Magnesium in PDB 8dr3: Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with Ntd

The binding sites of Magnesium atom in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with Ntd (pdb code 8dr3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Closed State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction (DNA2) with Ntd, PDB code: 8dr3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Closed 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 Closed 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:Mg1002 b:7.0 occ:1.00 HOG2 A:AGS1001 1.9 19.2 1.0 HG1 A:THR360 1.9 16.0 1.0 O A:HOH1103 1.9 16.2 1.0 O2G A:AGS1001 2.0 17.8 1.0 O A:HOH1101 2.1 9.7 1.0 OG1 A:THR360 2.3 15.4 1.0 O1B A:AGS1001 2.4 16.3 1.0 O A:HOH1102 2.5 15.6 1.0 PG A:AGS1001 3.0 2.5 1.0 O3B A:AGS1001 3.4 10.2 1.0 HB A:THR360 3.4 15.2 1.0 O3G A:AGS1001 3.5 15.3 1.0 CB A:THR360 3.5 14.8 1.0 PB A:AGS1001 3.5 0.0 1.0 HH22 B:ARG157 3.6 12.7 1.0 H A:THR360 3.6 15.0 1.0 OD2 A:ASP424 3.8 25.9 1.0 O1A A:AGS1001 3.8 17.2 1.0 HH22 A:ARG515 3.8 24.8 1.0 HH21 B:ARG128 3.9 12.2 1.0 H21 A:AGS1001 4.0 18.4 1.0 HG21 A:THR360 4.1 14.9 1.0 OD1 A:ASP424 4.2 23.8 1.0 OE1 B:GLU132 4.2 13.2 1.0 NH2 B:ARG157 4.2 10.2 1.0 N A:THR360 4.3 12.5 1.0 HH21 B:ARG157 4.3 11.1 1.0 CG2 A:THR360 4.4 15.8 1.0 CG A:ASP424 4.4 20.3 1.0 HH21 A:ARG515 4.5 25.6 1.0 NH2 A:ARG515 4.5 12.5 1.0 CA A:THR360 4.5 16.3 1.0 O2B A:AGS1001 4.5 21.6 1.0 HB2 A:LYS359 4.5 16.2 1.0 O3A A:AGS1001 4.5 20.4 1.0 NH2 B:ARG128 4.6 7.8 1.0 HD3 B:ARG129 4.6 13.3 1.0 HG21 A:ILE454 4.6 19.9 1.0 PA A:AGS1001 4.7 6.4 1.0 HH22 B:ARG128 4.7 12.6 1.0 HG3 A:GLU425 4.8 19.0 1.0 S1G A:AGS1001 4.8 9.4 1.0 HG23 A:THR360 4.8 16.0 1.0 HE2 A:LYS359 4.8 17.2 1.0 HA A:THR360 4.9 15.6 1.0 O2A A:AGS1001 4.9 16.9 1.0

Magnesium binding site 2 out of 4 in the Closed 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 Closed 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:10.1 occ:1.00 HOG2 B:AGS402 1.7 18.4 1.0 O B:HOH502 2.0 10.1 1.0 O2G B:AGS402 2.0 19.9 1.0 O B:HOH501 2.4 14.9 1.0 O B:HOH503 2.4 16.8 1.0 O2B B:AGS402 2.4 7.7 1.0 OG1 B:THR56 2.5 12.8 1.0 HG1 B:THR56 3.0 10.1 1.0 PG B:AGS402 3.1 6.2 1.0 O3B B:AGS402 3.2 17.7 1.0 PB B:AGS402 3.4 0.0 1.0 HB B:THR56 3.4 8.9 1.0 CB B:THR56 3.5 5.8 1.0 H B:THR56 3.7 8.8 1.0 HH21 C:ARG131 3.8 10.9 1.0 HH22 C:ARG160 3.8 12.3 1.0 O2A B:AGS402 3.8 10.8 1.0 O3G B:AGS402 3.8 17.2 1.0 HH22 B:ARG203 3.9 18.2 1.0 OD2 B:ASP114 3.9 8.1 1.0 OD1 B:ASP114 4.2 19.4 1.0 HG21 B:THR56 4.2 8.5 1.0 HD3 C:ARG132 4.3 9.0 1.0 OE2 B:GLU115 4.3 20.2 1.0 N B:THR56 4.4 2.5 1.0 H21 B:AGS402 4.4 17.9 1.0 O1B B:AGS402 4.4 17.5 1.0 O3A B:AGS402 4.5 25.7 1.0 CG2 B:THR56 4.5 10.7 1.0 CG B:ASP114 4.5 10.9 1.0 NH2 C:ARG160 4.5 14.4 1.0 HH21 B:ARG203 4.5 17.5 1.0 HB2 B:LYS55 4.5 10.8 1.0 OE1 C:GLU135 4.5 19.1 1.0 NH2 B:ARG203 4.6 13.5 1.0 HH21 C:ARG160 4.6 11.5 1.0 CA B:THR56 4.6 10.1 1.0 NH2 C:ARG131 4.6 12.5 1.0 PA B:AGS402 4.6 2.8 1.0 S1G B:AGS402 4.7 20.4 1.0 HH22 C:ARG131 4.8 11.1 1.0 HE2 B:LYS55 4.8 12.8 1.0 HG3 B:GLU115 4.9 10.0 1.0 O1A B:AGS402 4.9 9.9 1.0 HA B:THR56 4.9 10.1 1.0

