Magnesium in PDB 8rjw: Human RAD52 Open Ring - Ssdna Complex

The binding sites of Magnesium atom in the Human RAD52 Open Ring - Ssdna Complex (pdb code 8rjw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Human RAD52 Open Ring - Ssdna Complex, PDB code: 8rjw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Human RAD52 Open Ring - Ssdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human RAD52 Open Ring - Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:68.1 occ:1.00 O B:HOH502 2.0 56.1 1.0 OE2 C:GLU140 2.6 55.9 1.0 O B:HOH504 2.8 60.1 1.0 O C:HOH602 3.2 87.5 1.0 OE2 B:GLU145 3.5 57.7 1.0 CD C:GLU140 3.6 53.9 1.0 HZ2 C:LYS144 3.9 45.8 1.0 H4' J:DT20 3.9 89.3 1.0 O B:HOH503 3.9 58.2 1.0 OD2 B:ASP149 3.9 38.1 1.0 HZ1 C:LYS144 4.0 47.4 1.0 OE1 C:GLU140 4.1 55.7 1.0 O B:TYR126 4.2 46.2 1.0 H5'' J:DT20 4.2 86.5 1.0 HB3 B:TYR126 4.3 37.0 1.0 HG21 B:VAL128 4.3 41.2 1.0 CG B:ASP149 4.3 42.2 1.0 NZ C:LYS144 4.3 45.4 1.0 OD1 B:ASP149 4.5 46.5 1.0 HG3 C:GLU140 4.6 49.2 1.0 CD B:GLU145 4.6 54.6 1.0 HZ3 C:LYS144 4.7 46.0 1.0 CG C:GLU140 4.7 48.4 1.0 C4' J:DT20 4.7 90.7 1.0 HG2 B:GLU145 4.8 42.8 1.0 HA2 B:GLY127 4.8 39.5 1.0 C5' J:DT20 4.8 87.8 1.0 HB2 B:ASP149 4.8 39.2 1.0 H5' J:DT20 4.8 82.7 1.0 C B:TYR126 4.9 41.5 1.0 HD2 B:TYR126 5.0 42.6 1.0

Magnesium binding site 2 out of 5 in the Human RAD52 Open Ring - Ssdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human RAD52 Open Ring - Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:63.3 occ:1.00 O C:HOH601 1.8 48.0 1.0 O J:HOH105 1.8 47.8 1.0 O J:HOH106 3.0 51.4 1.0 OE1 D:GLU140 3.2 65.1 1.0 CD D:GLU140 3.6 61.5 1.0 HZ1 D:LYS144 3.8 55.9 1.0 OE2 D:GLU140 3.8 59.3 1.0 HZ2 D:LYS144 3.8 55.8 1.0 OE2 C:GLU145 3.9 52.5 1.0 O C:TYR126 4.0 49.6 1.0 OD2 C:ASP149 4.2 42.0 1.0 NZ D:LYS144 4.2 54.7 1.0 HG2 D:GLU140 4.3 54.1 1.0 HZ3 D:LYS144 4.5 54.9 1.0 O J:HOH101 4.5 47.5 1.0 CG D:GLU140 4.6 53.9 1.0 CG C:ASP149 4.6 37.5 1.0 OP2 J:DT17 4.7 45.0 1.0 HG21 C:VAL128 4.7 40.1 1.0 O J:HOH110 4.7 55.6 1.0 OD1 C:ASP149 4.7 42.9 1.0 OP1 J:DT17 4.9 52.1 1.0 HG3 D:GLU140 4.9 53.9 1.0 CD C:GLU145 5.0 46.4 1.0

