Magnesium in PDB 9gm8: Mukbef in A Nucleotide-Bound State with Open Neck Gate

The binding sites of Magnesium atom in the Mukbef in A Nucleotide-Bound State with Open Neck Gate (pdb code 9gm8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mukbef in A Nucleotide-Bound State with Open Neck Gate, PDB code: 9gm8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mukbef in A Nucleotide-Bound State with Open Neck Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mukbef in A Nucleotide-Bound State with Open Neck Gate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1501 b:77.4 occ:1.00 O2G A:ATP1502 2.0 83.6 1.0 O2B A:ATP1502 2.2 83.6 1.0 OG A:SER41 2.3 78.2 1.0 O3G A:ATP1502 2.5 83.6 1.0 PG A:ATP1502 2.6 83.6 1.0 HG A:SER41 2.7 78.2 1.0 O3B A:ATP1502 2.9 83.6 1.0 PB A:ATP1502 3.1 83.6 1.0 H A:SER41 3.3 78.2 1.0 CB A:SER41 3.5 78.2 1.0 HB2 A:SER41 3.5 78.2 1.0 OE2 A:GLU1407 3.6 84.8 1.0 HG1 B:THR1367 3.8 87.5 1.0 HE2 A:LYS40 4.0 79.4 1.0 HB2 A:LYS40 4.0 79.4 1.0 O3A A:ATP1502 4.0 83.6 1.0 O1G A:ATP1502 4.0 83.6 1.0 H B:THR1367 4.0 87.5 1.0 O1A A:ATP1502 4.0 83.6 1.0 HG B:SER1366 4.1 93.0 1.0 N A:SER41 4.1 78.2 1.0 HB3 A:SER41 4.1 78.2 1.0 OG1 B:THR1367 4.1 87.5 1.0 HZ2 A:LYS40 4.2 79.4 1.0 HB B:THR1367 4.3 87.5 1.0 O1B A:ATP1502 4.3 83.6 1.0 OD1 A:ASP1406 4.3 83.4 1.0 CA A:SER41 4.4 78.2 1.0 HZ1 A:LYS40 4.5 79.4 1.0 PA A:ATP1502 4.6 83.6 1.0 OD2 A:ASP1406 4.6 83.4 1.0 NZ A:LYS40 4.6 79.4 1.0 CD A:GLU1407 4.7 84.8 1.0 OG B:SER1366 4.7 93.0 1.0 HA A:SER41 4.7 78.2 1.0 CE A:LYS40 4.8 79.4 1.0 CB B:THR1367 4.8 87.5 1.0 N B:THR1367 4.9 87.5 1.0 CG A:ASP1406 4.9 83.4 1.0 CB A:LYS40 4.9 79.4 1.0 HG1 A:THR63 5.0 83.9 1.0 H A:LYS40 5.0 79.4 1.0

Magnesium binding site 2 out of 2 in the Mukbef in A Nucleotide-Bound State with Open Neck Gate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mukbef in A Nucleotide-Bound State with Open Neck Gate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1501 b:82.3 occ:1.00 O2G B:ATP1502 1.9 82.2 1.0 O2B B:ATP1502 2.0 82.2 1.0 OG B:SER41 2.1 84.1 1.0 O1A B:ATP1502 2.3 82.2 1.0 O3B B:ATP1502 2.6 82.2 1.0 HB2 B:SER41 2.7 84.1 1.0 PB B:ATP1502 2.7 82.2 1.0 HG B:SER41 2.8 84.1 1.0 PG B:ATP1502 2.8 82.2 1.0 CB B:SER41 2.9 84.1 1.0 H B:SER41 2.9 84.1 1.0 O3A B:ATP1502 3.1 82.2 1.0 PA B:ATP1502 3.1 82.2 1.0 HB2 A:SER1366 3.4 78.3 1.0 HG1 A:THR1367 3.5 77.4 1.0 O3G B:ATP1502 3.6 82.2 1.0 H A:THR1367 3.6 77.4 1.0 HB3 B:SER41 3.6 84.1 1.0 N B:SER41 3.7 84.1 1.0 O2A B:ATP1502 3.8 82.2 1.0 CA B:SER41 3.9 84.1 1.0 HA A:SER1366 4.0 78.3 1.0 O1G B:ATP1502 4.1 82.2 1.0 O1B B:ATP1502 4.1 82.2 1.0 CB A:SER1366 4.1 78.3 1.0 HB3 A:SER1366 4.2 78.3 1.0 OG1 A:THR1367 4.3 77.4 1.0 HB2 B:LYS40 4.3 86.3 1.0 N A:THR1367 4.4 77.4 1.0 HA B:SER41 4.5 84.1 1.0 CA A:SER1366 4.5 78.3 1.0 O5' B:ATP1502 4.5 82.2 1.0 H B:LYS40 4.6 86.3 1.0 HE2 B:LYS40 4.6 86.3 1.0 H B:THR42 4.7 83.3 1.0 HZ2 B:LYS40 4.7 86.3 1.0 HB A:THR1367 4.7 77.4 1.0 H B:GLY37 4.8 91.3 1.0 HZ3 B:LYS40 4.8 86.3 1.0 C B:LYS40 4.9 86.3 1.0 OD2 B:ASP1406 4.9 90.3 1.0 N B:LYS40 4.9 86.3 1.0

F.Burmann, M.Dillingham, F.Lowe. Structural Basis For Dna Capture By the Mukbef Smc Complex and Its Inhibition By A Viral Dna Mimic To Be Published.