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

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

Magnesium binding site 1 out of 4 in the Open 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 Open 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:2.6 occ:1.00 O A:HOH1035 1.9 1.0 1.0 O2G A:AGS901 2.0 4.5 1.0 O A:HOH1057 2.2 2.4 1.0 O A:HOH1076 2.3 1.8 1.0 OG1 A:THR360 2.3 3.8 1.0 O1B A:AGS901 2.3 4.5 1.0 HOG2 A:AGS901 2.5 4.5 1.0 HB A:THR360 3.1 3.8 1.0 PG A:AGS901 3.3 4.5 1.0 CB A:THR360 3.3 3.8 1.0 HH22 B:ARG157 3.5 2.0 1.0 PB A:AGS901 3.5 4.5 1.0 H A:THR360 3.6 3.8 1.0 O1A A:AGS901 3.7 4.5 1.0 O3B A:AGS901 3.7 4.5 1.0 HH21 B:ARG128 3.8 2.0 1.0 O3G A:AGS901 3.8 4.5 1.0 HG21 A:THR360 3.9 3.8 1.0 OD2 A:ASP424 3.9 3.9 1.0 HH12 A:ARG515 4.0 3.4 1.0 H21 A:AGS901 4.1 4.5 1.0 NH2 B:ARG157 4.2 2.0 1.0 OD1 A:ASP424 4.2 3.9 1.0 CG2 A:THR360 4.2 3.8 1.0 HH21 B:ARG157 4.3 2.0 1.0 OE1 B:GLU132 4.3 2.4 1.0 N A:THR360 4.3 3.8 1.0 HD3 B:ARG129 4.3 2.3 1.0 CA A:THR360 4.4 3.8 1.0 CG A:ASP424 4.4 3.9 1.0 O3A A:AGS901 4.5 4.5 1.0 NH2 B:ARG128 4.5 2.0 1.0 PA A:AGS901 4.6 4.5 1.0 HH22 B:ARG128 4.6 2.0 1.0 HB2 A:LYS359 4.6 3.8 1.0 O2B A:AGS901 4.6 4.5 1.0 HA A:THR360 4.7 3.8 1.0 HH22 A:ARG515 4.8 3.4 1.0 HG3 A:GLU425 4.8 4.1 1.0 HG23 A:THR360 4.8 3.8 1.0 OE2 A:GLU425 4.8 4.1 1.0 OE2 B:GLU132 4.8 2.4 1.0 NH1 A:ARG515 4.8 3.4 1.0 HG22 A:THR360 4.9 3.8 1.0 HG22 A:ILE454 4.9 4.4 1.0 S1G A:AGS901 4.9 4.5 1.0 HZ3 A:LYS359 4.9 3.8 1.0 CD B:GLU132 5.0 2.4 1.0 HE2 A:LYS359 5.0 3.8 1.0

Magnesium binding site 2 out of 4 in the Open 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 Open 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:1.4 occ:1.00 O B:HOH548 2.1 1.3 1.0 O2G B:AGS402 2.1 3.1 1.0 O2B B:AGS402 2.1 3.1 1.0 OG1 B:THR56 2.2 2.7 1.0 O B:HOH592 2.3 1.8 1.0 O B:HOH597 2.4 2.2 1.0 HOG2 B:AGS402 2.7 3.1 1.0 HB B:THR56 3.0 2.7 1.0 CB B:THR56 3.2 2.7 1.0 PG B:AGS402 3.3 3.1 1.0 HH22 C:ARG160 3.3 1.6 1.0 PB B:AGS402 3.3 3.1 1.0 H B:THR56 3.4 2.7 1.0 H21 B:AGS402 3.5 3.1 1.0 O3B B:AGS402 3.5 3.1 1.0 HH21 C:ARG131 3.7 0.8 1.0 HH22 B:ARG203 3.8 4.3 1.0 O3G B:AGS402 3.8 3.1 1.0 O2A B:AGS402 3.9 3.1 1.0 NH2 C:ARG160 3.9 1.6 1.0 HG21 B:THR56 4.0 2.7 1.0 HH21 C:ARG160 4.0 1.6 1.0 N B:THR56 4.1 2.7 1.0 OD1 B:ASP114 4.2 2.7 1.0 OD2 B:ASP114 4.2 2.7 1.0 CG2 B:THR56 4.2 2.7 1.0 CA B:THR56 4.2 2.7 1.0 O3A B:AGS402 4.3 3.1 1.0 HB2 B:LYS55 4.3 2.8 1.0 HD3 C:ARG132 4.4 1.2 1.0 O1B B:AGS402 4.4 3.1 1.0 NH2 B:ARG203 4.4 4.3 1.0 HH21 B:ARG203 4.5 4.3 1.0 NH2 C:ARG131 4.5 0.8 1.0 O B:HOH546 4.5 2.8 1.0 CG B:ASP114 4.6 2.7 1.0 HA B:THR56 4.6 2.7 1.0 OE1 C:GLU135 4.6 1.9 1.0 PA B:AGS402 4.6 3.1 1.0 HH22 C:ARG131 4.7 0.8 1.0 HE2 B:LYS55 4.7 2.8 1.0 HG23 B:THR56 4.7 2.7 1.0 HG3 B:GLU115 4.8 3.0 1.0 HG22 B:THR56 4.9 2.7 1.0 S1G B:AGS402 4.9 3.1 1.0 HZ1 B:LYS55 5.0 2.8 1.0 O1A B:AGS402 5.0 3.1 1.0

