Atomistry » Sodium » PDB 6lfw-6mc0 » 6lzk
Atomistry »
  Sodium »
    PDB 6lfw-6mc0 »
      6lzk »

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

Protein crystallography data

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

Sodium Binding Sites:

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 6lzk

Go back to Sodium Binding Sites List in 6lzk
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 6lzk

Go back to Sodium Binding Sites List in 6lzk
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

Reference:

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
Page generated: Tue Dec 15 12:34:26 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy