Magnesium in PDB 8dr6: Closed State of Rfc:Pcna Bound to A Nicked Dsdna

The binding sites of Magnesium atom in the Closed State of Rfc:Pcna Bound to A Nicked Dsdna (pdb code 8dr6). 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 Nicked Dsdna, PDB code: 8dr6:
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 Nicked Dsdna


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 Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:38.8 occ:1.00 HG1 A:THR360 1.7 48.4 1.0 O A:HOH1001 2.0 37.3 1.0 O A:HOH1003 2.0 40.4 1.0 O A:HOH1002 2.0 42.2 1.0 O2G A:AGS901 2.0 47.9 1.0 OG1 A:THR360 2.3 48.4 1.0 O1B A:AGS901 2.5 47.9 1.0 HB A:THR360 3.2 48.4 1.0 CB A:THR360 3.3 48.4 1.0 PG A:AGS901 3.4 47.9 1.0 OD2 A:ASP424 3.6 49.1 1.0 HH22 B:ARG157 3.6 38.9 1.0 HG21 A:THR360 3.7 48.4 1.0 PB A:AGS901 3.7 47.9 1.0 O3G A:AGS901 3.8 47.9 1.0 O1A A:AGS901 3.8 47.9 1.0 HH21 B:ARG157 3.8 38.9 1.0 H A:THR360 3.9 48.4 1.0 HH22 A:ARG515 4.0 44.8 1.0 NH2 B:ARG157 4.0 38.9 1.0 O3B A:AGS901 4.1 47.9 1.0 CG2 A:THR360 4.1 48.4 1.0 HH21 B:ARG128 4.1 37.2 1.0 OE2 A:GLU425 4.1 47.1 1.0 O3A A:AGS901 4.3 47.9 1.0 OD1 A:ASP424 4.3 49.1 1.0 HH11 B:ARG129 4.3 39.8 1.0 CG A:ASP424 4.3 49.1 1.0 PA A:AGS901 4.5 47.9 1.0 CA A:THR360 4.5 48.4 1.0 HD3 B:ARG129 4.5 39.8 1.0 N A:THR360 4.5 48.4 1.0 OE1 B:GLU132 4.6 37.9 1.0 HG23 A:THR360 4.7 48.4 1.0 NH2 A:ARG515 4.7 44.8 1.0 HH21 A:ARG515 4.7 44.8 1.0 HG21 A:ILE454 4.7 51.4 1.0 HG22 A:THR360 4.8 48.4 1.0 NH2 B:ARG128 4.8 37.2 1.0 O2A A:AGS901 4.8 47.9 1.0 NH1 B:ARG129 4.9 39.8 1.0 OE2 B:GLU132 4.9 37.9 1.0 HH22 B:ARG128 4.9 37.2 1.0 S1G A:AGS901 4.9 47.9 1.0 HA A:THR360 4.9 48.4 1.0

Magnesium binding site 2 out of 4 in the Closed State of Rfc:Pcna Bound to A Nicked Dsdna


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 Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:46.1 occ:1.00 HG21 B:THR56 2.0 31.1 1.0 HH11 C:ARG132 2.4 28.6 1.0 NH1 C:ARG132 2.5 28.6 1.0 HD3 C:ARG132 2.6 28.6 1.0 OD2 B:ASP114 2.7 30.5 1.0 CZ C:ARG132 2.8 28.6 1.0 O B:HOH503 2.8 28.5 1.0 CG2 B:THR56 2.9 31.1 1.0 O B:HOH502 2.9 32.8 1.0 HH12 C:ARG132 2.9 28.6 1.0 OG1 B:THR56 3.0 31.1 1.0 NE C:ARG132 3.0 28.6 1.0 CD C:ARG132 3.1 28.6 1.0 HD2 C:ARG132 3.2 28.6 1.0 CB B:THR56 3.3 31.1 1.0 HB B:THR56 3.3 31.1 1.0 HG1 B:THR56 3.3 31.1 1.0 HG22 B:THR56 3.3 31.1 1.0 HG23 B:THR56 3.5 31.1 1.0 HE C:ARG132 3.6 28.6 1.0 NH2 C:ARG132 3.6 28.6 1.0 OE1 C:GLU135 3.8 28.5 1.0 HH22 C:ARG132 3.9 28.6 1.0 CG B:ASP114 3.9 30.5 1.0 HH21 C:ARG132 4.1 28.6 1.0 O2A B:AGS402 4.6 30.6 1.0 OD1 B:ASP114 4.6 30.5 1.0 O B:HOH501 4.6 33.5 1.0 CG C:ARG132 4.6 28.6 1.0 HH22 B:ARG16 4.6 33.7 1.0 HH21 C:ARG160 4.7 27.6 1.0 CD C:GLU135 4.7 28.5 1.0 CA B:THR56 4.8 31.1 1.0 HE1 B:HIS60 4.8 31.5 1.0 O2G B:AGS402 4.8 30.6 1.0 O2B B:AGS402 4.8 30.6 1.0 HG3 C:ARG132 4.8 28.6 1.0 HG2 C:ARG132 4.9 28.6 1.0 OE2 B:GLU115 5.0 30.5 1.0

Magnesium binding site 3 out of 4 in the Closed State of Rfc:Pcna Bound to A Nicked Dsdna


