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Sodium in PDB 6l18: Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp

Enzymatic activity of Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp

All present enzymatic activity of Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp:
2.1.2.8;

Protein crystallography data

The structure of Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp, PDB code: 6l18 was solved by S.H.Park, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.50 / 1.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 55.860, 74.970, 157.620, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.1

Other elements in 6l18:

The structure of Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp also contains other interesting chemical elements:

Iodine (I) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp (pdb code 6l18). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp, PDB code: 6l18:

Sodium binding site 1 out of 1 in 6l18

Go back to Sodium Binding Sites List in 6l18
Sodium binding site 1 out of 1 in the Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xfel Structure of T4DCH D179N Mutant Complex with Natively Expressed Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:50.4
occ:1.00
 O A:ILE74 2.3 52.0 1.0
O A:GLY76 2.3 53.8 1.0
O A:HOH450 2.4 44.9 0.7
O A:LYS72 2.5 47.0 1.0
O A:HOH446 2.6 54.6 1.0
OG1 A:THR78 2.7 53.9 1.0
C A:ILE74 3.5 46.9 1.0
C A:LYS72 3.5 54.2 1.0
C A:GLY76 3.6 62.7 1.0
N A:THR78 3.7 50.4 1.0
CB A:THR78 3.9 58.4 1.0
N A:ILE74 4.0 45.6 1.0
CA A:LYS72 4.1 45.1 1.0
CA A:ILE74 4.1 46.7 1.0
CA A:THR78 4.2 49.1 1.0
N A:GLY76 4.2 46.0 1.0
C A:GLU77 4.2 57.9 1.0
C A:PRO75 4.3 46.9 1.0
CB A:ILE74 4.3 50.0 1.0
O A:VAL71 4.3 47.0 1.0
C A:ASP73 4.4 54.2 1.0
CA A:GLU77 4.5 54.8 1.0
N A:GLU77 4.5 55.0 1.0
O A:PRO75 4.5 50.2 1.0
N A:ASP73 4.5 47.1 1.0
N A:PRO75 4.5 45.6 1.0
CA A:GLY76 4.5 50.1 1.0
CG A:LYS72 4.6 50.0 1.0
CA A:PRO75 4.7 48.6 1.0
CA A:ASP73 4.8 47.1 1.0
CB A:LYS72 4.9 46.6 1.0
CG2 A:ILE74 5.0 50.1 1.0

Reference:

S.H.Park, J.Park, S.J.Lee, W.S.Yang, S.Park, K.Kim, Z.Y.Park, H.K.Song. A Host Dtmp-Bound Structure of T4 Phage Dcmp Hydroxymethylase Mutant Using An X-Ray Free Electron Laser. Sci Rep V. 9 16316 2019.
ISSN: ESSN 2045-2322
PubMed: 31705139
DOI: 10.1038/S41598-019-52825-Y
Page generated: Tue Oct 8 11:35:18 2024

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