Magnesium in PDB 8dr0: Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction

The binding sites of Magnesium atom in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (pdb code 8dr0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction, PDB code: 8dr0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:34.0 occ:1.00 O2G A:AGS901 2.3 44.7 1.0 OG1 A:THR360 2.3 40.5 1.0 O1B A:AGS901 2.5 37.9 1.0 HOG2 A:AGS901 2.9 41.5 1.0 PG A:AGS901 3.3 28.5 1.0 HB A:THR360 3.3 41.0 1.0 CB A:THR360 3.4 41.6 1.0 H A:THR360 3.5 41.1 1.0 O3G A:AGS901 3.5 42.2 1.0 OD1 A:ASP424 3.5 46.8 1.0 OD2 A:ASP424 3.5 43.8 1.0 PB A:AGS901 3.7 18.0 1.0 O3B A:AGS901 3.8 36.3 1.0 HG21 A:ILE454 3.8 45.4 1.0 CG A:ASP424 3.9 46.2 1.0 H21 A:AGS901 3.9 40.4 1.0 N A:THR360 4.0 38.3 1.0 HB2 A:LYS359 4.0 42.3 1.0 HE2 A:LYS359 4.1 43.1 1.0 CA A:THR360 4.2 40.8 1.0 HH21 B:ARG128 4.3 32.7 1.0 HG21 A:THR360 4.3 40.4 1.0 HG3 A:GLU425 4.4 39.0 1.0 HA A:THR360 4.4 41.3 1.0 HH22 B:ARG157 4.4 33.1 1.0 HZ1 A:LYS359 4.5 42.4 1.0 O2B A:AGS901 4.5 45.8 1.0 CG2 A:THR360 4.5 39.5 1.0 HZ3 A:LYS359 4.5 42.4 1.0 O1A A:AGS901 4.5 45.9 1.0 HG22 A:ILE454 4.6 45.5 1.0 CG2 A:ILE454 4.6 44.0 1.0 HH22 B:ARG128 4.7 33.0 1.0 NH2 B:ARG128 4.8 33.0 1.0 NZ A:LYS359 4.8 40.2 1.0 HH22 A:ARG515 4.9 37.9 1.0 HD12 A:ILE454 4.9 45.7 1.0 CE A:LYS359 4.9 41.4 1.0 O3A A:AGS901 4.9 37.1 1.0 CB A:LYS359 4.9 41.9 1.0

Magnesium binding site 2 out of 4 in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:25.6 occ:1.00 O2G B:AGS402 2.1 35.2 1.0 O2B B:AGS402 2.1 29.6 1.0 OG1 B:THR56 2.4 29.1 1.0 HOG2 B:AGS402 2.5 25.5 1.0 HG1 B:THR56 3.0 23.8 1.0 HB B:THR56 3.1 23.5 1.0 CB B:THR56 3.3 22.7 1.0 PB B:AGS402 3.3 11.7 1.0 PG B:AGS402 3.4 12.5 1.0 O3B B:AGS402 3.5 13.5 1.0 O2A B:AGS402 3.6 26.1 1.0 HH22 C:ARG160 3.7 20.4 1.0 H B:THR56 3.8 22.4 1.0 HG21 B:THR56 3.9 22.1 1.0 HH22 B:ARG203 3.9 23.6 1.0 OD2 B:ASP114 4.0 35.1 1.0 OE1 C:GLU135 4.1 32.8 1.0 HH21 C:ARG160 4.1 19.0 1.0 CG2 B:THR56 4.2 19.3 1.0 NH2 C:ARG160 4.2 21.8 1.0 O3G B:AGS402 4.3 29.9 1.0 O3A B:AGS402 4.3 24.0 1.0 O1B B:AGS402 4.4 14.2 1.0 PA B:AGS402 4.4 14.9 1.0 OD1 B:ASP114 4.4 28.1 1.0 HH21 B:ARG203 4.4 22.9 1.0 N B:THR56 4.4 16.8 1.0 HH21 C:ARG131 4.5 19.5 1.0 CA B:THR56 4.5 19.2 1.0 NH2 B:ARG203 4.5 23.3 1.0 CG B:ASP114 4.6 29.3 1.0 O1A B:AGS402 4.7 15.2 1.0 H21 B:AGS402 4.7 26.1 1.0 HG23 B:THR56 4.8 23.9 1.0 HG3 B:GLU115 4.8 22.4 1.0 S1G B:AGS402 4.8 29.7 1.0 HG22 B:THR56 4.8 22.5 1.0 HB2 B:LYS55 4.8 24.4 1.0 HH22 B:ARG16 4.9 25.8 1.0 HA B:THR56 4.9 24.1 1.0 CD C:GLU135 5.0 28.4 1.0

