Magnesium in PDB 7jy9: Structure of A 9 Base Pair Reca-D Loop Complex

The binding sites of Magnesium atom in the Structure of A 9 Base Pair Reca-D Loop Complex (pdb code 7jy9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of A 9 Base Pair Reca-D Loop Complex, PDB code: 7jy9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:24.3 occ:1.00 OG1 A:THR73 2.2 23.5 1.0 O2G A:AGS402 2.2 24.5 1.0 O1B A:AGS402 2.2 24.0 1.0 HG1 A:THR73 2.7 23.1 1.0 HOG2 A:AGS402 2.9 24.2 1.0 PG A:AGS402 3.1 25.4 1.0 HB A:THR73 3.2 24.0 1.0 CB A:THR73 3.3 23.6 1.0 OE1 A:GLU96 3.3 24.2 1.0 PB A:AGS402 3.4 24.5 1.0 O3B A:AGS402 3.4 25.4 1.0 O3G A:AGS402 3.5 26.2 1.0 H A:THR73 3.7 23.1 1.0 O2A A:AGS402 3.8 25.6 1.0 HG22 A:THR73 3.9 24.4 1.0 CG2 A:THR73 4.1 23.9 1.0 OD2 A:ASP144 4.2 23.2 1.0 OD1 A:ASP144 4.3 22.7 1.0 N A:THR73 4.3 22.8 1.0 CD A:GLU96 4.4 24.4 1.0 CA A:THR73 4.4 23.0 1.0 O2B A:AGS402 4.4 24.2 1.0 O3A A:AGS402 4.5 24.9 1.0 HG23 A:THR73 4.5 23.6 1.0 HB2 A:LYS72 4.5 22.4 1.0 PA A:AGS402 4.6 25.3 1.0 CG A:ASP144 4.7 22.9 1.0 HA A:THR73 4.7 22.6 1.0 OE2 A:GLU96 4.8 24.1 1.0 HE2 A:LYS72 4.8 22.6 1.0 HG21 A:THR73 4.9 24.1 1.0 S1G A:AGS402 5.0 25.7 1.0

Magnesium binding site 2 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:21.7 occ:1.00 O2G B:AGS402 2.2 21.8 1.0 OG1 B:THR73 2.2 21.7 1.0 O1B B:AGS402 2.2 21.8 1.0 HOG2 B:AGS402 2.6 21.7 1.0 HG1 B:THR73 2.7 21.6 1.0 HB B:THR73 3.2 22.1 1.0 CB B:THR73 3.2 21.9 1.0 HZ2 A:LYS250 3.3 20.1 1.0 PG B:AGS402 3.5 22.1 1.0 PB B:AGS402 3.6 22.0 1.0 HE3 A:LYS250 3.7 20.5 1.0 OE1 B:GLU96 3.7 21.4 1.0 H B:THR73 3.8 21.7 1.0 HG22 B:THR73 3.8 22.3 1.0 OD2 B:ASP144 3.9 21.5 1.0 O3B B:AGS402 3.9 22.2 1.0 OD1 B:ASP144 4.1 21.1 1.0 NZ A:LYS250 4.1 19.9 1.0 O2A B:AGS402 4.1 22.6 1.0 CG2 B:THR73 4.1 22.2 1.0 O3G B:AGS402 4.1 22.5 1.0 CE A:LYS250 4.2 20.3 1.0 HZ1 A:LYS250 4.3 19.7 1.0 N B:THR73 4.3 21.7 1.0 CA B:THR73 4.3 21.8 1.0 HE2 A:LYS250 4.3 20.6 1.0 CG B:ASP144 4.4 21.3 1.0 HB2 B:LYS72 4.4 21.2 1.0 HG23 B:THR73 4.5 22.1 1.0 O2B B:AGS402 4.6 21.9 1.0 HA B:THR73 4.6 21.7 1.0 HE2 B:LYS72 4.6 21.1 1.0 O3A B:AGS402 4.7 22.4 1.0 CD B:GLU96 4.8 21.4 1.0 HZ3 A:LYS250 4.8 19.8 1.0 PA B:AGS402 4.9 22.6 1.0 HD13 B:ILE192 4.9 21.0 1.0 HG21 B:THR73 4.9 22.5 1.0 HG22 B:ILE192 5.0 20.8 1.0 S1G B:AGS402 5.0 22.0 1.0

