Magnesium in PDB 7st9: 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 7st9). 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: 7st9:
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 A:Mg902 b:10.1 occ:1.00 O A:HOH1001 1.8 10.1 1.0 O2A A:AGS901 1.9 5.6 1.0 OG A:SER116 2.0 6.5 1.0 O A:HOH1036 2.0 5.3 1.0 O2G A:AGS901 2.8 5.6 1.0 O2B A:AGS901 3.0 5.6 1.0 PA A:AGS901 3.0 5.6 1.0 O A:HOH1003 3.0 10.1 1.0 O A:HOH1027 3.0 6.7 1.0 CB A:SER116 3.1 6.5 1.0 HB3 A:SER116 3.1 6.5 1.0 O1A A:AGS901 3.3 5.6 1.0 OE2 A:GLU187 3.3 9.6 1.0 HB2 A:SER116 3.6 6.5 1.0 O3A A:AGS901 3.6 5.6 1.0 HH22 A:ARG312 3.6 5.8 1.0 HH21 A:ARG312 3.7 5.8 1.0 H A:SER116 3.9 6.5 1.0 HZ1 A:LYS120 3.9 9.7 1.0 PB A:AGS901 3.9 5.6 1.0 OE1 A:GLU187 3.9 9.6 1.0 H3' A:AGS901 4.0 5.6 1.0 HG1 A:THR117 4.0 6.4 1.0 CD A:GLU187 4.0 9.6 1.0 NH2 A:ARG312 4.0 5.8 1.0 H A:THR117 4.1 6.4 1.0 PG A:AGS901 4.2 5.6 1.0 CA A:SER116 4.3 6.5 1.0 O5' A:AGS901 4.3 5.6 1.0 N A:SER116 4.4 6.5 1.0 HZ2 A:LYS120 4.4 9.7 1.0 HZ3 A:LYS120 4.4 9.7 1.0 NZ A:LYS120 4.4 9.7 1.0 N A:THR117 4.6 6.4 1.0 O3B A:AGS901 4.6 5.6 1.0 OG1 A:THR117 4.6 6.4 1.0 C A:SER116 4.7 6.5 1.0 H5'2 A:AGS901 4.8 5.6 1.0 O3G A:AGS901 4.8 5.6 1.0 C3' A:AGS901 4.9 5.6 1.0 O A:HOH1017 4.9 10.1 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 B:Mg401 b:10.1 occ:1.00 O2G B:AGS402 1.9 8.6 1.0 OG1 B:THR56 1.9 7.7 1.0 O B:HOH527 2.0 7.1 1.0 O2B B:AGS402 2.2 8.6 1.0 O B:HOH506 2.6 10.1 1.0 O B:HOH505 2.7 10.1 1.0 PG B:AGS402 3.1 8.6 1.0 CB B:THR56 3.2 7.7 1.0 HB B:THR56 3.3 7.7 1.0 H B:THR56 3.3 7.7 1.0 O3G B:AGS402 3.5 8.6 1.0 PB B:AGS402 3.6 8.6 1.0 HH22 C:ARG160 3.6 10.0 1.0 OD1 B:ASP114 3.7 4.8 1.0 HH21 C:ARG131 3.7 9.7 1.0 O3B B:AGS402 3.8 8.6 1.0 N B:THR56 3.9 7.7 1.0 HG21 B:THR56 4.0 7.7 1.0 OD2 B:ASP114 4.0 4.8 1.0 CA B:THR56 4.1 7.7 1.0 O2A B:AGS402 4.1 8.6 1.0 HB2 B:LYS55 4.1 7.7 1.0 CG2 B:THR56 4.2 7.7 1.0 CG B:ASP114 4.2 4.8 1.0 HA B:THR56 4.3 7.7 1.0 HH22 B:ARG203 4.3 11.8 1.0 NH2 C:ARG160 4.4 10.0 1.0 HE2 B:LYS55 4.4 7.7 1.0 O3A B:AGS402 4.4 8.6 1.0 HH21 C:ARG160 4.4 10.0 1.0 NH2 C:ARG131 4.5 9.7 1.0 HG23 B:THR56 4.6 7.7 1.0 HH22 C:ARG131 4.6 9.7 1.0 O1B B:AGS402 4.6 8.6 1.0 PA B:AGS402 4.7 8.6 1.0 S1G B:AGS402 4.7 8.6 1.0 OE2 B:GLU115 4.7 7.7 1.0 HH21 B:ARG203 4.8 11.8 1.0 O1A B:AGS402 4.9 8.6 1.0 HZ3 B:LYS55 4.9 7.7 1.0 NH2 B:ARG203 4.9 11.8 1.0 HG22 B:THR56 4.9 7.7 1.0 HZ1 B:LYS55 5.0 7.7 1.0 HG3 B:GLU115 5.0 7.7 1.0 OE1 C:GLU135 5.0 11.7 1.0 HB1 B:ALA143 5.0 10.1 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 C:Mg403 b:10.1 occ:1.00 O2B C:AGS404 1.9 10.1 1.0 OG1 C:THR60 2.0 2.5 