Magnesium in PDB 8dr4: Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) Without Ntd

The binding sites of Magnesium atom in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) Without Ntd (pdb code 8dr4). 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 (DNA2) Without Ntd, PDB code: 8dr4:
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 (DNA2) Without Ntd


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 (DNA2) Without Ntd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:27.3 occ:1.00 O2G A:AGS1001 2.0 28.3 1.0 HOG2 A:AGS1001 2.2 24.2 1.0 OG1 A:THR360 2.3 35.9 1.0 O1B A:AGS1001 2.4 27.5 1.0 HG1 A:THR360 2.9 34.3 1.0 HB A:THR360 3.0 33.8 1.0 CB A:THR360 3.2 29.2 1.0 PG A:AGS1001 3.4 5.8 1.0 PB A:AGS1001 3.4 15.2 1.0 HH22 B:ARG157 3.5 21.8 1.0 O3A A:AGS1001 3.6 23.1 1.0 OD2 A:ASP424 3.7 37.0 1.0 H A:THR360 3.7 33.3 1.0 HG21 A:THR360 3.7 33.4 1.0 O3B A:AGS1001 3.8 20.8 1.0 O1A A:AGS1001 3.8 34.8 1.0 HH21 B:ARG128 3.9 23.8 1.0 HH21 B:ARG157 4.0 22.5 1.0 CG2 A:THR360 4.1 34.3 1.0 OE1 B:GLU132 4.1 27.1 1.0 HH12 A:ARG515 4.1 22.8 1.0 NH2 B:ARG157 4.1 14.2 1.0 O3G A:AGS1001 4.1 28.8 1.0 OD1 A:ASP424 4.3 36.9 1.0 PA A:AGS1001 4.3 21.9 1.0 N A:THR360 4.3 29.7 1.0 CA A:THR360 4.4 29.9 1.0 HH22 A:ARG515 4.4 24.6 1.0 CG A:ASP424 4.4 33.9 1.0 HG21 A:ILE454 4.6 38.6 1.0 NH2 B:ARG128 4.6 21.0 1.0 OE2 B:GLU132 4.7 33.1 1.0 HG23 A:THR360 4.7 34.7 1.0 O2A A:AGS1001 4.7 10.9 1.0 HG22 A:THR360 4.7 34.6 1.0 HA A:THR360 4.7 33.7 1.0 O2B A:AGS1001 4.7 27.8 1.0 HH22 B:ARG128 4.8 23.9 1.0 CD B:GLU132 4.8 28.4 1.0 HB2 A:LYS359 4.8 32.1 1.0 H21 A:AGS1001 4.8 25.6 1.0 S1G A:AGS1001 4.9 25.6 1.0 NH1 A:ARG515 4.9 20.5 1.0

Magnesium binding site 2 out of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) Without Ntd


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 (DNA2) Without Ntd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:16.5 occ:1.00 HG1 B:THR56 1.8 22.8 1.0 HOG2 B:AGS402 2.1 23.3 1.0 OG1 B:THR56 2.2 30.6 1.0 O2G B:AGS402 2.2 33.3 1.0 O2B B:AGS402 2.6 23.2 1.0 HB B:THR56 3.2 20.7 1.0 CB B:THR56 3.3 15.5 1.0 PG B:AGS402 3.3 5.8 1.0 O3B B:AGS402 3.3 16.5 1.0 PB B:AGS402 3.6 6.3 1.0 H B:THR56 3.6 19.8 1.0 HH22 C:ARG160 3.6 18.7 1.0 OE1 B:GLU115 3.8 30.9 1.0 OD2 B:ASP114 3.8 26.1 1.0 HH21 C:ARG131 3.8 18.8 1.0 O2A B:AGS402 3.9 25.8 1.0 HG21 B:THR56 4.0 19.6 1.0 O3G B:AGS402 4.0 30.4 1.0 OD1 B:ASP114 4.1 27.6 1.0 HH22 B:ARG203 4.1 21.0 1.0 CG2 B:THR56 4.2 19.3 1.0 N B:THR56 4.3 14.1 1.0 H21 B:AGS402 4.3 23.9 1.0 NH2 C:ARG160 4.3 16.7 1.0 HH21 C:ARG160 4.3 17.8 1.0 CA B:THR56 4.4 19.8 1.0 CG B:ASP114 4.4 24.9 1.0 HB2 B:LYS55 4.5 19.9 1.0 OE1 C:GLU135 4.5 28.2 1.0 NH2 C:ARG131 4.5 14.8 1.0 HD3 C:ARG132 4.6 19.1 1.0 O3A B:AGS402 4.6 30.5 1.0 HH22 C:ARG131 4.6 17.9 1.0 O1B B:AGS402 4.7 23.6 1.0 HA B:THR56 4.7 21.4 1.0 HE2 B:LYS55 4.7 21.6 1.0 PA B:AGS402 4.7 14.3 1.0 HH11 C:ARG132 4.7 18.7 1.0 HH21 B:ARG203 4.7 20.6 1.0 HG23 B:THR56 4.8 22.3 1.0 NH2 B:ARG203 4.8 12.3 1.0 O1A B:AGS402 4.8 19.6 1.0 S1G B:AGS402 4.9 25.1 1.0 HG22 B:THR56 4.9 21.7 1.0 CD B:GLU115 5.0 26.1 1.0