Magnesium binding site 3 out of 4 in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:14.9 occ:1.00 HOG2 C:AGS402 1.8 29.9 1.0 O2G C:AGS402 2.2 29.0 1.0 OG1 C:THR60 2.3 15.3 1.0 O2B C:AGS402 2.4 23.8 1.0 HG1 C:THR60 2.9 23.2 1.0 HB C:THR60 3.1 23.6 1.0 PG C:AGS402 3.2 0.0 1.0 CB C:THR60 3.3 11.2 1.0 O3B C:AGS402 3.3 19.1 1.0 HH22 D:ARG183 3.4 12.7 1.0 PB C:AGS402 3.4 0.0 1.0 H C:THR60 3.6 21.0 1.0 O3G C:AGS402 3.7 29.3 1.0 HH21 D:ARG154 3.7 13.9 1.0 OD2 C:ASP117 3.8 21.3 1.0 HH21 D:ARG183 3.9 12.6 1.0 O2A C:AGS402 3.9 26.6 1.0 NH2 D:ARG183 3.9 8.5 1.0 OD1 C:ASP117 4.0 26.1 1.0 HG21 C:THR60 4.1 22.1 1.0 HD3 D:ARG155 4.1 14.5 1.0 H21 C:AGS402 4.2 28.3 1.0 N C:THR60 4.2 1.6 1.0 CG2 C:THR60 4.3 14.4 1.0 CA C:THR60 4.3 13.0 1.0 CG C:ASP117 4.3 16.5 1.0 NH2 D:ARG154 4.4 7.2 1.0 HB2 C:LYS59 4.4 10.1 1.0 HD23 C:LEU146 4.5 14.9 1.0 O1B C:AGS402 4.5 16.2 1.0 HH22 D:ARG154 4.5 12.7 1.0 O3A C:AGS402 4.5 16.1 1.0 HH12 C:ARG206 4.6 9.5 1.0 HG3 C:GLU118 4.6 12.8 1.0 HA C:THR60 4.6 23.2 1.0 HE2 C:LYS59 4.7 12.0 1.0 OE2 C:GLU118 4.7 26.5 1.0 PA C:AGS402 4.7 0.0 1.0 HH22 C:ARG206 4.7 15.9 1.0 OE1 D:GLU158 4.8 24.5 1.0 HD22 C:LEU146 4.8 12.9 1.0 HH11 D:ARG155 4.9 15.4 1.0 HG23 C:THR60 4.9 23.6 1.0 S1G C:AGS402 4.9 8.3 1.0 HG22 C:THR60 4.9 24.0 1.0 CD D:ARG155 5.0 11.5 1.0

Magnesium binding site 4 out of 4 in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:12.0 occ:1.00 HOG2 D:AGS402 1.6 29.7 1.0 O2B D:AGS402 2.2 32.6 1.0 OG1 D:THR72 2.3 18.7 1.0 O2G D:AGS402 2.4 23.3 1.0 HG1 D:THR72 3.0 18.1 1.0 HB D:THR72 3.0 17.1 1.0 CB D:THR72 3.2 7.8 1.0 H D:THR72 3.4 15.2 1.0 PB D:AGS402 3.4 0.0 1.0 PG D:AGS402 3.4 0.0 1.0 HH22 E:ARG184 3.5 17.5 1.0 O3B D:AGS402 3.5 24.4 1.0 HH21 E:ARG155 3.7 15.4 1.0 OD2 D:ASP140 3.8 16.7 1.0 O3G D:AGS402 3.9 33.4 1.0 HH21 E:ARG184 4.0 17.3 1.0 N D:THR72 4.0 4.9 1.0 OD1 D:ASP140 4.1 23.7 1.0 NH2 E:ARG184 4.1 8.1 1.0 O2A D:AGS402 4.1 31.9 1.0 HG21 D:THR72 4.2 16.3 1.0 HB2 D:LYS71 4.2 12.8 1.0 CA D:THR72 4.2 7.6 1.0 HG21 D:ILE169 4.2 13.5 1.0 O1B D:AGS402 4.3 9.8 1.0 OE1 E:GLU159 4.3 31.1 1.0 CG2 D:THR72 4.3 13.7 1.0 HH22 D:ARG229 4.3 29.5 1.0 CG D:ASP140 4.3 18.8 1.0 HD3 E:ARG156 4.4 19.9 1.0 NH2 E:ARG155 4.4 6.8 1.0 HE2 D:LYS71 4.4 12.3 1.0 OE2 D:GLU141 4.5 26.3 1.0 HA D:THR72 4.5 17.5 1.0 H21 D:AGS402 4.6 28.2 1.0 HH22 E:ARG155 4.6 16.3 1.0 O3A D:AGS402 4.6 27.5 1.0 HH11 E:ARG156 4.8 21.1 1.0 PA D:AGS402 4.8 4.3 1.0 HG22 D:ILE169 4.9 11.3 1.0 HG22 D:THR72 4.9 16.3 1.0 HG23 D:THR72 5.0 18.1 1.0 HH21 D:ARG229 5.0 30.9 1.0 O1A D:AGS402 5.0 8.3 1.0

M.Schrecker, J.C.Castaneda, S.Devbhandari, C.Kumar, D.Remus, R.K.Hite. Multistep Loading of A Dna Sliding Clamp Onto Dna By Replication Factor C. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35939393
DOI: 10.7554/ELIFE.78253