Magnesium binding site 3 out of 4 in the Closed 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 Closed 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:5.2 occ:1.00 O2G C:AGS402 2.1 11.7 1.0 O2B C:AGS402 2.3 0.0 1.0 OG1 C:THR60 2.3 6.3 1.0 O C:HOH503 2.3 6.6 1.0 O C:HOH502 2.4 0.0 1.0 O C:HOH501 2.5 2.7 1.0 HOG2 C:AGS402 2.8 10.7 1.0 HB C:THR60 3.1 11.1 1.0 PG C:AGS402 3.2 0.0 1.0 O3B C:AGS402 3.3 1.1 1.0 CB C:THR60 3.3 5.4 1.0 PB C:AGS402 3.3 0.0 1.0 HH22 D:ARG183 3.4 16.1 1.0 H C:THR60 3.4 10.6 1.0 O3G C:AGS402 3.8 10.1 1.0 O2A C:AGS402 3.8 5.2 1.0 H21 C:AGS402 3.9 9.7 1.0 HH21 D:ARG154 4.0 15.5 1.0 OD2 C:ASP117 4.0 7.9 1.0 HG21 C:THR60 4.1 9.3 1.0 N C:THR60 4.1 2.1 1.0 NH2 D:ARG183 4.1 12.0 1.0 OD1 C:ASP117 4.2 9.3 1.0 CA C:THR60 4.3 7.3 1.0 HB2 C:LYS59 4.3 16.5 1.0 CG2 C:THR60 4.3 4.4 1.0 HH12 C:ARG206 4.3 16.3 1.0 O1B C:AGS402 4.3 6.6 1.0 HD3 D:ARG155 4.4 8.0 1.0 HH21 D:ARG183 4.4 16.4 1.0 O3A C:AGS402 4.4 13.2 1.0 OE2 C:GLU118 4.5 17.6 1.0 CG C:ASP117 4.6 6.6 1.0 PA C:AGS402 4.6 1.6 1.0 HA C:THR60 4.6 10.8 1.0 HE2 C:LYS59 4.6 18.2 1.0 HH11 D:ARG155 4.7 9.0 1.0 HD22 C:LEU146 4.7 7.1 1.0 HD23 C:LEU146 4.7 9.3 1.0 NH2 D:ARG154 4.8 9.6 1.0 HH12 D:ARG183 4.8 16.2 1.0 HH22 C:ARG206 4.8 18.3 1.0 HG3 C:GLU118 4.8 6.8 1.0 S1G C:AGS402 4.9 2.0 1.0 HG23 C:THR60 4.9 10.3 1.0 OE1 D:GLU158 4.9 6.6 1.0 O1A C:AGS402 4.9 0.0 1.0 HZ3 C:LYS59 4.9 15.6 1.0 HH22 D:ARG154 4.9 16.0 1.0 HZ1 C:LYS59 5.0 15.9 1.0 HG22 C:THR60 5.0 10.5 1.0

Magnesium binding site 4 out of 4 in the Closed 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 Closed 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:5.6 occ:1.00 O D:HOH501 1.9 2.8 1.0 O2G D:AGS402 2.2 15.8 1.0 O D:HOH503 2.2 12.3 1.0 O2B D:AGS402 2.2 15.1 1.0 O D:HOH502 2.4 11.0 1.0 OG1 D:THR72 2.6 10.0 1.0 HOG2 D:AGS402 2.9 18.1 1.0 HB D:THR72 2.9 9.5 1.0 PG D:AGS402 3.2 0.0 1.0 O3B D:AGS402 3.2 8.8 1.0 HH22 E:ARG184 3.3 15.9 1.0 PB D:AGS402 3.3 0.0 1.0 CB D:THR72 3.3 4.5 1.0 HG1 D:THR72 3.3 9.7 1.0 H D:THR72 3.4 10.1 1.0 O2A D:AGS402 3.8 7.8 1.0 O3G D:AGS402 3.8 11.9 1.0 NH2 E:ARG184 3.9 4.7 1.0 HH22 D:ARG229 4.0 16.9 1.0 HH21 E:ARG155 4.0 12.2 1.0 H21 D:AGS402 4.0 16.8 1.0 HH21 E:ARG184 4.1 16.3 1.0 OD2 D:ASP140 4.1 8.1 1.0 N D:THR72 4.1 4.5 1.0 HG21 D:THR72 4.2 8.0 1.0 HD3 E:ARG156 4.2 10.6 1.0 O1B D:AGS402 4.3 1.2 1.0 CA D:THR72 4.3 7.8 1.0 HB2 D:LYS71 4.3 17.7 1.0 CG2 D:THR72 4.3 8.9 1.0 OD1 D:ASP140 4.4 10.6 1.0 O3A D:AGS402 4.4 17.7 1.0 OE1 E:GLU159 4.4 14.5 1.0 HH21 D:ARG229 4.5 18.4 1.0 PA D:AGS402 4.5 0.0 1.0 HG21 D:ILE169 4.6 12.4 1.0 NH2 D:ARG229 4.6 6.6 1.0 CG D:ASP140 4.7 6.0 1.0 HE2 D:LYS71 4.7 18.6 1.0 HA D:THR72 4.7 10.7 1.0 NH2 E:ARG155 4.7 7.1 1.0 O1A D:AGS402 4.8 8.6 1.0 HG22 D:THR72 4.9 9.5 1.0 OE2 D:GLU141 4.9 15.2 1.0 S1G D:AGS402 4.9 0.0 1.0 HH22 E:ARG155 4.9 12.6 1.0 HH12 E:ARG184 4.9 16.4 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