Magnesium in PDB 8dr7: Open State of Rfc:Pcna Bound to A Nicked Dsdna

The binding sites of Magnesium atom in the Open State of Rfc:Pcna Bound to A Nicked Dsdna (pdb code 8dr7). 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 Nicked Dsdna, PDB code: 8dr7:
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 Nicked Dsdna


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 Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:51.6 occ:1.00 HOG2 A:AGS1001 1.9 58.2 1.0 O2G A:AGS1001 2.0 62.8 1.0 O1A A:AGS1001 2.5 65.5 1.0 O1B A:AGS1001 2.8 53.7 1.0 OE2 B:GLU132 2.9 47.4 1.0 HH12 A:ARG515 2.9 52.3 1.0 HH21 B:ARG157 3.0 45.6 1.0 HH22 B:ARG157 3.1 46.5 1.0 HB A:THR360 3.2 68.9 1.0 OE1 B:GLU132 3.3 47.9 1.0 NH2 B:ARG157 3.3 44.1 1.0 OG1 A:THR360 3.4 74.0 1.0 CD B:GLU132 3.4 50.9 1.0 PG A:AGS1001 3.6 52.7 1.0 PA A:AGS1001 3.6 52.4 1.0 PB A:AGS1001 3.7 44.4 1.0 NH1 A:ARG515 3.7 46.9 1.0 CB A:THR360 3.7 68.9 1.0 HH22 A:ARG515 3.8 53.2 1.0 O3A A:AGS1001 3.9 60.5 1.0 HG21 A:THR360 3.9 69.3 1.0 O2A A:AGS1001 4.0 52.8 1.0 O3B A:AGS1001 4.0 51.2 1.0 HH11 B:ARG129 4.0 49.8 1.0 HG1 A:THR360 4.1 70.2 1.0 HH11 A:ARG515 4.2 52.8 1.0 CG2 A:THR360 4.4 68.4 1.0 CZ B:ARG157 4.4 43.5 1.0 HD3 B:ARG129 4.4 50.2 1.0 NH2 A:ARG515 4.4 49.0 1.0 H A:THR360 4.5 69.2 1.0 CZ A:ARG515 4.6 43.7 1.0 OD2 A:ASP424 4.6 69.5 1.0 O3G A:AGS1001 4.6 58.4 1.0 NH1 B:ARG129 4.7 50.6 1.0 S1G A:AGS1001 4.7 46.0 1.0 HG22 A:THR360 4.8 69.2 1.0 HH21 B:ARG128 4.9 47.5 1.0 HH12 B:ARG129 4.9 50.2 1.0 CG B:GLU132 4.9 45.2 1.0 HE B:ARG157 4.9 44.7 1.0 HD2 B:ARG129 5.0 49.9 1.0 OE2 A:GLU425 5.0 61.6 1.0

Magnesium binding site 2 out of 4 in the Open 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 Open State of Rfc:Pcna Bound to A Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:28.1 occ:1.00 O2G B:AGS403 2.0 46.5 1.0 OG1 B:THR56 2.1 34.6 1.0 HOG2 B:AGS403 2.5 34.5 1.0 O2B B:AGS403 2.7 28.1 1.0 HB B:THR56 2.9 33.7 1.0 CB B:THR56 3.0 27.1 1.0 PG B:AGS403 3.2 22.3 1.0 O3B B:AGS403 3.3 24.9 1.0 HH22 C:ARG160 3.5 32.3 1.0 HG21 B:THR56 3.5 33.4 1.0 HH21 C:ARG160 3.5 31.8 1.0 PB B:AGS403 3.6 14.1 1.0 H B:THR56 3.7 34.4 1.0 O2A B:AGS403 3.8 39.6 1.0 NH2 C:ARG160 3.8 35.5 1.0 CG2 B:THR56 3.9 31.8 1.0 HH11 C:ARG132 3.9 34.8 1.0 HH21 C:ARG131 4.0 31.8 1.0 OD2 B:ASP114 4.0 37.0 1.0 OE1 C:GLU135 4.1 46.4 1.0 HH22 B:ARG203 4.2 36.6 1.0 CA B:THR56 4.3 27.9 1.0 N B:THR56 4.3 28.1 1.0 O3G B:AGS403 4.4 32.1 1.0 OD1 B:ASP114 4.4 47.7 1.0 HG23 B:THR56 4.4 34.4 1.0 O1A B:AGS403 4.5 23.1 1.0 HD3 C:ARG132 4.5 34.5 1.0 PA B:AGS403 4.5 23.0 1.0 HG22 B:THR56 4.5 34.7 1.0 S1G B:AGS403 4.6 40.1 1.0 O3A B:AGS403 4.6 32.5 1.0 NH1 C:ARG132 4.6 33.9 1.0 HH21 B:ARG203 4.6 36.1 1.0 CG B:ASP114 4.6 38.1 1.0 HA B:THR56 4.7 33.9 1.0 H21 B:AGS403 4.7 33.7 1.0 NH2 B:ARG203 4.7 31.8 1.0 NH2 C:ARG131 4.7 31.1 1.0 HH12 C:ARG132 4.7 34.7 1.0 O1B B:AGS403 4.8 32.1 1.0 OE1 B:GLU115 4.8 45.7 1.0 HH22 B:ARG16 4.9 44.0 1.0 HD2 C:ARG132 4.9 34.4 1.0 HH22 C:ARG131 4.9 32.3 1.0 HB2 B:LYS55 5.0 36.0 1.0

