Magnesium in PDB 8dqw: Open State of RAD24-Rfc:9-1-1 Bound to A 5' Ss/Dsdna Junction

The binding sites of Magnesium atom in the Open State of RAD24-Rfc:9-1-1 Bound to A 5' Ss/Dsdna Junction (pdb code 8dqw). 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 RAD24-Rfc:9-1-1 Bound to A 5' Ss/Dsdna Junction, PDB code: 8dqw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Open State of RAD24-Rfc:9-1-1 Bound to A 5' 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 Open State of RAD24-Rfc:9-1-1 Bound to A 5' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:0.5 occ:1.00 O2G B:AGS402 1.8 9.7 1.0 OG1 B:THR56 1.9 4.1 1.0 O B:HOH536 2.2 1.7 1.0 O B:HOH518 2.2 3.3 1.0 HOG2 B:AGS402 2.4 5.8 1.0 O B:HOH508 2.5 2.9 1.0 O2B B:AGS402 2.5 7.0 1.0 CB B:THR56 3.0 1.7 1.0 HB B:THR56 3.1 3.2 1.0 PG B:AGS402 3.1 0.2 1.0 H B:THR56 3.4 4.1 1.0 O3B B:AGS402 3.6 1.4 1.0 HH22 C:ARG160 3.6 1.7 1.0 PB B:AGS402 3.6 3.3 1.0 O3G B:AGS402 3.7 3.8 1.0 HG21 B:THR56 3.8 9.8 1.0 H21 B:AGS402 3.8 3.5 1.0 HH21 C:ARG131 3.8 3.8 1.0 OD1 B:ASP114 3.8 5.1 1.0 N B:THR56 4.0 4.1 1.0 O2A B:AGS402 4.0 2.6 1.0 CG2 B:THR56 4.0 2.4 1.0 OD2 B:ASP114 4.1 8.7 1.0 CA B:THR56 4.1 6.5 1.0 HH22 B:ARG203 4.2 7.7 1.0 HB2 B:LYS55 4.3 2.9 1.0 NH2 C:ARG160 4.3 2.1 1.0 HA B:THR56 4.3 9.8 1.0 CG B:ASP114 4.3 8.2 1.0 HH21 C:ARG160 4.4 6.5 1.0 HG23 B:THR56 4.5 3.7 1.0 NH2 C:ARG131 4.6 6.3 1.0 HE2 B:LYS55 4.6 0.4 1.0 OE1 C:GLU135 4.6 2.7 1.0 O1B B:AGS402 4.7 8.2 1.0 O3A B:AGS402 4.7 7.5 1.0 S1G B:AGS402 4.7 3.7 1.0 HG22 B:THR56 4.7 6.4 1.0 HH21 B:ARG203 4.8 0.3 1.0 HH22 C:ARG131 4.8 5.6 1.0 PA B:AGS402 4.8 6.5 1.0 NH2 B:ARG203 4.8 6.7 1.0 OE2 B:GLU115 4.9 6.6 1.0 HE C:ARG132 4.9 0.3 1.0 HZ3 B:LYS55 4.9 0.2 1.0 HG3 B:GLU115 5.0 10.6 1.0

Magnesium binding site 2 out of 4 in the Open State of RAD24-Rfc:9-1-1 Bound to A 5' 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 Open State of RAD24-Rfc:9-1-1 Bound to A 5' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:7.2 occ:1.00 OG1 C:THR60 2.1 0.6 1.0 O2G C:AGS402 2.2 0.8 1.0 O C:HOH511 2.3 9.3 1.0 O2B C:AGS402 2.3 4.3 1.0 O C:HOH528 2.3 6.4 1.0 O C:HOH554 2.4 5.6 1.0 HOG2 C:AGS402 2.7 4.9 1.0 HB C:THR60 2.9 6.5 1.0 CB C:THR60 3.0 3.5 1.0 H C:THR60 3.3 7.1 1.0 PG C:AGS402 3.4 4.0 1.0 PB C:AGS402 3.5 4.4 1.0 HH22 D:ARG183 3.5 7.0 1.0 O3B C:AGS402 3.6 2.1 1.0 H21 C:AGS402 3.8 9.6 1.0 O2A C:AGS402 3.8 2.5 1.0 OD2 C:ASP117 3.9 9.6 1.0 HG21 C:THR60 3.9 1.7 1.0 N C:THR60 3.9 6.9 1.0 OD1 C:ASP117 3.9 5.5 1.0 HH22 C:ARG206 4.0 2.7 1.0 HH21 D:ARG154 4.0 0.1 1.0 CA C:THR60 4.0 2.3 1.0 CG2 C:THR60 4.1 6.3 1.0 HD3 D:ARG155 4.2 4.5 1.0 O3G C:AGS402 4.2 4.7 1.0 HB2 C:LYS59 4.2 4.2 1.0 NH2 D:ARG183 4.2 5.9 1.0 HH21 D:ARG183 4.3 6.2 1.0 CG C:ASP117 4.3 9.3 1.0 HA C:THR60 4.4 6.1 1.0 HH21 C:ARG206 4.5 8.8 1.0 HD23 C:LEU146 4.5 7.3 1.0 OE1 D:GLU158 4.5 7.2 1.0 HE2 C:LYS59 4.5 1.4 1.0 O3A C:AGS402 4.5 9.2 1.0 NH2 C:ARG206 4.5 7.9 1.0 O1B C:AGS402 4.6 5.3 1.0 HD22 C:LEU146 4.6 1.1 1.0 PA C:AGS402 4.6 6.1 1.0 HG23 C:THR60 4.7 5.1 1.0 HG22 C:THR60 4.7 1.5 1.0 NH2 D:ARG154 4.8 5.6 1.0 O1A C:AGS402 4.9 3.0 1.0 HG2 C:GLU118 4.9 2.2 1.0 HH22 D:ARG154 5.0 1.9 1.0

