Magnesium in PDB 8dr5: Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with Ntd

The binding sites of Magnesium atom in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with Ntd (pdb code 8dr5). 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) with Ntd, PDB code: 8dr5:
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) with 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) with Ntd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:15.1 occ:1.00 HG1 A:THR360 1.7 28.8 1.0 OG1 A:THR360 2.0 29.3 1.0 O2G A:AGS1002 2.4 37.7 1.0 O1B A:AGS1002 2.6 25.3 1.0 H21 A:AGS1002 3.0 27.1 1.0 HOG2 A:AGS1002 3.1 27.2 1.0 CB A:THR360 3.3 25.5 1.0 OD2 A:ASP424 3.3 42.5 1.0 PG A:AGS1002 3.3 21.7 1.0 HB A:THR360 3.4 28.8 1.0 H A:THR360 3.5 29.3 1.0 OD1 A:ASP424 3.6 43.6 1.0 O3G A:AGS1002 3.6 26.3 1.0 O3B A:AGS1002 3.7 22.8 1.0 PB A:AGS1002 3.7 0.5 1.0 HH22 B:ARG157 3.8 21.1 1.0 CG A:ASP424 3.8 37.7 1.0 HH21 B:ARG128 3.9 21.8 1.0 HG21 A:THR360 3.9 28.8 1.0 HG21 A:ILE454 4.0 37.1 1.0 O1A A:AGS1002 4.1 33.1 1.0 N A:THR360 4.1 27.3 1.0 CG2 A:THR360 4.2 30.8 1.0 CA A:THR360 4.3 26.5 1.0 HB2 A:LYS359 4.4 30.2 1.0 NH2 B:ARG128 4.5 19.9 1.0 NH2 B:ARG157 4.6 20.6 1.0 HG23 A:THR360 4.6 29.6 1.0 HA A:THR360 4.6 29.6 1.0 HH22 B:ARG128 4.6 24.3 1.0 HG3 A:GLU425 4.7 36.1 1.0 O2B A:AGS1002 4.7 28.4 1.0 HG2 A:GLU425 4.7 35.9 1.0 HE2 A:LYS359 4.7 31.4 1.0 HH21 B:ARG157 4.8 21.6 1.0 HH22 A:ARG515 4.8 23.5 1.0 HG22 A:ILE454 4.8 37.2 1.0 CG2 A:ILE454 4.8 35.9 1.0 HH12 A:ARG515 4.8 21.8 1.0 O3A A:AGS1002 4.8 27.8 1.0 HD12 A:ILE454 4.9 36.3 1.0 PA A:AGS1002 4.9 15.2 1.0 HG22 A:THR360 5.0 29.5 1.0 HD13 A:ILE454 5.0 36.1 1.0

Magnesium binding site 2 out of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with 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) with Ntd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:6.4 occ:1.00 HOG2 B:AGS402 2.1 22.9 1.0 O2B B:AGS402 2.5 19.7 1.0 OG1 B:THR56 2.6 25.9 1.0 O2G B:AGS402 2.7 28.6 1.0 HB B:THR56 2.8 19.3 1.0 O3B B:AGS402 3.0 25.2 1.0 HH22 C:ARG160 3.2 18.0 1.0 CB B:THR56 3.2 13.8 1.0 PB B:AGS402 3.3 1.8 1.0 O2A B:AGS402 3.4 29.3 1.0 HG1 B:THR56 3.4 21.0 1.0 PG B:AGS402 3.4 17.7 1.0 HH21 C:ARG160 3.6 18.3 1.0 H B:THR56 3.7 19.7 1.0 NH2 C:ARG160 3.7 17.0 1.0 HH22 B:ARG203 3.7 20.9 1.0 HG21 B:THR56 3.8 20.6 1.0 OD2 B:ASP114 4.0 29.1 1.0 HH21 C:ARG131 4.0 18.0 1.0 CG2 B:THR56 4.1 19.9 1.0 O3A B:AGS402 4.1 23.0 1.0 PA B:AGS402 4.2 11.2 1.0 HH21 B:ARG203 4.2 19.9 1.0 OE1 C:GLU135 4.2 30.1 1.0 NH2 B:ARG203 4.3 17.2 1.0 HH11 C:ARG132 4.3 19.2 1.0 N B:THR56 4.3 7.4 1.0 CA B:THR56 4.4 16.1 1.0 O1A B:AGS402 4.4 15.8 1.0 OE2 B:GLU115 4.4 21.7 1.0 O3G B:AGS402 4.5 19.5 1.0 HD3 C:ARG132 4.5 19.4 1.0 O1B B:AGS402 4.6 23.2 1.0 HG22 B:THR56 4.6 21.3 1.0 OD1 B:ASP114 4.7 21.4 1.0 H21 B:AGS402 4.7 20.8 1.0 CG B:ASP114 4.7 18.5 1.0 OE2 C:GLU135 4.8 29.0 1.0 HA B:THR56 4.8 20.5 1.0 NH2 C:ARG131 4.8 21.7 1.0 HB2 B:LYS55 4.8 17.9 1.0 HG23 B:THR56 4.9 20.6 1.0 HD2 C:ARG132 4.9 20.4 1.0 CD C:GLU135 4.9 31.2 1.0 S1G B:AGS402 5.0 32.6 1.0 CZ C:ARG160 5.0 17.7 1.0

