B:AGS500 4.6 64.7 1.0 CG C:GLU135 4.7 64.8 1.0 NH1 C:ARG160 4.8 62.2 1.0 NE C:ARG160 4.8 59.8 1.0 OE2 B:GLU115 4.8 75.9 1.0 NH2 B:ARG16 4.9 70.6 1.0 NH2 C:ARG132 4.9 67.7 1.0 CA B:THR56 4.9 59.0 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 4 (Partially 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 4 (Partially Closed 9-1-1 and Stably Bound Chamber Dna) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:63.7 occ:1.00 OG1 D:THR72 2.1 63.9 1.0 O3G D:AGS401 2.1 78.1 1.0 O2B D:AGS401 2.3 58.4 1.0 CB D:THR72 3.3 49.4 1.0 PG D:AGS401 3.3 51.2 1.0 OD2 D:ASP140 3.6 71.8 1.0 PB D:AGS401 3.6 46.9 1.0 NH2 E:ARG184 3.7 70.4 1.0 S1G D:AGS401 3.7 82.0 1.0 CG2 D:THR72 3.8 44.7 1.0 OE1 E:GLU159 3.9 83.0 1.0 O3B D:AGS401 4.0 61.6 1.0 OD1 D:ASP140 4.0 74.3 1.0 O3A D:AGS401 4.2 69.5 1.0 CG D:ASP140 4.2 72.1 1.0 OE2 D:GLU141 4.3 75.1 1.0 NH2 E:ARG155 4.4 66.5 1.0 O2A D:AGS401 4.4 71.8 1.0 CA D:THR72 4.5 42.6 1.0 NE E:ARG156 4.6 78.1 1.0 N D:THR72 4.6 42.5 1.0 O2G D:AGS401 4.6 38.5 1.0 PA D:AGS401 4.8 49.4 1.0 CZ E:ARG184 4.8 64.8 1.0 O1B D:AGS401 4.8 53.2 1.0 CD E:ARG156 4.9 71.5 1.0 CD E:GLU159 4.9 83.7 1.0 O1A D:AGS401 5.0 61.4 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