Magnesium binding site 3 out of 4 in the Open 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 Open State of Rfc:Pcna Bound to A Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:37.5 occ:1.00 HG1 C:THR60 2.2 39.5 1.0 OG1 C:THR60 2.3 42.9 1.0 O2G C:AGS402 2.3 54.5 1.0 O2B C:AGS402 2.4 51.5 1.0 HOG2 C:AGS402 2.9 47.5 1.0 HH22 D:ARG183 3.0 109.6 1.0 HB C:THR60 3.0 38.7 1.0 CB C:THR60 3.2 31.1 1.0 O3B C:AGS402 3.4 34.6 1.0 HH21 D:ARG183 3.4 109.8 1.0 PG C:AGS402 3.5 36.3 1.0 PB C:AGS402 3.5 9.9 1.0 NH2 D:ARG183 3.5 106.0 1.0 O2A C:AGS402 3.6 57.4 1.0 HG21 C:THR60 3.6 37.9 1.0 H C:THR60 3.8 40.7 1.0 HH22 C:ARG206 3.8 62.6 1.0 OD2 C:ASP117 3.9 36.3 1.0 CG2 C:THR60 4.0 32.5 1.0 OE1 D:GLU158 4.0 50.8 1.0 HD3 D:ARG155 4.2 38.5 1.0 HH21 C:ARG206 4.2 62.6 1.0 HH11 D:ARG155 4.2 39.3 1.0 HH21 D:ARG154 4.2 46.7 1.0 NH2 C:ARG206 4.3 56.9 1.0 PA C:AGS402 4.4 21.6 1.0 CA C:THR60 4.4 32.9 1.0 O3A C:AGS402 4.4 44.6 1.0 N C:THR60 4.4 34.7 1.0 O1A C:AGS402 4.5 22.8 1.0 OD1 C:ASP117 4.5 37.1 1.0 O3G C:AGS402 4.6 49.5 1.0 HG23 C:THR60 4.6 37.7 1.0 HD2 D:ARG155 4.6 37.8 1.0 HG22 C:THR60 4.6 38.1 1.0 O1B C:AGS402 4.6 36.5 1.0 CG C:ASP117 4.6 32.8 1.0 CZ D:ARG183 4.7 104.9 1.0 HA C:THR60 4.8 39.8 1.0 S1G C:AGS402 4.8 24.8 1.0 OE2 C:GLU118 4.8 46.1 1.0 H21 C:AGS402 4.8 46.6 1.0 CD D:ARG155 4.8 32.8 1.0 HH12 D:ARG183 4.8 110.3 1.0 NH1 D:ARG155 4.9 41.3 1.0 CD D:GLU158 4.9 50.8 1.0 NH2 D:ARG154 5.0 40.0 1.0 HH12 C:ARG20 5.0 47.4 1.0

Magnesium binding site 4 out of 4 in the Open 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 Open State of Rfc:Pcna Bound to A Nicked Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:31.1 occ:1.00 HG21 D:THR72 2.2 33.2 1.0 HOG2 D:AGS402 2.3 49.1 1.0 O2B D:AGS402 2.3 46.6 1.0 O2G D:AGS402 2.4 44.9 1.0 HH22 E:ARG184 2.8 36.6 1.0 HG22 D:THR72 2.8 34.9 1.0 CG2 D:THR72 2.9 35.1 1.0 HB D:THR72 3.0 33.0 1.0 HH21 E:ARG184 3.1 36.3 1.0 NH2 E:ARG184 3.3 36.2 1.0 CB D:THR72 3.5 29.1 1.0 O2A D:AGS402 3.5 54.5 1.0 PB D:AGS402 3.6 17.0 1.0 PG D:AGS402 3.7 26.7 1.0 HG23 D:THR72 3.7 34.1 1.0 O3B D:AGS402 3.7 43.9 1.0 H D:THR72 3.8 33.4 1.0 HH11 E:ARG156 3.8 36.4 1.0 HH22 D:ARG229 3.9 45.5 1.0 OE1 E:GLU159 3.9 44.5 1.0 HG1 D:THR72 4.0 33.6 1.0 HH21 D:ARG229 4.1 46.6 1.0 HH21 E:ARG155 4.2 32.6 1.0 O1A D:AGS402 4.3 26.5 1.0 PA D:AGS402 4.3 34.9 1.0 OG1 D:THR72 4.3 35.5 1.0 NH2 D:ARG229 4.3 33.0 1.0 HD3 E:ARG156 4.3 35.8 1.0 O3A D:AGS402 4.4 50.8 1.0 OD2 D:ASP140 4.4 34.3 1.0 CZ E:ARG184 4.5 32.7 1.0 HD2 E:ARG156 4.5 35.6 1.0 N D:THR72 4.5 27.9 1.0 NH1 E:ARG156 4.6 37.6 1.0 CA D:THR72 4.6 32.7 1.0 O1B D:AGS402 4.7 33.6 1.0 S1G D:AGS402 4.8 39.3 1.0 OE2 D:GLU141 4.8 35.2 1.0 HH12 E:ARG156 4.8 36.7 1.0 HH12 E:ARG184 4.9 35.7 1.0 CD E:GLU159 4.9 47.3 1.0 O3G D:AGS402 4.9 52.5 1.0 CD E:ARG156 4.9 31.2 1.0 HH12 D:ARG32 5.0 35.1 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