Magnesium binding site 3 out of 4 in the Open 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 Open 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:3.2 occ:1.00 O2B C:AGS402 1.9 3.2 1.0 O2G C:AGS402 2.0 3.2 1.0 O C:HOH595 2.3 3.2 1.0 O C:HOH515 2.3 3.2 1.0 OG1 C:THR60 2.3 1.1 1.0 O C:HOH581 2.4 3.2 1.0 HOG2 C:AGS402 2.7 3.2 1.0 HG1 C:THR60 3.0 1.1 1.0 HB C:THR60 3.0 1.1 1.0 PG C:AGS402 3.1 3.2 1.0 PB C:AGS402 3.1 3.2 1.0 CB C:THR60 3.2 1.1 1.0 H C:THR60 3.3 1.1 1.0 O3B C:AGS402 3.4 3.2 1.0 HH22 D:ARG183 3.5 1.2 1.0 O3G C:AGS402 3.7 3.2 1.0 HH22 C:ARG206 3.8 1.3 1.0 HH21 D:ARG154 3.8 0.9 1.0 O2A C:AGS402 3.9 3.2 1.0 H21 C:AGS402 3.9 3.2 1.0 N C:THR60 4.0 1.1 1.0 HB2 C:LYS59 4.1 0.7 1.0 O3A C:AGS402 4.1 3.2 1.0 NH2 D:ARG183 4.2 1.2 1.0 OD1 C:ASP117 4.2 0.7 1.0 CA C:THR60 4.2 1.1 1.0 O1B C:AGS402 4.2 3.2 1.0 HG21 C:THR60 4.2 1.1 1.0 OD2 C:ASP117 4.2 0.7 1.0 HH21 D:ARG183 4.3 1.2 1.0 CG2 C:THR60 4.4 1.1 1.0 HD3 D:ARG155 4.4 0.9 1.0 HH21 C:ARG206 4.5 1.3 1.0 NH2 C:ARG206 4.5 1.3 1.0 HE2 C:LYS59 4.5 0.7 1.0 NH2 D:ARG154 4.5 0.9 1.0 PA C:AGS402 4.5 3.2 1.0 HD23 C:LEU146 4.5 0.3 1.0 HH22 D:ARG154 4.6 0.9 1.0 O C:HOH568 4.6 1.1 1.0 HA C:THR60 4.6 1.1 1.0 CG C:ASP117 4.6 0.7 1.0 HZ3 C:LYS59 4.8 0.7 1.0 OE1 D:GLU158 4.8 1.2 1.0 HD22 C:LEU146 4.8 0.3 1.0 S1G C:AGS402 4.8 3.2 1.0 HG3 C:GLU118 4.8 0.7 1.0 HH12 D:ARG183 4.9 1.2 1.0 O1A C:AGS402 4.9 3.2 1.0 HG23 C:THR60 5.0 1.1 1.0 HG22 C:THR60 5.0 1.1 1.0 HZ1 C:LYS59 5.0 0.7 1.0 OE2 C:GLU118 5.0 0.7 1.0

Magnesium binding site 4 out of 4 in the Open 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 Open 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:0.8 occ:1.00 O2G D:AGS402 2.0 1.2 1.0 O2B D:AGS402 2.0 1.2 1.0 O D:HOH508 2.3 0.0 1.0 O D:HOH630 2.3 0.7 1.0 O D:HOH530 2.5 1.2 1.0 OG1 D:THR72 2.6 1.5 1.0 HOG2 D:AGS402 2.6 1.2 1.0 PG D:AGS402 3.0 1.2 1.0 PB D:AGS402 3.2 1.2 1.0 HG1 D:THR72 3.2 1.5 1.0 HH22 E:ARG184 3.2 0.7 1.0 HB D:THR72 3.2 1.5 1.0 O3B D:AGS402 3.3 1.2 1.0 H21 D:AGS402 3.4 1.2 1.0 CB D:THR72 3.5 1.5 1.0 HH21 E:ARG155 3.6 0.7 1.0 H D:THR72 3.6 1.5 1.0 O3G D:AGS402 3.6 1.2 1.0 HH22 D:ARG229 3.7 5.3 1.0 NH2 E:ARG184 3.9 0.7 1.0 O2A D:AGS402 4.0 1.2 1.0 HH21 E:ARG184 4.1 0.7 1.0 OD2 D:ASP140 4.2 1.0 1.0 O1B D:AGS402 4.2 1.2 1.0 O3A D:AGS402 4.2 1.2 1.0 HG21 D:THR72 4.3 1.5 1.0 N D:THR72 4.3 1.5 1.0 OD1 D:ASP140 4.3 1.0 1.0 NH2 E:ARG155 4.3 0.7 1.0 HB2 D:LYS71 4.4 1.2 1.0 HH21 D:ARG229 4.4 5.3 1.0 NH2 D:ARG229 4.4 5.3 1.0 HD3 E:ARG156 4.4 1.8 1.0 HE2 D:LYS71 4.4 1.2 1.0 CA D:THR72 4.5 1.5 1.0 CG2 D:THR72 4.5 1.5 1.0 OE1 E:GLU159 4.5 1.8 1.0 O D:HOH576 4.6 1.0 1.0 HH22 E:ARG155 4.6 0.7 1.0 HG21 D:ILE169 4.6 0.8 1.0 PA D:AGS402 4.6 1.2 1.0 CG D:ASP140 4.7 1.0 1.0 S1G D:AGS402 4.7 1.2 1.0 OE2 D:GLU141 4.8 1.7 1.0 HZ1 D:LYS71 4.8 1.2 1.0 HH12 E:ARG184 4.8 0.7 1.0 HA D:THR72 4.9 1.5 1.0 HZ3 D:LYS71 4.9 1.2 1.0 HE E:ARG155 5.0 0.7 1.0 HG22 D:ILE169 5.0 0.8 1.0 O1A D:AGS402 5.0 1.2 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