Sodium in PDB 6lzk: Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation

The structure of Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation, PDB code: 6lzk was solved by K.Fukui, K.Izuhara, T.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.36 / 3.16
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	128.900, 146.295, 175.585, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 27.2

The binding sites of Sodium atom in the Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation (pdb code 6lzk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation, PDB code: 6lzk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:69.8 occ:1.00 OE2 A:GLU115 3.3 67.3 1.0 OE1 A:GLU117 3.6 1.0 1.0 CB A:GLU117 3.7 69.4 1.0 O A:GLY125 4.1 61.6 1.0 N A:GLU117 4.2 58.2 1.0 CD A:GLU115 4.3 70.5 1.0 C A:GLY125 4.3 45.9 1.0 CG A:ARG127 4.4 49.9 1.0 NH1 A:ARG127 4.5 0.4 1.0 CD A:GLU117 4.5 0.3 1.0 N A:THR126 4.5 53.3 1.0 CG A:GLU115 4.5 57.4 1.0 CA A:THR126 4.5 53.7 1.0 CA A:GLU117 4.6 54.8 1.0 C A:THR126 4.6 53.5 1.0 CG A:GLU117 4.7 80.0 1.0 N A:ARG127 4.7 48.5 1.0 CD A:ARG127 4.7 77.5 1.0 O A:GLU115 4.8 48.8 1.0 C A:ILE116 4.9 39.6 1.0 CB A:ARG127 5.0 44.0 1.0 O A:THR126 5.0 62.0 1.0

Sodium binding site 2 out of 2 in the Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Aquifex Aeolicus Mutl Atpase Domain with K252N Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:56.2 occ:1.00 CB A:ASN26 4.0 47.5 1.0 OD2 A:ASP51 4.2 85.2 1.0 O A:ASN26 4.2 46.1 1.0 OG1 A:THR135 4.2 49.9 1.0 C A:ASN26 4.3 54.8 1.0 CB A:ALA30 4.4 57.9 1.0 CD1 A:ILE56 4.4 37.7 1.0 CB A:THR135 4.5 44.1 1.0 CG2 A:THR135 4.5 44.5 1.0 N A:SER27 4.5 61.4 1.0 CG1 A:ILE56 4.6 37.8 1.0 CA A:ASN26 4.7 51.5 1.0 CG A:ASN26 4.8 61.1 1.0 ND2 A:ASN26 4.8 44.5 1.0 CA A:SER27 4.9 42.9 1.0

K.Izuhara, K.Fukui, T.Murakawa, S.Baba, T.Kumasaka, K.Uchiyama, T.Yano. A Lynch Syndrome-Associated Mutation at A Bergerat Atp-Binding Fold Destabilizes the Structure of the Dna Mismatch Repair Endonuclease Mutl. J.Biol.Chem. V. 295 11643 2020.
ISSN: ESSN 1083-351X
PubMed: 32571878
DOI: 10.1074/JBC.RA120.013576