Magnesium in PDB 6fk5: Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion

The structure of Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion, PDB code: 6fk5 was solved by J.Silhan, Q.Zhao, E.Boura, H.Thomson, A.Foster, C.M.Tang, P.S.Freemont, G.S.Baldwin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.43 / 2.02
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.940, 58.940, 292.260, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 25.8

The binding sites of Magnesium atom in the Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion (pdb code 6fk5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion, PDB code: 6fk5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:47.3 occ:0.48 O A:HOH502 2.4 51.1 1.0 OE2 A:GLU34 2.7 50.1 1.0 O B:HOH106 2.8 50.6 1.0 O5' B:DA18 3.2 53.5 0.8 OD1 A:ASP246 3.2 39.8 1.0 OD2 A:ASP246 3.2 45.4 1.0 CG A:ASN9 3.5 46.0 1.0 CG A:ASP246 3.6 44.0 1.0 O A:HOH482 3.7 53.3 1.0 CB A:ASN9 3.7 41.2 1.0 O3' B:DG17 3.7 56.3 1.0 CD A:GLU34 3.8 52.7 1.0 OD1 A:ASN9 3.8 45.7 1.0 ND2 A:ASN9 3.8 47.5 1.0 P B:DA18 4.0 55.0 0.8 OD1 A:ASN7 4.1 40.8 1.0 OE1 A:GLU34 4.1 51.8 1.0 OP2 B:DA18 4.2 50.9 0.8 CD2 A:HIS247 4.3 37.8 1.0 NE2 A:HIS247 4.4 37.9 1.0 CA A:ASN9 4.7 44.1 1.0 C4' B:DG17 4.8 48.6 1.0 C3' B:DG17 4.8 51.0 1.0 C1' B:DG17 5.0 50.8 1.0

Magnesium binding site 2 out of 2 in the Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Dna Substrate in Presence of Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:63.8 occ:1.00 O A:HOH509 2.0 61.8 1.0 OD1 A:ASP153 3.4 53.2 1.0 OD2 A:ASP153 3.4 58.1 1.0 O A:HOH470 3.5 49.8 1.0 CG A:ASP153 3.8 51.4 1.0 O A:HOH485 3.8 45.8 1.0 ND1 A:HIS163 3.9 51.7 1.0 O A:PRO159 4.3 43.3 1.0 CB A:PRO159 4.5 48.0 1.0 O A:HOH483 4.6 49.0 1.0 CE1 A:HIS163 4.7 48.5 1.0 NH1 A:ARG173 4.7 45.5 1.0 C A:PRO159 4.9 47.6 1.0 O A:HOH456 4.9 49.2 1.0 CG A:HIS163 4.9 44.9 1.0

J.Silhan, Q.Zhao, E.Boura, H.Thomson, A.Forster, C.M.Tang, P.S.Freemont, G.S.Baldwin. Structural Basis For Recognition and Repair of the 3'-Phosphate By Nexo, A Base Excision Dna Repair Nuclease From Neisseria Meningitidis. Nucleic Acids Res. V. 46 11980 2018.
ISSN: ESSN 1362-4962
PubMed: 30329088
DOI: 10.1093/NAR/GKY934