Magnesium in PDB 7u1p: Rfc:Pcna Bound to Dna with A Ssdna Gap of Five Nucleotides

The binding sites of Magnesium atom in the Rfc:Pcna Bound to Dna with A Ssdna Gap of Five Nucleotides (pdb code 7u1p). 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 Dna with A Ssdna Gap of Five Nucleotides, PDB code: 7u1p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Rfc:Pcna Bound to Dna with A Ssdna Gap of Five 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 Dna with A Ssdna Gap of Five Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:19.6 occ:1.00 OG1 A:THR360 2.2 26.2 1.0 O1B A:AGS901 2.4 24.9 1.0 O3G A:AGS901 2.6 24.9 1.0 S1G A:AGS901 2.8 24.9 1.0 PG A:AGS901 3.2 24.9 1.0 CB A:THR360 3.5 26.2 1.0 PB A:AGS901 3.6 24.9 1.0 OD1 A:ASP424 3.7 30.7 1.0 O3B A:AGS901 3.8 24.9 1.0 O1A A:AGS901 4.0 24.9 1.0 CG2 A:THR360 4.3 26.2 1.0 OE2 A:GLU425 4.3 30.8 1.0 NH2 B:ARG157 4.4 19.8 1.0 CG A:ASP424 4.4 30.7 1.0 O3A A:AGS901 4.5 24.9 1.0 N A:THR360 4.5 26.2 1.0 O2G A:AGS901 4.6 24.9 1.0 PA A:AGS901 4.6 24.9 1.0 CA A:THR360 4.6 26.2 1.0 O2A A:AGS901 4.7 24.9 1.0 O2B A:AGS901 4.7 24.9 1.0 CG2 A:ILE454 4.9 29.0 1.0 NH2 A:ARG515 4.9 15.7 1.0 CD A:GLU425 5.0 30.8 1.0

Magnesium binding site 2 out of 4 in the Rfc:Pcna Bound to Dna with A Ssdna Gap of Five 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 Dna with A Ssdna Gap of Five Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:24.1 occ:1.00 O1B B:ADP401 2.1 25.7 1.0 OG1 B:THR56 2.2 22.1 1.0 OD1 B:ASP114 3.3 20.9 1.0 CB B:THR56 3.5 22.1 1.0 PB B:ADP401 3.5 25.7 1.0 OD2 B:ASP114 3.6 20.9 1.0 OE2 B:GLU115 3.7 21.8 1.0 CG B:ASP114 3.8 20.9 1.0 O1A B:ADP401 3.9 25.7 1.0 O3B B:ADP401 4.1 25.7 1.0 CG2 B:THR56 4.2 22.1 1.0 NH1 C:ARG160 4.4 23.7 1.0 CD B:GLU115 4.4 21.8 1.0 O3A B:ADP401 4.4 25.7 1.0 N B:THR56 4.4 22.1 1.0 OE1 C:GLU135 4.5 24.4 1.0 O2B B:ADP401 4.5 25.7 1.0 CA B:THR56 4.5 22.1 1.0 OE1 B:GLU115 4.6 21.8 1.0 NH1 C:ARG132 4.6 22.2 1.0 PA B:ADP401 4.7 25.7 1.0 NH2 C:ARG160 4.7 23.7 1.0 NH2 B:ARG203 4.8 24.5 1.0 CE B:LYS55 4.9 21.9 1.0

Magnesium binding site 3 out of 4 in the Rfc:Pcna Bound to Dna with A Ssdna Gap of Five 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 Dna with A Ssdna Gap of Five Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:24.2 occ:1.00 OG1 C:THR60 2.2 22.3 1.0 O3G C:AGS401 2.3 36.0 1.0 O1B C:AGS401 2.5 36.0 1.0 S1G C:AGS401 3.0 36.0 1.0 PG C:AGS401 3.1 36.0 1.0 CB C:THR60 3.4 22.3 1.0 NH2 D:ARG183 3.6 19.0 1.0 PB C:AGS401 3.7 36.0 1.0 OE2 C:GLU118 3.9 24.1 1.0 O3B C:AGS401 3.9 36.0 1.0 CG2 C:THR60 4.0 22.3 1.0 O1A C:AGS401 4.1 36.0 1.0 O3A C:AGS401 4.4 36.0 1.0 O2G C:AGS401 4.5 36.0 1.0 NH2 C:ARG206 4.5 20.2 1.0 OE1 D:GLU158 4.5 29.9 1.0 CA C:THR60 4.5 22.3 1.0 N C:THR60 4.6 22.3 1.0 PA C:AGS401 4.6 36.0 1.0 OD1 C:ASP117 4.7 24.4 1.0 CD C:GLU118 4.7 24.1 1.0 O2A C:AGS401 4.8 36.0 1.0 CG C:ASP117 4.8 24.4 1.0 CZ D:ARG183 4.9 19.0 1.0 OD2 C:ASP117 4.9 24.4 1.0 OE2 D:GLU158 4.9 29.9 1.0 O2B C:AGS401 5.0 36.0 1.0

Magnesium binding site 4 out of 4 in the Rfc:Pcna Bound to Dna with A Ssdna Gap of Five 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 Dna with A Ssdna Gap of Five Nucleotides within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:27.8 occ:1.00 OG1 D:THR72 2.1 22.6 1.0 O3G D:AGS401 2.1 36.0 1.0 O2B D:AGS401 2.3 36.0 1.0 CB D:THR72 3.3 22.6 1.0 PG D:AGS401 3.5 36.0 1.0 NH2 E:ARG184 3.6 26.5 1.0 PB D:AGS401 3.7 36.0 1.0 CG2 D:THR72 3.9 22.6 1.0 O2A D:AGS401 4.0 36.0 1.0 O3B D:AGS401 4.1 36.0 1.0 S1G D:AGS401 4.1 36.0 1.0 NH2 E:ARG155 4.3 29.1 1.0 OE2 E:GLU159 4.3 34.7 1.0 OD1 D:ASP140 4.4 27.7 1.0 CA D:THR72 4.5 22.6 1.0 O1B D:AGS401 4.5 36.0 1.0 OD2 D:ASP140 4.5 27.7 1.0 N D:THR72 4.5 22.6 1.0 CG D:ASP140 4.6 27.7 1.0 O2G D:AGS401 4.6 36.0 1.0 CD E:ARG156 4.7 33.2 1.0 O3A D:AGS401 4.7 36.0 1.0 PA D:AGS401 4.8 36.0 1.0 CZ E:ARG184 4.9 26.5 1.0 O1A D:AGS401 5.0 36.0 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