Magnesium binding site 3 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:17.9 occ:1.00 O2G C:AGS402 2.2 18.1 1.0 OG1 C:THR73 2.2 17.7 1.0 O1B C:AGS402 2.2 17.8 1.0 HOG2 C:AGS402 2.6 18.0 1.0 HG1 C:THR73 2.8 17.5 1.0 HB C:THR73 3.2 18.4 1.0 CB C:THR73 3.2 18.1 1.0 PG C:AGS402 3.5 18.4 1.0 HZ2 B:LYS250 3.5 22.4 1.0 PB C:AGS402 3.5 18.0 1.0 OE1 C:GLU96 3.7 17.8 1.0 H C:THR73 3.7 17.5 1.0 HE3 B:LYS250 3.8 22.7 1.0 O3B C:AGS402 3.8 18.4 1.0 HG22 C:THR73 3.8 18.9 1.0 OD2 C:ASP144 3.9 17.6 1.0 CG2 C:THR73 4.1 18.6 1.0 O2A C:AGS402 4.1 19.3 1.0 OD1 C:ASP144 4.1 17.0 1.0 O3G C:AGS402 4.1 19.1 1.0 NZ B:LYS250 4.2 22.3 1.0 N C:THR73 4.3 17.4 1.0 CA C:THR73 4.3 17.7 1.0 CE B:LYS250 4.3 22.6 1.0 HE2 B:LYS250 4.4 22.8 1.0 CG C:ASP144 4.4 17.4 1.0 HB2 C:LYS72 4.4 16.6 1.0 HZ1 B:LYS250 4.5 22.1 1.0 HG23 C:THR73 4.5 18.5 1.0 O2B C:AGS402 4.5 17.6 1.0 O3A C:AGS402 4.6 18.6 1.0 HA C:THR73 4.6 17.5 1.0 HE2 C:LYS72 4.7 16.5 1.0 CD C:GLU96 4.7 17.7 1.0 PA C:AGS402 4.8 19.1 1.0 HD13 C:ILE192 4.9 16.5 1.0 HG21 C:THR73 4.9 19.0 1.0 HZ3 B:LYS250 5.0 22.2 1.0

Magnesium binding site 4 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:17.3 occ:1.00 O2G D:AGS402 2.2 17.3 1.0 OG1 D:THR73 2.2 17.5 1.0 O1B D:AGS402 2.2 17.3 1.0 HOG2 D:AGS402 2.6 17.3 1.0 HG1 D:THR73 2.6 17.4 1.0 HZ2 C:LYS250 3.3 18.0 1.0 CB D:THR73 3.4 17.8 1.0 OE1 D:GLU96 3.4 17.6 1.0 PG D:AGS402 3.5 17.4 1.0 HB D:THR73 3.5 17.8 1.0 PB D:AGS402 3.6 17.4 1.0 H D:THR73 3.6 17.4 1.0 OD2 D:ASP144 3.7 17.7 1.0 O3B D:AGS402 3.8 17.4 1.0 HE3 C:LYS250 3.8 18.2 1.0 OD1 D:ASP144 3.8 17.3 1.0 HG22 D:THR73 4.0 18.2 1.0 NZ C:LYS250 4.1 17.7 1.0 O3G D:AGS402 4.1 17.6 1.0 CG D:ASP144 4.2 17.6 1.0 O2A D:AGS402 4.2 17.9 1.0 N D:THR73 4.2 17.5 1.0 HB2 D:LYS72 4.2 17.1 1.0 CG2 D:THR73 4.3 18.1 1.0 HZ1 C:LYS250 4.3 17.4 1.0 CE C:LYS250 4.3 18.0 1.0 HE2 D:LYS72 4.3 17.0 1.0 CA D:THR73 4.4 17.7 1.0 HE2 C:LYS250 4.4 18.4 1.0 CD D:GLU96 4.4 17.6 1.0 O2B D:AGS402 4.5 17.4 1.0 HG23 D:THR73 4.5 18.1 1.0 OE2 D:GLU96 4.6 17.4 1.0 HA D:THR73 4.6 17.7 1.0 O3A D:AGS402 4.6 17.7 1.0 HG22 D:ILE192 4.7 17.0 1.0 HD13 D:ILE192 4.7 17.2 1.0 HZ3 C:LYS250 4.8 17.6 1.0 S1G D:AGS402 4.9 17.4 1.0 PA D:AGS402 4.9 18.0 1.0

