Magnesium in PDB 7u1a: Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides

The binding sites of Magnesium atom in the Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides (pdb code 7u1a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides, PDB code: 7u1a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:54.0 occ:1.00 O3G A:AGS901 2.1 62.1 1.0 OG1 A:THR360 2.2 58.1 1.0 O1B A:AGS901 2.5 62.1 1.0 OD2 A:ASP424 2.6 59.5 1.0 S1G A:AGS901 3.0 62.1 1.0 PG A:AGS901 3.0 62.1 1.0 CB A:THR360 3.2 58.1 1.0 CG A:ASP424 3.4 59.5 1.0 OD1 A:ASP424 3.5 59.5 1.0 PB A:AGS901 3.6 62.1 1.0 O3B A:AGS901 3.8 62.1 1.0 CG2 A:THR360 3.9 58.1 1.0 O1A A:AGS901 3.9 62.1 1.0 NH2 B:ARG157 4.2 53.2 1.0 O2G A:AGS901 4.3 62.1 1.0 CA A:THR360 4.4 58.1 1.0 O3A A:AGS901 4.4 62.1 1.0 N A:THR360 4.5 58.1 1.0 PA A:AGS901 4.5 62.1 1.0 OE2 A:GLU425 4.6 59.9 1.0 O2A A:AGS901 4.7 62.1 1.0 CB A:ASP424 4.8 59.5 1.0 CG2 A:ILE454 4.9 55.5 1.0 O2B A:AGS901 4.9 62.1 1.0 NH1 B:ARG129 5.0 56.4 1.0

Magnesium binding site 2 out of 4 in the Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:54.8 occ:1.00 OG1 B:THR56 2.1 49.2 1.0 O1B B:ADP401 2.4 53.5 1.0 CB B:THR56 3.4 49.2 1.0 PB B:ADP401 3.8 53.5 1.0 O1A B:ADP401 3.8 53.5 1.0 OE1 B:GLU115 3.8 52.9 1.0 OE1 C:GLU135 4.1 51.9 1.0 NH2 B:ARG203 4.1 54.2 1.0 O3B B:ADP401 4.1 53.5 1.0 NH2 C:ARG160 4.1 50.8 1.0 CG2 B:THR56 4.1 49.2 1.0 N B:THR56 4.4 49.2 1.0 O3A B:ADP401 4.5 53.5 1.0 CA B:THR56 4.5 49.2 1.0 OE2 C:GLU135 4.7 51.9 1.0 PA B:ADP401 4.7 53.5 1.0 CD C:GLU135 4.8 51.9 1.0 O2B B:ADP401 4.9 53.5 1.0 CD B:GLU115 4.9 52.9 1.0

Magnesium binding site 3 out of 4 in the Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:49.1 occ:1.00 OG1 C:THR60 2.2 48.4 1.0 O3G C:AGS401 2.2 58.6 1.0 O1B C:AGS401 2.4 58.6 1.0 PG C:AGS401 3.1 58.6 1.0 S1G C:AGS401 3.1 58.6 1.0 CB C:THR60 3.5 48.4 1.0 NH2 D:ARG183 3.5 44.1 1.0 PB C:AGS401 3.6 58.6 1.0 OD1 C:ASP117 3.7 51.1 1.0 O3B C:AGS401 3.8 58.6 1.0 OD2 C:ASP117 3.8 51.1 1.0 CG C:ASP117 4.1 51.1 1.0 O1A C:AGS401 4.2 58.6 1.0 NH1 D:ARG155 4.2 52.9 1.0 CG2 C:THR60 4.2 48.4 1.0 O3A C:AGS401 4.2 58.6 1.0 NH2 C:ARG206 4.3 46.6 1.0 OE2 C:GLU118 4.4 51.3 1.0 OE1 D:GLU158 4.4 53.1 1.0 N C:THR60 4.4 48.4 1.0 O2G C:AGS401 4.5 58.6 1.0 CA C:THR60 4.5 48.4 1.0 PA C:AGS401 4.6 58.6 1.0 CZ D:ARG183 4.6 44.1 1.0 CG C:GLU118 4.8 51.3 1.0 O2A C:AGS401 4.8 58.6 1.0 O2B C:AGS401 4.8 58.6 1.0 NH1 D:ARG183 4.9 44.1 1.0 CZ D:ARG155 4.9 52.9 1.0

Magnesium binding site 4 out of 4 in the Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rfc:Pcna Bound to Dsdna with A Ssdna Gap of Six Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:50.7 occ:1.00 O3G D:AGS401 2.1 58.6 1.0 OG1 D:THR72 2.1 44.4 1.0 O2B D:AGS401 2.5 58.6 1.0 OD2 D:ASP140 3.2 49.3 1.0 CB D:THR72 3.3 44.4 1.0 PG D:AGS401 3.4 58.6 1.0 OD1 D:ASP140 3.6 49.3 1.0 CG D:ASP140 3.8 49.3 1.0 S1G D:AGS401 3.8 58.6 1.0 PB D:AGS401 3.9 58.6 1.0 CG2 D:THR72 3.9 44.4 1.0 O3B D:AGS401 4.1 58.6 1.0 O2A D:AGS401 4.1 58.6 1.0 CA D:THR72 4.5 44.4 1.0 OE2 D:GLU141 4.5 53.1 1.0 OE1 E:GLU159 4.5 58.9 1.0 N D:THR72 4.5 44.4 1.0 O2G D:AGS401 4.5 58.6 1.0 NH2 E:ARG184 4.6 49.1 1.0 O1B D:AGS401 4.8 58.6 1.0 CD E:ARG156 4.9 54.9 1.0 O3A D:AGS401 4.9 58.6 1.0 PA D:AGS401 4.9 58.6 1.0 O1A D:AGS401 4.9 58.6 1.0 CG2 D:ILE169 5.0 41.2 1.0

X.Liu, C.Gaubitz, J.Pajak, B.A.Kelch. A Second Dna Binding Site on Rfc Facilitates Clamp Loading at Gapped or Nicked Dna. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35731107
DOI: 10.7554/ELIFE.77483