Magnesium in PDB 3qkt: RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp

The structure of RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp, PDB code: 3qkt was solved by G.J.Williams, R.S.Williams, A.Arvai, G.Moncalian, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.65 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.390, 108.517, 150.366, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.4

The binding sites of Magnesium atom in the RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp (pdb code 3qkt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp, PDB code: 3qkt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:20.8 occ:1.00 O1G A:ANP901 2.0 16.4 1.0 O A:HOH685 2.1 18.8 1.0 O1B A:ANP901 2.2 17.0 1.0 OE1 A:GLN140 2.2 19.8 1.0 OG A:SER37 2.2 22.8 1.0 O A:HOH883 2.4 16.8 1.0 CD A:GLN140 3.1 21.2 1.0 PG A:ANP901 3.2 18.6 1.0 CB A:SER37 3.2 13.6 1.0 PB A:ANP901 3.3 19.2 1.0 N3B A:ANP901 3.5 25.8 1.0 NE2 A:GLN140 3.5 22.5 1.0 N A:SER37 4.0 18.6 1.0 OD1 A:ASP822 4.0 23.4 1.0 O3G A:ANP901 4.1 21.1 1.0 O2A A:ANP901 4.1 18.2 1.0 O3A A:ANP901 4.1 21.5 1.0 OD2 A:ASP822 4.1 26.5 1.0 CA A:SER37 4.2 18.3 1.0 O A:HOH906 4.3 23.0 1.0 N B:GLY794 4.3 19.9 1.0 O2G A:ANP901 4.3 15.8 1.0 OE2 A:GLU823 4.4 29.5 1.0 O2B A:ANP901 4.4 20.4 1.0 CG A:GLN140 4.5 17.6 1.0 CG A:ASP822 4.5 27.5 1.0 PA A:ANP901 4.6 19.0 1.0 CG A:GLU823 4.6 28.7 1.0 CB A:GLN140 4.7 18.4 1.0 CE A:LYS36 4.7 23.1 1.0 CA B:GLY794 4.8 22.2 1.0 NZ A:LYS36 4.9 30.9 1.0 CB A:LYS36 4.9 21.9 1.0 O B:HOH892 5.0 22.6 1.0 CB B:SER793 5.0 18.9 1.0

Magnesium binding site 2 out of 4 in the RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:19.3 occ:1.00 O1G B:ANP901 2.0 16.6 1.0 O B:HOH684 2.2 14.8 1.0 OE1 B:GLN140 2.2 16.1 1.0 O1B B:ANP901 2.2 14.7 1.0 OG B:SER37 2.2 14.4 1.0 O B:HOH883 2.3 15.1 1.0 CD B:GLN140 3.1 18.7 1.0 PG B:ANP901 3.2 17.8 1.0 PB B:ANP901 3.2 16.7 1.0 CB B:SER37 3.3 17.6 1.0 NE2 B:GLN140 3.5 18.2 1.0 N3B B:ANP901 3.5 21.6 1.0 O3G B:ANP901 4.0 17.5 1.0 N B:SER37 4.0 14.7 1.0 OD1 B:ASP822 4.1 25.2 1.0 O3A B:ANP901 4.1 15.3 1.0 OD2 B:ASP822 4.1 21.9 1.0 O2A B:ANP901 4.2 18.5 1.0 CA B:SER37 4.2 20.7 1.0 O B:HOH359 4.2 21.5 1.0 N A:GLY794 4.3 20.1 1.0 O2G B:ANP901 4.3 16.5 1.0 O2B B:ANP901 4.4 15.7 1.0 OE2 B:GLU823 4.4 27.8 1.0 CG B:GLN140 4.4 17.2 1.0 CG B:ASP822 4.5 24.4 1.0 CG B:GLU823 4.5 29.7 1.0 PA B:ANP901 4.6 17.2 1.0 CB B:GLN140 4.7 14.3 1.0 CE B:LYS36 4.7 24.4 1.0 CA A:GLY794 4.8 19.0 1.0 O A:HOH885 4.9 21.9 1.0 NZ B:LYS36 4.9 31.8 1.0 CB B:LYS36 4.9 18.6 1.0 CD B:GLU823 5.0 30.9 1.0