Magnesium binding site 5 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:19.0 occ:1.00 OG1 E:THR73 2.2 19.0 1.0 O2G E:AGS402 2.2 19.1 1.0 O1B E:AGS402 2.2 19.1 1.0 HOG2 E:AGS402 2.6 19.1 1.0 HG1 E:THR73 2.7 18.9 1.0 HB E:THR73 3.3 19.4 1.0 CB E:THR73 3.3 19.2 1.0 PG E:AGS402 3.4 19.3 1.0 PB E:AGS402 3.5 19.2 1.0 OE1 E:GLU96 3.5 19.1 1.0 H E:THR73 3.7 19.1 1.0 HE3 D:LYS250 3.7 22.8 1.0 O3B E:AGS402 3.8 19.4 1.0 HZ2 D:LYS250 3.8 22.4 1.0 HG22 E:THR73 3.9 19.6 1.0 OD2 E:ASP144 3.9 19.0 1.0 OD1 E:ASP144 4.0 18.7 1.0 O2A E:AGS402 4.0 19.7 1.0 CG2 E:THR73 4.2 19.5 1.0 HE2 D:LYS250 4.2 22.9 1.0 O3G E:AGS402 4.2 19.6 1.0 N E:THR73 4.2 19.1 1.0 HB2 E:LYS72 4.3 18.8 1.0 CE D:LYS250 4.3 22.6 1.0 CA E:THR73 4.3 19.2 1.0 CG E:ASP144 4.4 18.9 1.0 O2B E:AGS402 4.4 19.2 1.0 NZ D:LYS250 4.5 22.1 1.0 HE2 E:LYS72 4.5 18.7 1.0 HG23 E:THR73 4.5 19.5 1.0 O3A E:AGS402 4.6 19.6 1.0 CD E:GLU96 4.6 19.1 1.0 HA E:THR73 4.6 19.1 1.0 PA E:AGS402 4.8 19.8 1.0 HD13 E:ILE192 4.8 18.6 1.0 HZ1 D:LYS250 4.8 21.8 1.0 HG22 E:ILE192 4.9 18.5 1.0 OE2 E:GLU96 4.9 19.0 1.0 S1G E:AGS402 5.0 19.4 1.0 HG21 E:THR73 5.0 19.8 1.0

Magnesium binding site 6 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:19.8 occ:1.00 OG1 F:THR73 2.2 19.5 1.0 O2G F:AGS402 2.2 20.4 1.0 O1B F:AGS402 2.2 20.3 1.0 HOG2 F:AGS402 2.5 20.3 1.0 HG1 F:THR73 2.7 19.3 1.0 CB F:THR73 3.3 19.9 1.0 HB F:THR73 3.3 20.3 1.0 OE1 F:GLU96 3.5 19.9 1.0 PG F:AGS402 3.5 21.1 1.0 PB F:AGS402 3.6 20.8 1.0 H F:THR73 3.6 19.8 1.0 HZ2 E:LYS250 3.6 24.4 1.0 OD1 F:ASP144 3.7 18.8 1.0 HE3 E:LYS250 3.9 25.0 1.0 OD2 F:ASP144 4.0 18.9 1.0 O3B F:AGS402 4.0 21.3 1.0 O3G F:AGS402 4.0 21.6 1.0 N F:THR73 4.1 19.6 1.0 HB2 F:LYS72 4.1 19.3 1.0 HG22 F:THR73 4.1 20.4 1.0 HE2 E:LYS250 4.2 25.0 1.0 CA F:THR73 4.2 19.6 1.0 CG F:ASP144 4.2 18.8 1.0 CG2 F:THR73 4.3 20.2 1.0 O2B F:AGS402 4.3 20.7 1.0 O2A F:AGS402 4.3 21.6 1.0 CE E:LYS250 4.3 24.6 1.0 NZ E:LYS250 4.3 24.1 1.0 HE2 F:LYS72 4.4 19.3 1.0 CD F:GLU96 4.5 19.9 1.0 HA F:THR73 4.5 19.3 1.0 HD13 F:ILE192 4.6 18.3 1.0 HG23 F:THR73 4.6 19.9 1.0 HG22 F:ILE192 4.6 18.3 1.0 OE2 F:GLU96 4.7 19.9 1.0 O3A F:AGS402 4.7 21.4 1.0 HZ1 E:LYS250 4.8 23.8 1.0 S1G F:AGS402 4.9 21.4 1.0 PA F:AGS402 5.0 21.7 1.0 HZ3 E:LYS250 5.0 23.8 1.0

