Sodium in PDB 8k4r: Structure of Vinm-Vinl Complex

The structure of Structure of Vinm-Vinl Complex, PDB code: 8k4r was solved by A.Miyanaga, K.Nagata, J.Nakajima, T.Chisuga, F.Kudo, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.04 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.501, 72.987, 80.209, 94.18, 90.87, 103.34
R / Rfree (%)	20.7 / 25.1

The binding sites of Sodium atom in the Structure of Vinm-Vinl Complex (pdb code 8k4r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Vinm-Vinl Complex, PDB code: 8k4r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Vinm-Vinl Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vinm-Vinl Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:65.2 occ:1.00 O A:GLY340 2.3 58.5 1.0 O A:VAL338 2.4 56.4 1.0 O C:VAL448 2.5 66.2 1.0 O A:PRO337 2.8 50.9 1.0 C A:VAL338 3.3 53.6 1.0 O C:GLN443 3.4 95.4 1.0 C A:GLY340 3.5 55.8 1.0 CA A:VAL338 3.7 53.3 1.0 C C:VAL448 3.8 68.5 1.0 C A:PRO337 3.8 50.5 1.0 O C:GLY449 4.0 69.9 1.0 C A:VAL339 4.2 53.8 1.0 N A:GLY340 4.2 54.6 1.0 N A:VAL338 4.2 52.1 1.0 O C:CYS445 4.3 74.4 1.0 O A:VAL339 4.3 54.8 1.0 N A:VAL339 4.3 53.1 1.0 N A:ALA341 4.4 56.0 1.0 CA A:GLY340 4.5 55.1 1.0 CA A:ALA341 4.5 56.3 1.0 C C:GLN443 4.6 89.8 1.0 N C:VAL448 4.6 72.9 1.0 CA C:VAL448 4.6 71.3 1.0 N C:GLY449 4.7 66.3 1.0 CA A:VAL339 4.8 52.9 1.0 CA C:GLY449 4.8 68.2 1.0 C C:GLY449 4.8 70.7 1.0 CB C:VAL448 4.8 71.6 1.0

Sodium binding site 2 out of 2 in the Structure of Vinm-Vinl Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Vinm-Vinl Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na601 b:64.9 occ:1.00 O C:GLY340 2.1 63.3 1.0 O A:GLU521 2.4 66.4 1.0 O C:VAL338 2.9 64.3 1.0 O A:GLY524 3.0 59.0 1.0 O C:PRO337 3.0 57.1 1.0 C C:GLY340 3.3 60.5 1.0 C A:GLU521 3.4 67.5 1.0 CA A:GLU521 3.6 70.2 1.0 C C:VAL338 3.7 63.5 1.0 CB A:GLU521 3.8 72.1 1.0 CA C:ALA341 4.1 59.6 1.0 N C:ALA341 4.1 59.8 1.0 C C:PRO337 4.1 57.9 1.0 C A:GLY524 4.2 57.4 1.0 CA C:VAL338 4.2 62.4 1.0 N C:GLY340 4.4 60.0 1.0 C C:VAL339 4.4 62.2 1.0 O C:VAL339 4.4 63.6 1.0 CA C:GLY340 4.4 60.2 1.0 N C:VAL338 4.6 60.0 1.0 N A:LEU522 4.6 66.4 1.0 N C:VAL339 4.7 64.0 1.0 CA A:GLY524 4.8 57.0 1.0 N A:GLY524 4.9 55.8 1.0 CB C:ALA341 4.9 60.8 1.0 N A:GLU521 5.0 69.3 1.0

A.Miyanaga, K.Nagata, J.Nakajima, T.Chisuga, F.Kudo, T.Eguchi. Structural Basis of Amide-Forming Adenylation Enzyme Vinm in Vicenistatin Biosynthesis. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 37870408
DOI: 10.1021/ACSCHEMBIO.3C00517