Magnesium binding site 3 out of 4 in the RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:24.2 occ:1.00 O1G C:ANP901 2.0 19.1 1.0 OG C:SER37 2.1 23.2 1.0 O1B C:ANP901 2.2 20.3 1.0 OE1 C:GLN140 2.2 20.7 1.0 O C:HOH603 2.2 22.1 1.0 O C:HOH701 2.3 19.0 1.0 CB C:SER37 3.1 22.2 1.0 CD C:GLN140 3.2 26.6 1.0 PB C:ANP901 3.2 21.6 1.0 PG C:ANP901 3.2 21.5 1.0 NE2 C:GLN140 3.5 22.4 1.0 N3B C:ANP901 3.5 26.9 1.0 N C:SER37 3.9 19.2 1.0 O3G C:ANP901 4.0 23.4 1.0 O2A C:ANP901 4.1 20.1 1.0 O3A C:ANP901 4.1 24.4 1.0 CA C:SER37 4.1 21.2 1.0 OD2 C:ASP822 4.1 26.5 1.0 OD1 C:ASP822 4.1 26.9 1.0 O C:HOH262 4.2 26.3 1.0 N D:GLY794 4.2 26.7 1.0 O2G C:ANP901 4.4 18.9 1.0 O2B C:ANP901 4.4 21.4 1.0 OE2 C:GLU823 4.4 36.6 1.0 CG C:GLN140 4.5 16.6 1.0 CG C:ASP822 4.5 26.0 1.0 PA C:ANP901 4.6 21.6 1.0 CG C:GLU823 4.6 35.1 1.0 CB C:GLN140 4.7 16.4 1.0 CE C:LYS36 4.8 32.5 1.0 CA D:GLY794 4.8 26.2 1.0 CB D:SER793 4.9 21.2 1.0 O1A C:ANP901 4.9 17.6 1.0 O C:HOH922 4.9 29.4 1.0 CB C:LYS36 5.0 21.6 1.0

Magnesium binding site 4 out of 4 in the RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of RAD50 Abc-Atpase with Adjacent Coiled-Coil Region in Complex with Amp- Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:22.7 occ:1.00 O1G D:ANP901 2.0 16.9 1.0 OE1 D:GLN140 2.1 21.2 1.0 O1B D:ANP901 2.2 16.7 1.0 OG D:SER37 2.2 19.6 1.0 O D:HOH884 2.2 17.0 1.0 O D:HOH702 2.3 15.0 1.0 CD D:GLN140 3.1 26.9 1.0 CB D:SER37 3.2 20.9 1.0 PG D:ANP901 3.2 20.4 1.0 PB D:ANP901 3.3 19.9 1.0 NE2 D:GLN140 3.5 24.9 1.0 N3B D:ANP901 3.5 24.8 1.0 O3G D:ANP901 4.0 16.8 1.0 N D:SER37 4.0 19.4 1.0 O2A D:ANP901 4.1 19.0 1.0 OD1 D:ASP822 4.1 24.1 1.0 O3A D:ANP901 4.1 18.8 1.0 CA D:SER37 4.2 22.0 1.0 OD2 D:ASP822 4.2 21.4 1.0 O D:HOH358 4.3 26.2 1.0 N C:GLY794 4.3 23.1 1.0 O2G D:ANP901 4.4 20.5 1.0 O2B D:ANP901 4.4 20.6 1.0 CG D:GLN140 4.4 20.9 1.0 OE2 D:GLU823 4.5 30.2 1.0 CG D:GLU823 4.6 34.5 1.0 PA D:ANP901 4.6 20.6 1.0 CG D:ASP822 4.6 25.0 1.0 CE D:LYS36 4.6 27.9 1.0 CB D:GLN140 4.7 17.6 1.0 CA C:GLY794 4.8 26.3 1.0 CB D:LYS36 4.9 24.7 1.0 NZ D:LYS36 4.9 34.6 1.0 CB C:SER793 4.9 26.2 1.0 O1A D:ANP901 5.0 16.4 1.0 O C:HOH891 5.0 27.2 1.0

G.J.Williams, R.S.Williams, J.S.Williams, G.Moncalian, A.S.Arvai, O.Limbo, G.Guenther, S.Sildas, M.Hammel, P.Russell, J.A.Tainer. Abc Atpase Signature Helices in RAD50 Link Nucleotide State to MRE11 Interface For Dna Repair. Nat.Struct.Mol.Biol. V. 18 423 2011.
ISSN: ISSN 1545-9993
PubMed: 21441914
DOI: 10.1038/NSMB.2038