Magnesium binding site 7 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg401 b:17.7 occ:1.00 O2G G:AGS402 2.1 17.8 1.0 OG1 G:THR73 2.2 17.7 1.0 O1B G:AGS402 2.2 17.9 1.0 HOG2 G:AGS402 2.6 17.8 1.0 HG1 G:THR73 2.7 17.6 1.0 HB G:THR73 3.2 18.2 1.0 CB G:THR73 3.2 18.0 1.0 PG G:AGS402 3.4 18.1 1.0 PB G:AGS402 3.5 18.2 1.0 HE3 F:LYS250 3.5 19.0 1.0 HZ2 F:LYS250 3.6 18.5 1.0 O3B G:AGS402 3.6 18.3 1.0 H G:THR73 3.7 18.0 1.0 HG22 G:THR73 3.7 18.3 1.0 OE1 G:GLU96 3.8 17.5 1.0 O3G G:AGS402 4.0 18.3 1.0 CG2 G:THR73 4.0 18.2 1.0 O2A G:AGS402 4.1 18.7 1.0 OD2 G:ASP144 4.2 17.6 1.0 CE F:LYS250 4.2 18.7 1.0 NZ F:LYS250 4.2 18.3 1.0 HE2 F:LYS250 4.2 18.8 1.0 OD1 G:ASP144 4.2 17.4 1.0 N G:THR73 4.3 18.0 1.0 CA G:THR73 4.3 18.1 1.0 HG23 G:THR73 4.4 18.1 1.0 O3A G:AGS402 4.4 18.6 1.0 HZ1 F:LYS250 4.5 18.2 1.0 HB2 G:LYS72 4.6 17.8 1.0 CG G:ASP144 4.6 17.5 1.0 HE2 G:LYS72 4.6 17.7 1.0 O2B G:AGS402 4.6 18.4 1.0 HA G:THR73 4.7 17.9 1.0 PA G:AGS402 4.7 18.8 1.0 CD G:GLU96 4.8 17.6 1.0 HG21 G:THR73 4.9 18.5 1.0 S1G G:AGS402 4.9 18.3 1.0 HZ3 F:LYS250 5.0 18.1 1.0 HD13 G:ILE192 5.0 17.4 1.0