Magnesium binding site 3 out of 4 in the Open State of RAD24-Rfc:9-1-1 Bound to A 5' 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 Open State of RAD24-Rfc:9-1-1 Bound to A 5' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:3.1 occ:1.00 O D:HOH537 2.0 1.8 1.0 O2B D:AGS402 2.1 8.1 1.0 O2G D:AGS402 2.2 2.8 1.0 O D:HOH561 2.2 2.5 1.0 OG1 D:THR72 2.3 6.5 1.0 O D:HOH503 2.3 5.8 1.0 HOG2 D:AGS402 2.9 1.5 1.0 HB D:THR72 3.0 8.8 1.0 CB D:THR72 3.2 6.1 1.0 PG D:AGS402 3.3 2.8 1.0 HH22 E:ARG184 3.3 2.9 1.0 H D:THR72 3.3 1.5 1.0 PB D:AGS402 3.3 5.1 1.0 O3B D:AGS402 3.5 5.5 1.0 H21 D:AGS402 3.7 9.6 1.0 O2A D:AGS402 3.8 5.4 1.0 HH21 E:ARG155 3.8 7.9 1.0 O3G D:AGS402 3.8 9.5 1.0 NH2 E:ARG184 4.0 6.1 1.0 N D:THR72 4.0 3.5 1.0 OD2 D:ASP140 4.0 8.0 1.0 HH22 D:ARG229 4.1 7.8 1.0 HH21 E:ARG184 4.1 5.3 1.0 HG21 D:THR72 4.1 1.8 1.0 HB2 D:LYS71 4.2 1.8 1.0 CA D:THR72 4.2 0.6 1.0 OD1 D:ASP140 4.3 1.3 1.0 CG2 D:THR72 4.3 1.7 1.0 O1B D:AGS402 4.3 7.6 1.0 OE1 E:GLU159 4.3 1.5 1.0 O3A D:AGS402 4.4 2.1 1.0 HE2 D:LYS71 4.4 2.5 1.0 HG21 D:ILE169 4.5 2.8 1.0 HD3 E:ARG156 4.5 8.3 1.0 HA D:THR72 4.6 5.1 1.0 NH2 E:ARG155 4.6 5.5 1.0 PA D:AGS402 4.6 0.3 1.0 CG D:ASP140 4.6 8.7 1.0 NH2 D:ARG229 4.7 3.6 1.0 HH21 D:ARG229 4.7 8.8 1.0 HH22 E:ARG155 4.7 1.6 1.0 O1A D:AGS402 4.8 9.4 1.0 O D:HOH552 4.8 1.6 1.0 HG23 D:THR72 4.9 4.3 1.0 HG22 D:THR72 4.9 4.6 1.0 OE2 D:GLU141 4.9 5.7 1.0 S1G D:AGS402 5.0 2.8 1.0

Magnesium binding site 4 out of 4 in the Open State of RAD24-Rfc:9-1-1 Bound to A 5' 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 Open State of RAD24-Rfc:9-1-1 Bound to A 5' Ss/Dsdna Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:0.0 occ:1.00 O A:HOH1001 1.8 0.0 1.0 O2A A:AGS901 1.8 5.3 1.0 OG A:SER116 2.1 0.0 1.0 O A:HOH1025 2.2 0.0 1.0 O2B A:AGS901 2.6 0.2 1.0 HB3 A:SER116 2.8 1.0 1.0 PA A:AGS901 2.9 7.7 1.0 O A:HOH1002 2.9 0.0 1.0 O1A A:AGS901 2.9 5.5 1.0 O2G A:AGS901 3.0 1.8 1.0 CB A:SER116 3.0 0.0 1.0 HOG2 A:AGS901 3.4 9.0 1.0 O B:HOH520 3.4 1.9 1.0 H A:SER116 3.5 0.2 1.0 HB2 A:SER116 3.6 0.9 1.0 HH22 A:ARG312 3.6 0.0 1.0 OE2 A:GLU187 3.7 1.9 1.0 PB A:AGS901 3.7 8.2 1.0 OE1 A:GLU187 3.7 0.6 1.0 O3A A:AGS901 3.7 0.8 1.0 HG1 A:THR117 3.8 0.7 1.0 H A:THR117 3.9 0.0 1.0 HH21 A:ARG312 3.9 0.2 1.0 HZ2 A:LYS120 4.0 2.3 1.0 CA A:SER116 4.0 0.0 1.0 CD A:GLU187 4.1 4.8 1.0 N A:SER116 4.1 0.0 1.0 NH2 A:ARG312 4.1 0.0 1.0 O5' A:AGS901 4.2 6.9 1.0 PG A:AGS901 4.3 8.5 1.0 N A:THR117 4.3 0.0 1.0 O3B A:AGS901 4.4 2.8 1.0 C A:SER116 4.5 0.0 1.0 OG1 A:THR117 4.6 0.0 1.0 H3' A:AGS901 4.6 9.4 1.0 NZ A:LYS120 4.6 2.4 1.0 HZ1 A:LYS120 4.7 2.4 1.0 HZ3 A:LYS120 4.7 2.3 1.0 H5'2 A:AGS901 4.8 8.9 1.0 HA A:SER116 4.8 1.7 1.0 O A:HOH1005 4.9 3.0 1.0 O1B A:AGS901 4.9 3.2 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