Magnesium in PDB 3r8f: Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna

The structure of Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna, PDB code: 3r8f was solved by K.E.Duderstadt, K.Chuang, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.49 / 3.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.797, 114.219, 201.266, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 26.8

The binding sites of Magnesium atom in the Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna (pdb code 3r8f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna, PDB code: 3r8f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:65.4 occ:1.00 O3G A:ACP700 2.1 48.8 1.0 OG1 A:THR126 2.5 57.7 1.0 O2B A:ACP700 2.7 33.8 1.0 OD2 A:ASP181 3.1 71.0 1.0 OD1 A:ASP180 3.1 57.5 1.0 OD2 A:ASP180 3.3 55.3 1.0 PG A:ACP700 3.4 61.2 1.0 CG A:ASP180 3.5 53.7 1.0 OD1 A:ASP181 3.5 70.3 1.0 CG A:ASP181 3.6 68.1 1.0 PB A:ACP700 3.9 45.8 1.0 CB A:THR126 3.9 55.3 1.0 O2G A:ACP700 4.0 59.9 1.0 C3B A:ACP700 4.1 62.2 1.0 N A:THR126 4.3 54.8 1.0 O1B A:ACP700 4.4 43.8 1.0 O A:HOH3 4.4 50.3 1.0 CA A:THR126 4.5 50.1 1.0 O1G A:ACP700 4.5 78.0 1.0 CE A:LYS125 4.5 63.6 1.0 CB A:LYS125 4.6 44.7 1.0 CG2 A:THR126 4.8 52.1 1.0 CB A:ASP180 4.8 49.0 1.0 N A:ASP181 4.9 47.7 1.0 CB A:ASP181 5.0 64.0 1.0

Magnesium binding site 2 out of 4 in the Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:48.6 occ:1.00 O1G B:ACP700 2.3 62.2 1.0 OG1 B:THR126 2.5 53.1 1.0 O1B B:ACP700 2.5 43.9 1.0 OD2 B:ASP181 3.1 61.5 1.0 OD1 B:ASP180 3.1 61.7 1.0 OD2 B:ASP180 3.3 57.5 1.0 PG B:ACP700 3.4 71.5 1.0 O3G B:ACP700 3.4 69.6 1.0 CG B:ASP180 3.5 58.0 1.0 OD1 B:ASP181 3.5 62.7 1.0 CG B:ASP181 3.6 61.0 1.0 PB B:ACP700 3.8 53.3 1.0 CB B:THR126 3.9 49.0 1.0 N B:THR126 4.3 48.3 1.0 C3B B:ACP700 4.3 69.1 1.0 O2B B:ACP700 4.5 52.7 1.0 CA B:THR126 4.5 44.1 1.0 CE B:LYS125 4.5 80.5 1.0 O2G B:ACP700 4.6 88.6 1.0 CB B:LYS125 4.6 60.2 1.0 CG2 B:THR126 4.8 46.8 1.0 CB B:ASP180 4.8 55.9 1.0 N B:ASP181 4.9 41.5 1.0 NH2 A:ARG230 5.0 90.0 1.0 CB B:ASP181 5.0 60.5 1.0 O3A B:ACP700 5.0 55.2 1.0

Magnesium binding site 3 out of 4 in the Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:67.3 occ:1.00 O3G C:ACP700 2.1 71.6 1.0 O1B C:ACP700 2.5 58.3 1.0 OG1 C:THR126 2.5 60.4 1.0 OD2 C:ASP181 3.1 69.3 1.0 OD1 C:ASP180 3.1 70.9 1.0 OD2 C:ASP180 3.3 66.0 1.0 PG C:ACP700 3.4 79.3 1.0 CG C:ASP180 3.5 67.3 1.0 OD1 C:ASP181 3.5 67.4 1.0 CG C:ASP181 3.6 67.9 1.0 PB C:ACP700 3.8 65.2 1.0 CB C:THR126 3.9 57.5 1.0 O2G C:ACP700 4.0 82.4 1.0 C3B C:ACP700 4.1 75.8 1.0 N C:THR126 4.3 59.3 1.0 CA C:THR126 4.5 55.7 1.0 O2B C:ACP700 4.5 67.4 1.0 O1G C:ACP700 4.5 90.2 1.0 CE C:LYS125 4.5 74.2 1.0 CB C:LYS125 4.6 56.9 1.0 CG2 C:THR126 4.8 56.2 1.0 CB C:ASP180 4.8 66.3 1.0 O3A C:ACP700 4.9 65.2 1.0 NH2 B:ARG230 4.9 0.8 1.0 N C:ASP181 4.9 56.2 1.0 CB C:ASP181 5.0 68.6 1.0

Magnesium binding site 4 out of 4 in the Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Replication Initiator Dnaa Bound to Amppcp and Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:50.6 occ:1.00 O3G D:ACP700 1.8 62.5 1.0 OG1 D:THR126 2.5 71.8 1.0 O1B D:ACP700 2.6 43.2 1.0 OD2 D:ASP181 3.1 69.5 1.0 OD1 D:ASP180 3.1 62.8 1.0 PG D:ACP700 3.2 74.7 1.0 OD2 D:ASP180 3.3 60.6 1.0 CG D:ASP180 3.5 58.7 1.0 OD1 D:ASP181 3.5 70.2 1.0 CG D:ASP181 3.6 67.2 1.0 PB D:ACP700 3.8 55.2 1.0 O2G D:ACP700 3.8 72.9 1.0 CB D:THR126 3.9 67.9 1.0 C3B D:ACP700 4.1 73.9 1.0 O1G D:ACP700 4.2 93.1 1.0 N D:THR126 4.3 64.6 1.0 CA D:THR126 4.5 60.3 1.0 CE D:LYS125 4.5 73.9 1.0 O2B D:ACP700 4.6 52.5 1.0 CB D:LYS125 4.6 50.5 1.0 CG2 D:THR126 4.8 65.2 1.0 CB D:ASP180 4.8 53.5 1.0 N D:ASP181 4.9 41.6 1.0 CB D:ASP181 5.0 62.8 1.0 O3A D:ACP700 5.0 59.5 1.0

K.E.Duderstadt, K.Chuang, J.M.Berger. Dna Stretching By Bacterial Initiators Promotes Replication Origin Opening. Nature V. 478 209 2011.
ISSN: ISSN 0028-0836
PubMed: 21964332
DOI: 10.1038/NATURE10455