Magnesium in PDB 2hcb: Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus

The structure of Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus, PDB code: 2hcb was solved by J.P.Erzberger, M.L.Mott, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.076, 117.714, 200.994, 90.00, 90.00, 90.00
R / Rfree (%)	26.6 / 29.8

The binding sites of Magnesium atom in the Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus (pdb code 2hcb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus, PDB code: 2hcb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:16.0 occ:1.00 OG1 A:THR126 1.8 40.3 1.0 O1G A:ACP700 2.2 36.8 1.0 O2B A:ACP700 2.7 34.5 1.0 OD2 A:ASP181 2.9 45.6 1.0 CB A:THR126 3.2 40.5 1.0 OD1 A:ASP181 3.6 46.9 1.0 PG A:ACP700 3.6 35.0 1.0 OD1 A:ASP180 3.6 32.1 1.0 CG A:ASP181 3.6 45.5 1.0 PB A:ACP700 3.9 36.4 1.0 CA A:THR126 4.0 39.4 1.0 OD2 A:ASP180 4.0 28.6 1.0 CG A:ASP180 4.0 31.1 1.0 N A:THR126 4.0 40.1 1.0 O2G A:ACP700 4.1 35.0 1.0 CG2 A:THR126 4.2 40.9 1.0 C3B A:ACP700 4.3 34.9 1.0 O1B A:ACP700 4.5 35.6 1.0 O3G A:ACP700 4.7 35.0 1.0 CE A:LYS125 4.7 53.0 1.0 NZ A:LYS125 4.8 53.9 1.0 O2A A:ACP700 4.8 31.9 1.0 OH A:TYR145 4.8 40.8 1.0

Magnesium binding site 2 out of 4 in the Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:17.3 occ:1.00 OG1 B:THR126 2.3 43.4 1.0 O3G B:ACP700 2.3 46.7 1.0 O1B B:ACP700 3.2 41.2 1.0 OD1 B:ASP181 3.5 52.8 1.0 PG B:ACP700 3.5 46.7 1.0 CB B:THR126 3.5 44.0 1.0 OD2 B:ASP181 3.6 52.0 1.0 CG2 B:THR126 3.9 43.4 1.0 CG B:ASP181 3.9 51.7 1.0 O1G B:ACP700 3.9 45.0 1.0 C3B B:ACP700 4.0 43.3 1.0 OD2 B:ASP180 4.0 43.9 1.0 NH2 A:ARG230 4.1 60.1 1.0 OD1 B:ASP180 4.2 43.6 1.0 PB B:ACP700 4.2 40.4 1.0 CG B:ASP180 4.3 44.9 1.0 O2A B:ACP700 4.4 44.5 1.0 NZ B:LYS125 4.5 59.1 1.0 CA B:THR126 4.7 47.2 1.0 NH2 B:ARG277 4.7 48.6 1.0 OH B:TYR145 4.8 52.7 1.0 O2G B:ACP700 4.8 46.4 1.0 N B:THR126 4.9 48.1 1.0

Magnesium binding site 3 out of 4 in the Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:64.3 occ:1.00 O3G C:ACP700 2.1 49.5 1.0 OG1 C:THR126 2.1 52.8 1.0 OD1 C:ASP181 2.9 69.5 1.0 O1B C:ACP700 3.1 44.7 1.0 OD2 C:ASP181 3.2 70.4 1.0 NZ C:LYS125 3.3 61.2 1.0 CG C:ASP181 3.4 70.2 1.0 CB C:THR126 3.4 53.4 1.0 PG C:ACP700 3.5 47.6 1.0 OD1 C:ASP180 3.7 57.0 1.0 OD2 C:ASP180 3.8 55.9 1.0 CG2 C:THR126 3.9 53.1 1.0 CG C:ASP180 4.0 56.6 1.0 C3B C:ACP700 4.1 45.8 1.0 NH2 B:ARG230 4.2 51.0 1.0 PB C:ACP700 4.2 44.2 1.0 CA C:THR126 4.3 52.0 1.0 O1G C:ACP700 4.4 46.6 1.0 O2G C:ACP700 4.5 46.0 1.0 N C:THR126 4.5 51.5 1.0 CE C:LYS125 4.7 62.3 1.0 O1A C:ACP700 4.7 44.8 1.0 CB C:ASP181 4.9 70.0 1.0

Magnesium binding site 4 out of 4 in the Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Amppcp-Bound Dnaa From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:15.0 occ:1.00 OG1 D:THR126 2.0 41.2 1.0 O3G D:ACP700 2.2 49.8 1.0 O1B D:ACP700 2.6 43.0 1.0 NZ D:LYS125 3.3 56.3 1.0 OD2 D:ASP180 3.3 45.7 1.0 PG D:ACP700 3.4 50.1 1.0 OD1 D:ASP181 3.4 61.0 1.0 CB D:THR126 3.4 41.5 1.0 OD2 D:ASP181 3.5 59.3 1.0 C3B D:ACP700 3.6 45.9 1.0 PB D:ACP700 3.6 43.3 1.0 OD1 D:ASP180 3.7 45.8 1.0 CG D:ASP181 3.7 59.4 1.0 CG D:ASP180 3.8 46.2 1.0 O2G D:ACP700 4.0 49.1 1.0 N D:THR126 4.1 38.6 1.0 CG2 D:THR126 4.2 41.7 1.0 CA D:THR126 4.2 38.4 1.0 O2B D:ACP700 4.5 42.2 1.0 CE D:LYS125 4.6 54.6 1.0 O1G D:ACP700 4.6 50.6 1.0 O1A D:ACP700 4.8 35.8 1.0 NH2 C:ARG230 4.9 47.6 1.0 O3A D:ACP700 4.9 40.8 1.0

J.P.Erzberger, M.L.Mott, J.M.Berger. Structural Basis For Atp-Dependent Dnaa Assembly and Replication-Origin Remodeling. Nat.Struct.Mol.Biol. V. 13 676 2006.
ISSN: ISSN 1545-9993
PubMed: 16829961
DOI: 10.1038/NSMB1115