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 Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:24.5 occ:1.00 O2G C:AGS402 2.0 37.7 1.0 O2B C:AGS402 2.1 37.7 1.0 OG1 C:THR60 2.2 25.5 1.0 O C:HOH503 2.2 24.4 1.0 O C:HOH501 2.3 25.4 1.0 O C:HOH502 2.3 24.2 1.0 HG1 C:THR60 2.8 25.5 1.0 HB C:THR60 3.0 25.5 1.0 CB C:THR60 3.2 25.5 1.0 PG C:AGS402 3.4 37.7 1.0 HH22 D:ARG183 3.4 20.8 1.0 PB C:AGS402 3.5 37.7 1.0 H C:THR60 3.5 25.5 1.0 OD2 C:ASP117 3.6 25.1 1.0 HH21 D:ARG154 3.9 27.2 1.0 O3B C:AGS402 3.9 37.7 1.0 HG21 C:THR60 3.9 25.5 1.0 O2A C:AGS402 3.9 37.7 1.0 O3G C:AGS402 3.9 37.7 1.0 HH21 D:ARG183 3.9 20.8 1.0 NH2 D:ARG183 4.0 20.8 1.0 OD1 C:ASP117 4.1 25.1 1.0 N C:THR60 4.1 25.5 1.0 CG2 C:THR60 4.1 25.5 1.0 O3A C:AGS402 4.2 37.7 1.0 CA C:THR60 4.2 25.5 1.0 CG C:ASP117 4.3 25.1 1.0 HD3 D:ARG155 4.3 23.7 1.0 HB2 C:LYS59 4.5 24.3 1.0 PA C:AGS402 4.5 37.7 1.0 O1B C:AGS402 4.5 37.7 1.0 HH11 D:ARG155 4.5 23.7 1.0 HA C:THR60 4.5 25.5 1.0 NH2 D:ARG154 4.6 27.2 1.0 HD22 C:LEU146 4.6 21.6 1.0 HH12 C:ARG206 4.7 22.8 1.0 HH22 D:ARG154 4.7 27.2 1.0 HE2 C:LYS59 4.7 24.3 1.0 HG23 C:THR60 4.7 25.5 1.0 HD23 C:LEU146 4.7 21.6 1.0 O1A C:AGS402 4.7 37.7 1.0 HG22 C:THR60 4.8 25.5 1.0 S1G C:AGS402 4.9 37.7 1.0 HG3 C:GLU118 4.9 24.0 1.0 OE1 D:GLU158 5.0 25.7 1.0

Magnesium binding site 4 out of 4 in the Closed State of Rfc:Pcna Bound to A Nicked Dsdna


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 Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:24.7 occ:1.00 O D:HOH502 2.0 26.6 1.0 O D:HOH501 2.0 27.9 1.0 O2G D:AGS402 2.1 37.7 1.0 O D:HOH503 2.1 30.6 1.0 O2B D:AGS402 2.2 37.7 1.0 HG1 D:THR72 2.2 26.7 1.0 OG1 D:THR72 2.6 26.7 1.0 HB D:THR72 3.1 26.7 1.0 HH22 E:ARG184 3.3 23.4 1.0 CB D:THR72 3.4 26.7 1.0 PG D:AGS402 3.5 37.7 1.0 PB D:AGS402 3.6 37.7 1.0 HH21 E:ARG184 3.6 23.4 1.0 H D:THR72 3.7 26.7 1.0 HH21 E:ARG155 3.8 27.7 1.0 NH2 E:ARG184 3.8 23.4 1.0 O2A D:AGS402 3.9 37.7 1.0 OD2 D:ASP140 3.9 25.1 1.0 HD3 E:ARG156 4.0 30.7 1.0 O3B D:AGS402 4.1 37.7 1.0 HG21 D:THR72 4.1 26.7 1.0 O3G D:AGS402 4.2 37.7 1.0 O3A D:AGS402 4.3 37.7 1.0 OD1 D:ASP140 4.3 25.1 1.0 HH22 D:ARG229 4.3 21.4 1.0 N D:THR72 4.3 26.7 1.0 OE1 E:GLU159 4.4 32.8 1.0 HH11 E:ARG156 4.4 30.7 1.0 CG2 D:THR72 4.4 26.7 1.0 CA D:THR72 4.5 26.7 1.0 NH2 E:ARG155 4.5 27.7 1.0 PA D:AGS402 4.5 37.7 1.0 HG21 D:ILE169 4.6 22.6 1.0 CG D:ASP140 4.6 25.1 1.0 HB2 D:LYS71 4.6 23.5 1.0 HD2 E:ARG156 4.6 30.7 1.0 HE2 D:LYS71 4.6 23.5 1.0 O1B D:AGS402 4.7 37.7 1.0 OE2 D:GLU141 4.7 25.9 1.0 HH22 E:ARG155 4.7 27.7 1.0 O1A D:AGS402 4.7 37.7 1.0 CD E:ARG156 4.8 30.7 1.0 HA D:THR72 4.8 26.7 1.0 HH21 D:ARG229 4.9 21.4 1.0 HG22 D:THR72 4.9 26.7 1.0 NH2 D:ARG229 5.0 21.4 1.0 S1G D:AGS402 5.0 37.7 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