Magnesium in PDB 7u19: Rfc:Pcna Bound to Nicked Dna

The binding sites of Magnesium atom in the Rfc:Pcna Bound to Nicked Dna (pdb code 7u19). 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 Nicked Dna, PDB code: 7u19:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Rfc:Pcna Bound to Nicked Dna


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 Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:59.2 occ:1.00 O1B A:AGS901 2.2 64.6 1.0 O3G A:AGS901 2.2 64.6 1.0 OG1 A:THR360 2.3 59.9 1.0 OD1 A:ASP424 3.0 66.3 1.0 PG A:AGS901 3.1 64.6 1.0 S1G A:AGS901 3.3 64.6 1.0 PB A:AGS901 3.5 64.6 1.0 CB A:THR360 3.6 59.9 1.0 CG A:ASP424 3.7 66.3 1.0 O3B A:AGS901 3.8 64.6 1.0 O1A A:AGS901 3.8 64.6 1.0 OD2 A:ASP424 3.9 66.3 1.0 OE2 A:GLU425 4.3 66.3 1.0 CG2 A:THR360 4.4 59.9 1.0 O3A A:AGS901 4.4 64.6 1.0 PA A:AGS901 4.5 64.6 1.0 N A:THR360 4.5 59.9 1.0 O2G A:AGS901 4.5 64.6 1.0 O2B A:AGS901 4.5 64.6 1.0 O2A A:AGS901 4.5 64.6 1.0 CA A:THR360 4.6 59.9 1.0 NH1 B:ARG129 4.7 60.1 1.0 CG2 A:ILE454 4.7 63.4 1.0 NH2 B:ARG157 4.9 58.3 1.0 CB A:ASP424 4.9 66.3 1.0 CD A:GLU425 5.0 66.3 1.0

Magnesium binding site 2 out of 4 in the Rfc:Pcna Bound to Nicked Dna


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 Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:55.0 occ:1.00 O3G B:AGS401 2.1 64.7 1.0 OG1 B:THR56 2.3 57.3 1.0 O1B B:AGS401 2.4 64.7 1.0 S1G B:AGS401 2.7 64.7 1.0 PG B:AGS401 2.8 64.7 1.0 CB B:THR56 3.3 57.3 1.0 PB B:AGS401 3.4 64.7 1.0 O3B B:AGS401 3.5 64.7 1.0 OD2 B:ASP114 3.6 54.4 1.0 O1A B:AGS401 3.7 64.7 1.0 OE2 B:GLU115 3.7 55.8 1.0 O3A B:AGS401 3.9 64.7 1.0 O2G B:AGS401 4.2 64.7 1.0 N B:THR56 4.2 57.3 1.0 PA B:AGS401 4.2 64.7 1.0 OD1 B:ASP114 4.2 54.4 1.0 CG B:ASP114 4.3 54.4 1.0 CG2 B:THR56 4.3 57.3 1.0 CA B:THR56 4.4 57.3 1.0 NH2 B:ARG203 4.4 62.8 1.0 NH2 C:ARG160 4.4 57.3 1.0 O2A B:AGS401 4.5 64.7 1.0 CD B:GLU115 4.5 55.8 1.0 OE1 B:GLU115 4.6 55.8 1.0 O2B B:AGS401 4.7 64.7 1.0 NZ B:LYS55 4.8 58.2 1.0 NH1 C:ARG132 4.8 58.8 1.0

Magnesium binding site 3 out of 4 in the Rfc:Pcna Bound to Nicked Dna


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 Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:57.5 occ:1.00 OG1 C:THR60 2.1 52.1 1.0 O1B C:AGS401 2.2 66.5 1.0 O3G C:AGS401 2.2 66.5 1.0 CB C:THR60 3.2 52.1 1.0 PG C:AGS401 3.2 66.5 1.0 S1G C:AGS401 3.4 66.5 1.0 PB C:AGS401 3.5 66.5 1.0 OD1 C:ASP117 3.7 54.1 1.0 OE2 C:GLU118 3.8 55.1 1.0 O3B C:AGS401 3.8 66.5 1.0 OD2 C:ASP117 3.9 54.1 1.0 O1A C:AGS401 4.0 66.5 1.0 CG2 C:THR60 4.1 52.1 1.0 NH2 D:ARG183 4.1 45.2 1.0 CG C:ASP117 4.2 54.1 1.0 N C:THR60 4.2 52.1 1.0 O3A C:AGS401 4.2 66.5 1.0 CA C:THR60 4.3 52.1 1.0 PA C:AGS401 4.5 66.5 1.0 O2G C:AGS401 4.6 66.5 1.0 O2B C:AGS401 4.6 66.5 1.0 O2A C:AGS401 4.6 66.5 1.0 NH2 C:ARG206 4.9 50.9 1.0 CD C:GLU118 4.9 55.1 1.0 CD D:ARG155 5.0 50.0 1.0

Magnesium binding site 4 out of 4 in the Rfc:Pcna Bound to Nicked Dna


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 Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:57.6 occ:1.00 OG1 D:THR72 2.0 49.5 1.0 O3G D:AGS401 2.1 66.5 1.0 O2B D:AGS401 2.1 66.5 1.0 CB D:THR72 3.2 49.5 1.0 PG D:AGS401 3.4 66.5 1.0 PB D:AGS401 3.5 66.5 1.0 OD1 D:ASP140 3.6 51.6 1.0 O2A D:AGS401 3.7 66.5 1.0 CG2 D:THR72 4.0 49.5 1.0 O3B D:AGS401 4.0 66.5 1.0 NH2 E:ARG184 4.1 50.9 1.0 S1G D:AGS401 4.2 66.5 1.0 O1B D:AGS401 4.3 66.5 1.0 CA D:THR72 4.4 49.5 1.0 N D:THR72 4.4 49.5 1.0 OE1 E:GLU159 4.4 58.1 1.0 O3A D:AGS401 4.5 66.5 1.0 PA D:AGS401 4.6 66.5 1.0 CG D:ASP140 4.6 51.6 1.0 CD E:ARG156 4.6 55.1 1.0 O2G D:AGS401 4.6 66.5 1.0 OE2 E:GLU159 4.7 58.1 1.0 O1A D:AGS401 4.8 66.5 1.0 NH1 E:ARG156 4.8 55.1 1.0 NE E:ARG156 4.9 55.1 1.0 OE2 D:GLU141 5.0 51.8 1.0 CG2 D:ILE169 5.0 43.0 1.0 CD E:GLU159 5.0 58.1 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