Magnesium binding site 8 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg401 b:19.9 occ:1.00 OG1 H:THR73 2.2 20.0 1.0 O2G H:AGS402 2.2 20.0 1.0 O1B H:AGS402 2.2 20.4 1.0 HG1 H:THR73 2.6 19.8 1.0 HOG2 H:AGS402 2.7 19.8 1.0 OE1 H:GLU96 3.4 19.3 1.0 PG H:AGS402 3.4 20.5 1.0 CB H:THR73 3.4 20.4 1.0 HB H:THR73 3.5 20.7 1.0 HZ2 G:LYS250 3.5 25.3 1.0 PB H:AGS402 3.6 20.8 1.0 H H:THR73 3.7 20.5 1.0 HE3 G:LYS250 3.8 25.9 1.0 OD2 H:ASP144 3.8 19.5 1.0 O3B H:AGS402 3.9 20.8 1.0 OD1 H:ASP144 3.9 19.1 1.0 HE2 G:LYS250 4.1 25.9 1.0 O3G H:AGS402 4.1 20.7 1.0 HG22 H:THR73 4.1 20.6 1.0 O2A H:AGS402 4.2 21.3 1.0 CE G:LYS250 4.2 25.4 1.0 CG H:ASP144 4.3 19.2 1.0 NZ G:LYS250 4.3 24.9 1.0 N H:THR73 4.3 20.5 1.0 HB2 H:LYS72 4.3 20.1 1.0 CG2 H:THR73 4.3 20.5 1.0 CD H:GLU96 4.4 19.2 1.0 CA H:THR73 4.4 20.5 1.0 O2B H:AGS402 4.5 20.9 1.0 HE2 H:LYS72 4.5 19.9 1.0 HG23 H:THR73 4.6 20.3 1.0 OE2 H:GLU96 4.6 19.2 1.0 HA H:THR73 4.6 20.2 1.0 HZ1 G:LYS250 4.7 24.5 1.0 O3A H:AGS402 4.7 21.4 1.0 HD13 H:ILE192 4.7 19.5 1.0 HG22 H:ILE192 4.8 19.4 1.0 S1G H:AGS402 4.9 20.5 1.0 HZ3 G:LYS250 4.9 24.5 1.0 PA H:AGS402 4.9 21.6 1.0

Magnesium binding site 9 out of 9 in the Structure of A 9 Base Pair Reca-D Loop Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A 9 Base Pair Reca-D Loop Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg401 b:17.4 occ:1.00 O2G I:AGS402 2.2 17.2 1.0 OG1 I:THR73 2.2 17.9 1.0 O1B I:AGS402 2.2 18.1 1.0 HG1 I:THR73 2.6 17.9 1.0 HOG2 I:AGS402 2.6 16.9 1.0 OE1 I:GLU96 3.2 16.7 1.0 CB I:THR73 3.4 18.5 1.0 PG I:AGS402 3.5 17.6 1.0 HB I:THR73 3.5 18.7 1.0 PB I:AGS402 3.5 18.5 1.0 HZ2 H:LYS250 3.6 25.2 1.0 OD2 I:ASP144 3.7 17.2 1.0 H I:THR73 3.7 18.8 1.0 HE3 H:LYS250 3.7 25.7 1.0 OD1 I:ASP144 3.8 17.6 1.0 O3B I:AGS402 3.9 18.1 1.0 HE2 H:LYS250 4.1 25.7 1.0 HG22 I:THR73 4.1 18.5 1.0 CG I:ASP144 4.2 17.4 1.0 HB2 I:LYS72 4.2 18.5 1.0 CE H:LYS250 4.2 25.3 1.0 CD I:GLU96 4.2 16.5 1.0 O2A I:AGS402 4.3 18.9 1.0 N I:THR73 4.3 18.9 1.0 NZ H:LYS250 4.3 24.8 1.0 CG2 I:THR73 4.3 18.6 1.0 O3G I:AGS402 4.3 17.8 1.0 CA I:THR73 4.4 18.9 1.0 HE2 I:LYS72 4.4 17.9 1.0 O2B I:AGS402 4.4 18.8 1.0 OE2 I:GLU96 4.5 16.4 1.0 HG23 I:THR73 4.6 18.6 1.0 HD13 I:ILE192 4.6 18.0 1.0 HA I:THR73 4.6 18.7 1.0 HG22 I:ILE192 4.6 17.7 1.0 O3A I:AGS402 4.7 19.1 1.0 HZ1 H:LYS250 4.7 24.5 1.0 S1G I:AGS402 4.9 17.3 1.0 HZ3 H:LYS250 4.9 24.5 1.0 PA I:AGS402 4.9 19.4 1.0

H.Yang, C.Zhou, A.Dhar, N.P.Pavletich. Mechanism of Strand Exchange From Reca-Dna Synaptic and D-Loop Structures. Nature V. 586 801 2020.
ISSN: ESSN 1476-4687
PubMed: 33057191
DOI: 10.1038/S41586-020-2820-9