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

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

Magnesium binding site 1 out of 4 in the Intermediate 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 Intermediate 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:56.5 occ:1.00 HG1 A:THR360 1.9 77.8 1.0 O2G A:AGS901 2.2 76.7 1.0 O1B A:AGS901 2.3 74.7 1.0 OG1 A:THR360 2.3 82.7 1.0 O3G A:AGS901 2.9 73.3 1.0 PG A:AGS901 2.9 63.4 1.0 HOG2 A:AGS901 3.0 74.6 1.0 PB A:AGS901 3.3 68.6 1.0 HB A:THR360 3.3 76.7 1.0 CB A:THR360 3.4 75.5 1.0 O3B A:AGS901 3.4 71.4 1.0 H A:THR360 3.5 77.7 1.0 OD2 A:ASP424 3.6 81.8 1.0 H21 A:AGS901 3.7 75.0 1.0 HH21 B:ARG128 3.8 59.5 1.0 OD1 A:ASP424 3.8 84.9 1.0 O3A A:AGS901 4.0 72.8 1.0 HH22 B:ARG157 4.1 56.9 1.0 CG A:ASP424 4.2 80.5 1.0 N A:THR360 4.2 77.1 1.0 HG21 A:THR360 4.2 77.4 1.0 HG21 A:ILE454 4.2 86.4 1.0 HB2 A:LYS359 4.3 75.7 1.0 O1A A:AGS901 4.3 78.1 1.0 HH21 B:ARG157 4.4 55.6 1.0 CG2 A:THR360 4.4 76.3 1.0 CA A:THR360 4.4 75.1 1.0 HH22 A:ARG515 4.4 66.1 1.0 HE2 A:LYS359 4.4 75.8 1.0 NH2 B:ARG128 4.5 61.8 1.0 HH22 B:ARG128 4.5 60.5 1.0 NH2 B:ARG157 4.6 55.3 1.0 O2B A:AGS901 4.6 80.5 1.0 PA A:AGS901 4.7 69.1 1.0 S1G A:AGS901 4.7 66.6 1.0 HA A:THR360 4.8 77.6 1.0 HD3 B:ARG129 4.8 60.8 1.0 HG23 A:THR360 4.8 77.7 1.0 HZ1 A:LYS359 4.8 75.4 1.0 O2A A:AGS901 4.9 71.6 1.0 HG3 A:GLU425 4.9 79.9 1.0 HG22 A:ILE454 4.9 86.2 1.0 HZ3 A:LYS359 5.0 75.8 1.0 HG2 A:GLU425 5.0 79.2 1.0

Magnesium binding site 2 out of 4 in the Intermediate 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 Intermediate 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:38.3 occ:1.00 HG1 B:THR56 1.8 46.7 1.0 O2G B:AGS402 2.3 56.1 1.0 OG1 B:THR56 2.4 53.1 1.0 HOG2 B:AGS402 2.8 52.5 1.0 O2B B:AGS402 2.9 45.0 1.0 HH22 C:ARG160 3.0 40.9 1.0 HB B:THR56 3.1 44.7 1.0 CB B:THR56 3.3 37.5 1.0 PG B:AGS402 3.6 39.4 1.0 O3B B:AGS402 3.6 45.9 1.0 NH2 C:ARG160 3.6 39.4 1.0 HH21 C:ARG160 3.6 40.9 1.0 HG21 B:THR56 3.7 45.7 1.0 HH21 C:ARG131 3.8 40.8 1.0 OD2 B:ASP114 3.8 55.0 1.0 OE2 B:GLU115 3.8 47.4 1.0 PB B:AGS402 3.9 25.8 1.0 HD3 C:ARG132 4.0 43.0 1.0 O2A B:AGS402 4.0 58.9 1.0 H B:THR56 4.0 45.7 1.0 CG2 B:THR56 4.1 44.1 1.0 OE1 C:GLU135 4.1 54.4 1.0 HH11 C:ARG132 4.2 42.8 1.0 OD1 B:ASP114 4.2 44.4 1.0 HH22 B:ARG203 4.4 47.4 1.0 CG B:ASP114 4.5 50.3 1.0 NH2 C:ARG131 4.5 36.0 1.0 CA B:THR56 4.6 35.0 1.0 HD2 C:ARG132 4.6 43.3 1.0 N B:THR56 4.6 40.3 1.0 HG22 B:THR56 4.7 46.4 1.0 O3G B:AGS402 4.7 53.6 1.0 HG23 B:THR56 4.7 46.6 1.0 HH22 C:ARG131 4.7 40.4 1.0 CD C:ARG132 4.8 45.8 1.0 O3A B:AGS402 4.8 56.8 1.0 PA B:AGS402 4.8 45.7 1.0 HH21 B:ARG203 4.8 47.4 1.0 S1G B:AGS402 4.8 52.3 1.0 CZ C:ARG160 4.9 43.0 1.0 HH12 C:ARG160 4.9 42.2 1.0 O1A B:AGS402 4.9 46.3 1.0 NH2 B:ARG203 4.9 48.3 1.0 HA B:THR56 4.9 45.7 1.0 O1B B:AGS402 5.0 44.7 1.0 NH1 C:ARG132 5.0 46.1 1.0

