Magnesium in PDB 4r8u: S-Sad Structure of Dinb-Dna Complex

All present enzymatic activity of S-Sad Structure of Dinb-Dna Complex:
2.7.7.7;

The structure of S-Sad Structure of Dinb-Dna Complex, PDB code: 4r8u was solved by J.Kottur, D.T.Nair, T.Weinert, V.Oligeric, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.950, 57.210, 110.600, 90.00, 94.69, 90.00
R / Rfree (%)	18.1 / 22

The binding sites of Magnesium atom in the S-Sad Structure of Dinb-Dna Complex (pdb code 4r8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S-Sad Structure of Dinb-Dna Complex, PDB code: 4r8u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the S-Sad Structure of Dinb-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S-Sad Structure of Dinb-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:37.0 occ:1.00 O2B A:1FZ402 2.2 40.8 1.0 O A:MET10 2.2 54.3 1.0 O1A A:1FZ402 2.3 40.9 1.0 OD1 A:ASP9 2.3 51.0 1.0 OD2 A:ASP104 2.4 71.6 1.0 O1G A:1FZ402 2.4 40.4 1.0 OD1 A:ASP104 3.0 98.7 1.0 CG A:ASP104 3.0 72.8 1.0 PB A:1FZ402 3.4 40.6 1.0 CG A:ASP9 3.4 60.0 1.0 C A:MET10 3.4 49.3 1.0 PA A:1FZ402 3.5 40.8 1.0 PG A:1FZ402 3.6 40.3 1.0 N3A A:1FZ402 3.8 40.7 1.0 O3B A:1FZ402 3.9 40.4 1.0 NZ A:LYS158 3.9 49.8 1.0 OD2 A:ASP9 4.0 68.5 1.0 N A:MET10 4.0 40.4 1.0 C5' A:1FZ402 4.0 41.3 1.0 O3G A:1FZ402 4.2 40.2 1.0 O5' A:1FZ402 4.2 41.1 1.0 CA A:MET10 4.2 49.4 1.0 C A:ASP9 4.3 41.2 1.0 CB A:ASP104 4.4 43.2 1.0 N A:ASP11 4.4 54.4 1.0 CB A:ASP9 4.6 50.5 1.0 CA A:ASP11 4.6 48.9 1.0 OE1 A:GLU105 4.6 66.0 1.0 CE A:LYS158 4.6 59.7 1.0 N A:CYS12 4.6 45.2 1.0 O1B A:1FZ402 4.7 40.8 1.0 CB A:MET10 4.7 39.4 1.0 CB A:PHE13 4.7 39.6 1.0 CA A:ASP9 4.7 46.9 1.0 N A:PHE13 4.8 49.5 1.0 C A:ASP11 4.8 48.3 1.0 O2A A:1FZ402 4.8 40.9 1.0 O A:ASP9 4.8 51.0 1.0 O2G A:1FZ402 4.9 40.3 1.0

Magnesium binding site 2 out of 2 in the S-Sad Structure of Dinb-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S-Sad Structure of Dinb-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:30.5 occ:1.00 O1A B:1FZ401 2.0 52.9 1.0 O1G B:1FZ401 2.3 51.9 1.0 OD1 B:ASP9 2.3 68.1 1.0 O2B B:1FZ401 2.3 51.5 1.0 O B:MET10 2.3 57.5 1.0 OD2 B:ASP104 2.4 72.7 1.0 PB B:1FZ401 3.3 50.7 1.0 PA B:1FZ401 3.3 51.7 1.0 CG B:ASP9 3.4 74.0 1.0 PG B:1FZ401 3.4 51.8 1.0 C B:MET10 3.5 62.2 1.0 CG B:ASP104 3.6 76.8 1.0 N3A B:1FZ401 3.6 50.7 1.0 O3B B:1FZ401 3.8 51.3 1.0 O3G B:1FZ401 3.9 52.3 1.0 N B:MET10 4.0 65.5 1.0 C5' B:1FZ401 4.0 51.0 1.0 OD2 B:ASP9 4.1 81.1 1.0 NZ B:LYS158 4.1 66.0 1.0 O5' B:1FZ401 4.2 51.1 1.0 CA B:MET10 4.3 62.7 1.0 OD1 B:ASP104 4.3 88.5 1.0 C B:ASP9 4.4 65.4 1.0 OE1 B:GLU105 4.4 85.7 1.0 O2A B:1FZ401 4.5 51.5 1.0 N B:ASP11 4.5 71.0 1.0 CB B:ASP9 4.6 71.2 1.0 CB B:ASP104 4.6 76.3 1.0 O1B B:1FZ401 4.7 50.3 1.0 CB B:MET10 4.7 65.5 1.0 N B:CYS12 4.7 61.4 1.0 N B:PHE13 4.7 62.9 1.0 CB B:PHE13 4.7 62.3 1.0 CA B:ASP11 4.7 66.3 1.0 CA B:ASP9 4.8 67.7 1.0 O2G B:1FZ401 4.8 52.1 1.0 O B:ASP9 4.8 65.2 1.0 C B:ASP11 4.9 67.5 1.0

T.Weinert, V.Olieric, S.Waltersperger, E.Panepucci, L.Chen, H.Zhang, D.Zhou, J.Rose, A.Ebihara, S.Kuramitsu, D.Li, N.Howe, G.Schnapp, A.Pautsch, K.Bargsten, A.E.Prota, P.Surana, J.Kottur, D.T.Nair, F.Basilico, V.Cecatiello, S.Pasqualato, A.Boland, O.Weichenrieder, B.Wang, M.O.Steinmetz, M.Caffrey, M.Wang. Fast Native-Sad Phasing For Routine Macromolecular Structure Determination Nat.Methods 2014.
ISSN: ESSN 1548-7105
PubMed: 25506719
DOI: 10.1038/NMETH.3211