1.0 O2G C:AGS404 2.0 10.1 1.0 O C:HOH502 2.2 10.1 1.0 O C:HOH525 2.5 10.1 1.0 O C:HOH516 2.6 10.1 1.0 HB C:THR60 2.9 2.5 1.0 CB C:THR60 3.0 2.5 1.0 PG C:AGS404 3.3 10.1 1.0 H C:THR60 3.3 2.5 1.0 PB C:AGS404 3.3 10.1 1.0 HH22 D:ARG183 3.5 10.1 1.0 O3G C:AGS404 3.7 10.1 1.0 OD2 C:ASP117 3.7 3.4 1.0 O2A C:AGS404 3.7 10.1 1.0 O3B C:AGS404 3.7 10.1 1.0 HH22 C:ARG206 3.9 3.5 1.0 HG21 C:THR60 3.9 2.5 1.0 N C:THR60 3.9 2.5 1.0 OD1 C:ASP117 4.0 3.4 1.0 HH21 D:ARG154 4.0 2.1 1.0 CA C:THR60 4.0 2.5 1.0 CG2 C:THR60 4.1 2.5 1.0 O3A C:AGS404 4.1 10.1 1.0 NH2 D:ARG183 4.1 10.1 1.0 HH21 D:ARG183 4.1 10.1 1.0 HD3 D:ARG155 4.2 1.9 1.0 HB2 C:LYS59 4.2 3.5 1.0 CG C:ASP117 4.3 3.4 1.0 PA C:AGS404 4.3 10.1 1.0 HA C:THR60 4.4 2.5 1.0 O1B C:AGS404 4.4 10.1 1.0 HH21 C:ARG206 4.4 3.5 1.0 HE2 C:LYS59 4.5 3.5 1.0 NH2 C:ARG206 4.5 3.5 1.0 HD23 C:LEU146 4.5 3.6 1.0 HD22 C:LEU146 4.5 3.6 1.0 O1A C:AGS404 4.6 10.1 1.0 HG23 C:THR60 4.6 2.5 1.0 HG22 C:THR60 4.7 2.5 1.0 HH11 D:ARG155 4.7 1.9 1.0 NH2 D:ARG154 4.7 2.1 1.0 OE1 D:GLU158 4.8 1.1 1.0 HH22 D:ARG154 4.9 2.1 1.0 S1G C:AGS404 4.9 10.1 1.0 HG3 C:GLU118 5.0 2.9 1.0 CD2 C:LEU146 5.0 3.6 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 D:Mg401 b:10.1 occ:1.00 O2B D:AGS402 2.0 10.1 1.0 O D:HOH571 2.2 10.1 1.0 O2G D:AGS402 2.2 10.1 1.0 O D:HOH501 2.2 10.1 1.0 OG1 D:THR72 2.3 2.8 1.0 O D:HOH556 2.4 10.1 1.0 HB D:THR72 2.9 2.8 1.0 HG1 D:THR72 3.0 2.8 1.0 CB D:THR72 3.2 2.8 1.0 H D:THR72 3.3 2.8 1.0 PG D:AGS402 3.4 10.1 1.0 PB D:AGS402 3.4 10.1 1.0 HH22 E:ARG184 3.4 3.7 1.0 O2A D:AGS402 3.5 10.1 1.0 O3B D:AGS402 3.7 10.1 1.0 O3G D:AGS402 3.8 10.1 1.0 HH21 E:ARG184 3.9 3.7 1.0 HH21 E:ARG155 3.9 6.1 1.0 NH2 E:ARG184 4.0 3.7 1.0 N D:THR72 4.0 2.8 1.0 OD2 D:ASP140 4.0 1.6 1.0 HG21 D:THR72 4.1 2.8 1.0 HH22 D:ARG229 4.1 4.2 1.0 OD1 D:ASP140 4.1 1.6 1.0 CA D:THR72 4.2 2.8 1.0 HB2 D:LYS71 4.2 7.9 1.0 CG2 D:THR72 4.3 2.8 1.0 O1B D:AGS402 4.3 10.1 1.0 OE1 E:GLU159 4.3 6.0 1.0 O3A D:AGS402 4.3 10.1 1.0 PA D:AGS402 4.4 10.1 1.0 HE2 D:LYS71 4.4 7.9 1.0 HG21 D:ILE169 4.4 10.1 1.0 CG D:ASP140 4.5 1.6 1.0 HD3 E:ARG156 4.5 5.9 1.0 HA D:THR72 4.6 2.8 1.0 HH21 D:ARG229 4.6 4.2 1.0 NH2 E:ARG155 4.6 6.1 1.0 NH2 D:ARG229 4.7 4.2 1.0 O1A D:AGS402 4.7 10.1 1.0 HG22 D:THR72 4.8 2.8 1.0 HH22 E:ARG155 4.8 6.1 1.0 HH11 E:ARG156 4.9 5.9 1.0 HG23 D:THR72 4.9 2.8 1.0 O D:HOH567 4.9 10.1 1.0 H D:LYS71 5.0 7.9 1.0

J.C.Castaneda, M.Schrecker, D.Remus, R.K.Hite. Mechanisms of Loading and Release of the 9-1-1 Checkpoint Clamp. Nat.Struct.Mol.Biol. V. 29 369 2022.
ISSN: ESSN 1545-9985
PubMed: 35314831
DOI: 10.1038/S41594-022-00741-7