Magnesium binding site 3 out of 4 in the Intermediate 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 Intermediate 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:30.3 occ:1.00 HOG2 C:AGS402 2.1 61.3 1.0 OG1 C:THR60 2.4 48.6 1.0 O2G C:AGS402 2.4 61.7 1.0 O2B C:AGS402 2.4 65.5 1.0 HG1 C:THR60 2.8 49.6 1.0 HH22 D:ARG183 3.0 39.4 1.0 OE2 C:GLU118 3.1 50.2 1.0 OD2 C:ASP117 3.3 54.5 1.0 HB C:THR60 3.5 48.4 1.0 CB C:THR60 3.5 41.0 1.0 HD3 D:ARG155 3.6 43.2 1.0 OD1 C:ASP117 3.6 44.2 1.0 PB C:AGS402 3.7 43.1 1.0 NH2 D:ARG183 3.7 34.7 1.0 PG C:AGS402 3.7 31.1 1.0 HH21 D:ARG183 3.8 39.0 1.0 HH21 D:ARG154 3.8 34.5 1.0 CG C:ASP117 3.9 42.2 1.0 O3B C:AGS402 3.9 52.8 1.0 HG21 C:THR60 4.0 47.8 1.0 H C:THR60 4.1 48.0 1.0 CD C:GLU118 4.3 46.9 1.0 CG2 C:THR60 4.4 42.6 1.0 CD D:ARG155 4.4 44.8 1.0 NH2 D:ARG154 4.5 24.1 1.0 HH11 D:ARG155 4.5 44.2 1.0 HG3 C:GLU118 4.5 42.5 1.0 HD2 D:ARG155 4.5 44.1 1.0 HD22 C:LEU146 4.6 39.8 1.0 O3G C:AGS402 4.6 66.2 1.0 HH22 D:ARG154 4.6 35.5 1.0 CA C:THR60 4.6 40.1 1.0 N C:THR60 4.7 39.9 1.0 O1B C:AGS402 4.7 21.3 1.0 O3A C:AGS402 4.7 62.8 1.0 HA C:THR60 4.8 48.1 1.0 OE1 D:GLU158 4.8 46.9 1.0 HH12 D:ARG183 4.8 40.4 1.0 HD23 C:LEU146 4.9 39.2 1.0 HB2 C:LYS59 4.9 36.5 1.0 HG2 D:ARG155 4.9 44.4 1.0 HG23 C:THR60 4.9 48.9 1.0 CZ D:ARG183 4.9 28.7 1.0 HE2 C:LYS59 5.0 34.9 1.0 CG C:GLU118 5.0 42.0 1.0

Magnesium binding site 4 out of 4 in the Intermediate 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 Intermediate 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:43.8 occ:1.00 HOG2 D:AGS402 1.9 61.2 1.0 O2G D:AGS402 2.2 50.6 1.0 O2B D:AGS402 2.4 62.0 1.0 OG1 D:THR72 2.6 43.2 1.0 HH22 E:ARG184 3.0 41.3 1.0 HG1 D:THR72 3.2 46.4 1.0 HB D:THR72 3.4 44.6 1.0 HH21 E:ARG184 3.5 40.3 1.0 HD3 E:ARG156 3.5 47.9 1.0 HH21 E:ARG155 3.5 38.6 1.0 NH2 E:ARG184 3.6 40.0 1.0 CB D:THR72 3.6 32.5 1.0 PG D:AGS402 3.6 38.2 1.0 PB D:AGS402 3.7 33.2 1.0 O3B D:AGS402 3.9 59.6 1.0 H D:THR72 4.0 45.3 1.0 OD1 D:ASP140 4.1 44.4 1.0 OD2 D:ASP140 4.1 52.2 1.0 O2A D:AGS402 4.2 60.9 1.0 HG21 D:THR72 4.2 46.4 1.0 NH2 E:ARG155 4.2 34.5 1.0 OE2 E:GLU159 4.3 58.2 1.0 HH22 E:ARG155 4.3 38.5 1.0 HH22 D:ARG229 4.4 37.3 1.0 CD E:ARG156 4.5 48.4 1.0 CG D:ASP140 4.5 46.9 1.0 CG2 D:THR72 4.5 44.9 1.0 OE2 D:GLU141 4.6 50.0 1.0 O1B D:AGS402 4.6 48.8 1.0 N D:THR72 4.6 37.9 1.0 HD2 E:ARG156 4.7 48.3 1.0 O3G D:AGS402 4.7 68.5 1.0 CA D:THR72 4.7 39.1 1.0 H21 D:AGS402 4.7 60.2 1.0 HE2 D:LYS71 4.7 37.5 1.0 HG21 D:ILE169 4.8 37.4 1.0 HG2 E:ARG156 4.8 48.0 1.0 HB2 D:LYS71 4.8 35.9 1.0 S1G D:AGS402 4.8 38.6 1.0 O3A D:AGS402 4.8 56.3 1.0 CZ E:ARG184 4.9 32.9 1.0 HH11 E:ARG156 4.9 48.6 1.0 HG3 D:GLU141 4.9 37.6 1.0 PA D:AGS402 5.0 32.3 1.0 HH21 D:ARG229 5.0 37.5 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