Magnesium in PDB 4nmn: Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution

The structure of Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution, PDB code: 4nmn was solved by A.Y.Lyubimov, M.S.Strycharska, J.P.Erzberger, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.19 / 3.30
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	195.707, 195.707, 195.707, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 27.5

The structure of Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution also contains other interesting chemical elements:

Strontium

(Sr)

1 atom

The binding sites of Magnesium atom in the Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution (pdb code 4nmn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution, PDB code: 4nmn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:63.0 occ:1.00 O1B A:ADP1001 1.9 79.7 1.0 OE1 A:GLU237 2.0 73.8 1.0 OG1 A:THR213 2.1 59.0 1.0 OE2 A:GLU237 2.4 74.2 1.0 CD A:GLU237 2.5 73.5 1.0 CB A:THR213 3.3 58.8 1.0 PB A:ADP1001 3.4 78.6 1.0 CG A:GLU237 3.9 72.3 1.0 O2B A:ADP1001 4.0 78.6 1.0 O3A A:ADP1001 4.1 68.5 1.0 OD1 A:ASP316 4.1 69.7 1.0 CG2 A:THR213 4.1 56.9 1.0 O A:HOH1102 4.3 59.3 1.0 O3B A:ADP1001 4.4 77.8 1.0 CA A:THR213 4.5 60.4 1.0 NE2 A:GLN357 4.5 81.6 1.0 OD2 A:ASP316 4.5 68.4 1.0 CB A:GLU237 4.6 70.7 1.0 N A:THR213 4.6 60.4 1.0 O2A A:ADP1001 4.6 81.0 1.0 PA A:ADP1001 4.6 79.5 1.0 CG A:ASP316 4.7 67.6 1.0 SD A:MET238 4.7 89.9 1.0 O1A A:ADP1001 4.8 78.7 1.0 CD2 A:TYR317 4.8 59.8 1.0

Magnesium binding site 2 out of 2 in the Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aquifex Aeolicus Replicative Helicase (Dnab) Complexed with Adp, at 3.3 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:52.3 occ:1.00 OG1 B:THR213 2.1 64.8 1.0 O3B B:ADP1001 2.6 76.8 1.0 O1B B:ADP1001 3.0 76.5 1.0 PB B:ADP1001 3.3 76.2 1.0 CB B:THR213 3.4 64.2 1.0 OD2 B:ASP316 3.7 64.6 1.0 CG2 B:THR213 4.0 62.8 1.0 OE1 B:GLU237 4.2 71.5 1.0 O2A B:ADP1001 4.3 81.0 1.0 OD1 B:ASP316 4.4 64.5 1.0 O2B B:ADP1001 4.4 75.8 1.0 CG B:ASP316 4.4 64.2 1.0 CA B:THR213 4.5 65.0 1.0 O3A B:ADP1001 4.5 80.1 1.0 N B:THR213 4.6 65.9 1.0 NE2 B:GLN357 4.6 88.9 1.0 CD B:GLU237 4.7 70.6 1.0 PA B:ADP1001 4.8 80.2 1.0 CG B:GLU237 4.9 69.0 1.0

M.S.Strycharska, E.Arias-Palomo, A.Y.Lyubimov, J.P.Erzberger, V.L.O'shea, C.J.Bustamante, J.M.Berger. Nucleotide and Partner-Protein Control of Bacterial Replicative Helicase Structure and Function. Mol.Cell V. 52 844 2013.
ISSN: ISSN 1097-2765
PubMed: 24373746
DOI: 10.1016/J.MOLCEL.2013.11.016