Magnesium binding site 3 out of 5 in the Human RAD52 Open Ring - Ssdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human RAD52 Open Ring - Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:48.8 occ:1.00 O E:HOH503 1.9 62.2 1.0 OD2 D:ASP149 2.4 46.6 1.0 OE2 E:GLU140 2.4 64.7 1.0 O D:TYR126 3.0 43.9 1.0 O J:HOH109 3.2 56.5 1.0 OE2 D:GLU145 3.5 53.2 1.0 CG D:ASP149 3.6 45.6 1.0 O D:HOH603 3.6 52.0 1.0 CD E:GLU140 3.6 59.1 1.0 HZ2 E:LYS144 3.7 54.7 1.0 O E:HOH508 3.8 54.9 1.0 HG2 D:GLU145 3.9 45.4 1.0 HB2 D:ASP149 3.9 40.7 1.0 C D:TYR126 4.1 42.8 1.0 HB3 D:TYR126 4.2 41.5 1.0 H D:TYR126 4.2 39.7 1.0 OE1 E:GLU140 4.3 59.5 1.0 CB D:ASP149 4.3 40.4 1.0 OD1 D:ASP149 4.5 49.6 1.0 HA2 D:GLY127 4.5 40.1 1.0 CD D:GLU145 4.5 52.5 1.0 HG3 E:GLU140 4.5 53.6 1.0 HB3 D:ASP149 4.6 41.1 1.0 NZ E:LYS144 4.6 54.7 1.0 CG D:GLU145 4.6 46.1 1.0 O D:HOH601 4.7 57.1 1.0 HG23 D:VAL128 4.7 40.0 1.0 CG E:GLU140 4.7 52.9 1.0 O J:HOH107 4.8 54.0 1.0 OP2 J:DT13 4.8 43.1 1.0 N D:TYR126 4.9 37.7 1.0 HZ1 E:LYS144 4.9 53.6 1.0 CA D:TYR126 4.9 38.6 1.0 HZ3 E:LYS144 4.9 54.6 1.0 CB D:TYR126 4.9 41.4 1.0 HG3 D:GLU145 4.9 46.0 1.0

Magnesium binding site 4 out of 5 in the Human RAD52 Open Ring - Ssdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human RAD52 Open Ring - Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:61.0 occ:1.00 O J:HOH111 1.9 58.5 1.0 O E:HOH504 2.5 57.6 1.0 O F:HOH606 2.6 60.1 1.0 OE2 F:GLU140 2.7 62.3 1.0 O E:HOH501 2.9 55.5 1.0 CD F:GLU140 3.5 57.3 1.0 OE1 F:GLU140 3.6 56.5 1.0 HZ2 F:LYS144 3.7 53.4 1.0 HZ1 F:LYS144 3.8 53.0 1.0 OP1 J:DT9 4.0 54.9 1.0 O J:HOH103 4.0 53.6 1.0 NZ F:LYS144 4.1 52.4 1.0 OP2 J:DT9 4.2 45.2 1.0 HZ3 F:LYS144 4.2 52.6 1.0 HH22 E:ARG55 4.4 53.7 1.0 O E:HOH505 4.4 43.6 1.0 P J:DT9 4.5 50.8 1.0 OD1 E:ASP149 4.8 51.3 1.0 O E:HOH506 4.8 60.3 1.0 CG F:GLU140 4.9 52.1 1.0 H4' J:DT9 4.9 38.5 1.0 O5' J:DT9 5.0 39.6 1.0 O E:TYR126 5.0 39.2 1.0

Magnesium binding site 5 out of 5 in the Human RAD52 Open Ring - Ssdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human RAD52 Open Ring - Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg501 b:78.0 occ:1.00 O J:HOH108 2.6 68.7 1.0 O F:HOH601 2.8 47.5 1.0 OE2 G:GLU140 3.2 70.4 1.0 OE1 G:GLU140 3.3 65.1 1.0 CD G:GLU140 3.6 65.8 1.0 OE2 F:GLU145 4.2 52.4 1.0 HZ1 G:LYS144 4.5 62.4 1.0 H4' J:DT4 4.5 146.7 1.0 HZ2 G:LYS144 4.5 61.5 1.0 O3' J:DT4 4.6 123.5 1.0 OD2 F:ASP149 4.6 50.5 1.0 H2'' J:DT4 4.8 145.3 1.0 NZ G:LYS144 4.9 61.3 1.0 O F:TYR126 4.9 36.5 1.0 O G:HOH601 4.9 59.8 1.0 HG21 F:VAL128 4.9 33.2 1.0

C.C.Liang, L.A.Greenhough, L.Masino, S.Maslen, I.Bajrami, M.Tuppi, M.Skehel, I.A.Taylor, S.C.West. Mechanism of Single-Stranded Dna Annealing By RAD52-Rpa Complex Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07347-7