Magnesium binding site 3 out of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with 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) with Ntd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:15.2 occ:1.00 OG1 C:THR60 1.9 22.6 1.0 O2G C:AGS402 2.5 33.7 1.0 O2B C:AGS402 2.5 21.2 1.0 HOG2 C:AGS402 2.8 21.4 1.0 HB C:THR60 3.0 16.1 1.0 CB C:THR60 3.0 10.1 1.0 O3B C:AGS402 3.3 15.4 1.0 HH22 D:ARG183 3.4 30.9 1.0 H C:THR60 3.4 16.7 1.0 PG C:AGS402 3.5 2.1 1.0 PB C:AGS402 3.5 0.0 1.0 HG21 C:THR60 3.7 13.4 1.0 O2A C:AGS402 3.8 27.1 1.0 OD2 C:ASP117 3.8 24.4 1.0 CG2 C:THR60 4.0 7.3 1.0 NH2 D:ARG183 4.0 26.3 1.0 HH21 D:ARG183 4.0 30.6 1.0 N C:THR60 4.0 7.5 1.0 CA C:THR60 4.1 7.3 1.0 HD3 D:ARG155 4.1 24.1 1.0 HH22 C:ARG206 4.2 31.5 1.0 OD1 C:ASP117 4.2 26.7 1.0 HH11 D:ARG155 4.3 25.2 1.0 O3G C:AGS402 4.4 33.7 1.0 HA C:THR60 4.4 15.7 1.0 CG C:ASP117 4.4 15.1 1.0 HB2 C:LYS59 4.5 20.4 1.0 O3A C:AGS402 4.5 11.1 1.0 HG23 C:THR60 4.5 14.6 1.0 HH21 D:ARG154 4.5 50.7 1.0 PA C:AGS402 4.5 6.5 1.0 O1B C:AGS402 4.6 0.0 1.0 O1A C:AGS402 4.6 10.8 1.0 HH21 C:ARG206 4.7 30.3 1.0 OE1 D:GLU158 4.7 34.3 1.0 HD22 C:LEU146 4.7 16.9 1.0 HG22 C:THR60 4.7 16.4 1.0 HD2 D:ARG155 4.7 25.9 1.0 NH2 C:ARG206 4.8 18.7 1.0 H21 C:AGS402 4.8 20.8 1.0 HG3 C:GLU118 4.8 20.2 1.0 OE2 C:GLU118 4.8 30.3 1.0 HE2 C:LYS59 4.8 20.8 1.0 HD23 C:LEU146 4.9 17.5 1.0 CD D:ARG155 4.9 24.0 1.0 NH1 D:ARG155 5.0 29.7 1.0

Magnesium binding site 4 out of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with 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) with Ntd within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:24.6 occ:1.00 HG1 D:THR72 1.7 27.5 1.0 HOG2 D:AGS402 1.8 34.7 1.0 OG1 D:THR72 2.2 31.2 1.0 O2G D:AGS402 2.3 35.0 1.0 O2B D:AGS402 3.0 36.9 1.0 HH22 E:ARG184 3.2 20.9 1.0 PG D:AGS402 3.4 7.2 1.0 O3B D:AGS402 3.4 26.2 1.0 CB D:THR72 3.5 18.1 1.0 HH21 E:ARG155 3.6 22.2 1.0 OD2 D:ASP140 3.7 29.1 1.0 HH21 E:ARG184 3.8 21.0 1.0 H D:THR72 3.8 26.6 1.0 HB D:THR72 3.8 25.4 1.0 PB D:AGS402 3.8 0.0 1.0 NH2 E:ARG184 3.8 17.2 1.0 HG21 D:THR72 3.9 27.3 1.0 OD1 D:ASP140 4.1 32.0 1.0 OE1 E:GLU159 4.1 33.4 1.0 CG2 D:THR72 4.1 30.8 1.0 HD3 E:ARG156 4.2 22.6 1.0 HG23 D:THR72 4.2 27.5 1.0 NH2 E:ARG155 4.3 22.5 1.0 CG D:ASP140 4.3 30.0 1.0 O3G D:AGS402 4.3 35.4 1.0 O2A D:AGS402 4.3 32.6 1.0 OE2 D:GLU141 4.4 18.6 1.0 N D:THR72 4.4 19.9 1.0 HG21 D:ILE169 4.5 28.6 1.0 HH11 E:ARG156 4.5 24.3 1.0 HH22 E:ARG155 4.6 22.2 1.0 HH22 D:ARG229 4.6 23.4 1.0 CA D:THR72 4.6 21.4 1.0 HB2 D:LYS71 4.6 28.9 1.0 HE2 D:LYS71 4.7 28.4 1.0 H21 D:AGS402 4.7 32.8 1.0 HD2 E:ARG156 4.7 21.5 1.0 O1B D:AGS402 4.8 14.2 1.0 HG22 D:ILE169 4.8 28.8 1.0 HE E:ARG155 4.9 21.5 1.0 HA D:THR72 4.9 27.1 1.0 HG3 D:GLU141 4.9 23.7 1.0 CD E:ARG156 4.9 12.6 1.0 O3A D:AGS402 4.9 34.9 1.0 S1G D:AGS402 5.0 1.4 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