Magnesium binding site 3 out of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) Without Ntd


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 (DNA2) Without Ntd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:15.4 occ:1.00 HOG2 C:AGS402 1.8 32.9 1.0 OG1 C:THR60 2.0 24.9 1.0 O2B C:AGS402 2.4 23.6 1.0 O2G C:AGS402 2.4 35.9 1.0 HB C:THR60 3.0 21.4 1.0 CB C:THR60 3.1 16.1 1.0 O3B C:AGS402 3.2 22.6 1.0 PG C:AGS402 3.3 0.0 1.0 PB C:AGS402 3.4 0.0 1.0 HH22 D:ARG183 3.4 31.9 1.0 H C:THR60 3.4 20.9 1.0 HG21 C:THR60 3.8 20.4 1.0 O2A C:AGS402 3.8 26.1 1.0 HH21 D:ARG154 4.0 20.5 1.0 OD2 C:ASP117 4.0 18.0 1.0 NH2 D:ARG183 4.0 25.5 1.0 CG2 C:THR60 4.0 15.6 1.0 HH22 C:ARG206 4.0 23.6 1.0 N C:THR60 4.0 13.7 1.0 HH21 D:ARG183 4.1 31.1 1.0 O3G C:AGS402 4.1 33.4 1.0 CA C:THR60 4.1 13.3 1.0 OD1 C:ASP117 4.2 22.2 1.0 HD3 D:ARG155 4.2 17.8 1.0 OE1 D:GLU158 4.4 30.9 1.0 HD23 C:LEU146 4.4 17.3 1.0 HB2 C:LYS59 4.4 17.3 1.0 O3A C:AGS402 4.4 33.0 1.0 O1B C:AGS402 4.4 20.2 1.0 HA C:THR60 4.4 21.1 1.0 HD22 C:LEU146 4.5 15.6 1.0 HH11 D:ARG155 4.5 18.7 1.0 CG C:ASP117 4.5 14.2 1.0 PA C:AGS402 4.6 1.9 1.0 HG22 C:THR60 4.6 20.6 1.0 NH2 D:ARG154 4.6 10.9 1.0 NH2 C:ARG206 4.7 12.1 1.0 HH21 C:ARG206 4.7 24.4 1.0 HG23 C:THR60 4.7 21.5 1.0 HH22 D:ARG154 4.7 20.9 1.0 O1A C:AGS402 4.7 17.9 1.0 HE2 C:LYS59 4.8 16.4 1.0 H21 C:AGS402 4.9 30.2 1.0 HG3 C:GLU118 4.9 15.2 1.0 CD2 C:LEU146 4.9 16.9 1.0

Magnesium binding site 4 out of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) Without Ntd


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 (DNA2) Without Ntd within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:12.5 occ:1.00 HG1 D:THR72 2.2 23.1 1.0 O2G D:AGS402 2.2 32.9 1.0 O2B D:AGS402 2.4 30.9 1.0 OG1 D:THR72 2.6 27.5 1.0 HOG2 D:AGS402 2.9 33.4 1.0 HB D:THR72 3.1 20.0 1.0 PG D:AGS402 3.2 0.7 1.0 O3B D:AGS402 3.3 32.5 1.0 HH22 E:ARG184 3.4 18.6 1.0 CB D:THR72 3.4 13.3 1.0 PB D:AGS402 3.4 0.0 1.0 H D:THR72 3.6 20.5 1.0 O3G D:AGS402 3.8 32.8 1.0 HH21 E:ARG155 4.0 15.0 1.0 O2A D:AGS402 4.0 34.8 1.0 NH2 E:ARG184 4.0 16.6 1.0 H21 D:AGS402 4.1 31.1 1.0 OD1 D:ASP140 4.1 22.8 1.0 HH21 E:ARG184 4.1 18.0 1.0 HG21 D:THR72 4.2 19.8 1.0 HH22 D:ARG229 4.2 16.0 1.0 N D:THR72 4.3 12.7 1.0 OD2 D:ASP140 4.3 22.2 1.0 HG21 D:ILE169 4.3 16.4 1.0 HE2 D:LYS71 4.3 21.9 1.0 CG2 D:THR72 4.4 16.4 1.0 CA D:THR72 4.4 19.4 1.0 O1B D:AGS402 4.4 20.1 1.0 HD3 E:ARG156 4.4 20.6 1.0 HB2 D:LYS71 4.4 20.6 1.0 O3A D:AGS402 4.6 24.5 1.0 CG D:ASP140 4.6 20.0 1.0 OE1 E:GLU159 4.7 22.7 1.0 HH11 E:ARG156 4.7 21.5 1.0 NH2 E:ARG155 4.7 8.3 1.0 PA D:AGS402 4.8 3.8 1.0 HA D:THR72 4.8 21.6 1.0 HH21 D:ARG229 4.8 16.6 1.0 HZ1 D:LYS71 4.8 21.6 1.0 NH2 D:ARG229 4.8 4.7 1.0 HD2 E:ARG156 4.9 20.7 1.0 HG22 D:ILE169 4.9 15.7 1.0 O1A D:AGS402 4.9 20.6 1.0 HG22 D:THR72 4.9 20.9 1.0 S1G D:AGS402 4.9 19.1 1.0 HH22 E:ARG155 5.0 16.9 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