Manganese in PDB 6fke: Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Product Dna Hairpin

All present enzymatic activity of Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Product Dna Hairpin:
3.1.11.2;

The structure of Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Product Dna Hairpin, PDB code: 6fke 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)	40.08 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.929, 58.929, 292.591, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.4

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

Manganese binding site 1 out of 2 in the Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Product Dna Hairpin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Product Dna Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:68.7 occ:0.46 OE2 A:GLU34 2.9 41.9 1.0 O A:HOH464 3.3 56.6 1.0 OE1 A:GLU34 3.4 33.8 1.0 OD1 A:ASN9 3.5 45.3 1.0 CD A:GLU34 3.5 40.9 1.0 O B:HOH101 3.6 53.0 1.0 O4' B:DA15 3.7 61.0 1.0 CG A:ASN9 3.7 48.5 1.0 C4' B:DA15 3.7 61.0 1.0 C1' B:DA15 3.9 63.2 1.0 ND2 A:ASN9 4.0 49.9 1.0 O3' B:DA15 4.2 68.1 1.0 OD2 A:ASP246 4.2 47.6 1.0 O B:HOH109 4.2 61.7 1.0 NZ A:LYS36 4.3 45.0 1.0 C3' B:DA15 4.5 60.8 1.0 OD1 A:ASP246 4.5 40.1 1.0 CB A:ASN9 4.5 41.1 1.0 N3 B:DA15 4.6 62.9 1.0 C2' B:DA15 4.7 64.4 1.0 CG A:ASP246 4.8 45.5 1.0 CE A:LYS36 4.9 47.7 1.0 N9 B:DA15 4.9 63.7 1.0 C5' B:DA15 4.9 53.2 1.0 CG A:GLU34 4.9 29.4 1.0

Manganese binding site 2 out of 2 in the Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Product Dna Hairpin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of 3' Phosphatase Nexo (D146N) From Neisseria Bound to Product Dna Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:70.1 occ:0.52 O A:HOH451 3.5 45.2 1.0 OD1 A:ASP153 3.7 49.8 1.0 ND1 A:HIS163 3.8 46.5 1.0 OD2 A:ASP153 3.9 59.8 1.0 O A:PRO159 3.9 40.5 1.0 CG A:ASP153 4.2 47.0 1.0 O A:HOH468 4.2 40.0 1.0 CB A:PRO159 4.4 46.0 1.0 C A:PRO159 4.4 45.7 1.0 CG A:HIS163 4.7 38.4 1.0 CB A:HIS163 4.7 41.2 1.0 CE1 A:HIS163 4.7 45.0 1.0 CA A:HIS163 4.8 34.7 1.0 O A:HOH414 4.8 45.0 1.0 CA A:PRO159 4.8 44.6 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