Barium in PDB 6kaj: Crystal Structure of Fkrp in Complex with Ba Ion

The structure of Crystal Structure of Fkrp in Complex with Ba Ion, PDB code: 6kaj was solved by N.Kuwabara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.16 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.369, 118.820, 253.080, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.4

The structure of Crystal Structure of Fkrp in Complex with Ba Ion also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Barium atom in the Crystal Structure of Fkrp in Complex with Ba Ion (pdb code 6kaj). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 4 binding sites of Barium where determined in the Crystal Structure of Fkrp in Complex with Ba Ion, PDB code: 6kaj:
Jump to Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba506 b:0.4 occ:1.00 O2A A:CDP504 2.6 59.4 1.0 OD1 A:ASP362 2.6 47.8 1.0 OD2 A:ASP364 2.8 62.9 1.0 O3B A:CDP504 3.0 60.5 1.0 OD2 A:ASP360 3.2 51.3 1.0 OD1 A:ASP360 3.3 49.3 1.0 PA A:CDP504 3.6 59.8 1.0 CG A:ASP360 3.6 49.1 1.0 O A:ASP362 3.7 44.8 1.0 O5' A:CDP504 3.8 63.9 1.0 CG A:ASP362 3.8 50.8 1.0 O3A A:CDP504 4.0 64.5 1.0 CG A:ASP364 4.0 56.7 1.0 PB A:CDP504 4.1 66.8 1.0 CA A:GLY345 4.1 47.0 1.0 N A:GLY345 4.2 50.5 1.0 C A:ASP362 4.2 47.2 1.0 OD2 A:ASP362 4.5 55.2 1.0 N A:ASP362 4.6 46.9 1.0 C4' A:CDP504 4.7 57.7 1.0 C5' A:CDP504 4.7 58.3 1.0 C A:GLY345 4.7 43.3 1.0 N A:SER346 4.7 41.1 1.0 O A:HOH631 4.8 38.8 1.0 O1B A:CDP504 4.8 68.0 1.0 CA A:ASP362 4.8 46.3 1.0 OD1 A:ASP364 4.8 56.6 1.0 N A:VAL363 4.8 48.2 1.0 CB A:ASP364 4.9 50.4 1.0 OG A:SER346 4.9 43.5 1.0 CB A:ASP362 4.9 48.3 1.0 O1A A:CDP504 4.9 68.4 1.0 N A:ASP364 4.9 47.3 1.0

Barium binding site 2 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba506 b:0.3 occ:1.00 OD1 B:ASP362 2.6 37.0 1.0 O2A B:CDP504 2.6 39.3 1.0 OD1 B:ASP360 2.8 47.7 1.0 OD2 B:ASP360 2.8 45.4 1.0 OD2 B:ASP364 3.1 51.3 1.0 CG B:ASP360 3.1 44.8 1.0 O1B B:CDP504 3.3 41.2 1.0 O B:ASP362 3.5 37.9 1.0 PA B:CDP504 3.7 42.9 1.0 CG B:ASP362 3.8 37.8 1.0 O5' B:CDP504 4.0 45.5 1.0 C B:ASP362 4.1 39.4 1.0 CA B:GLY345 4.3 31.1 1.0 N B:ASP362 4.3 39.9 1.0 CG B:ASP364 4.3 49.5 1.0 O3A B:CDP504 4.3 47.9 1.0 PB B:CDP504 4.4 53.1 1.0 N B:GLY345 4.4 36.5 1.0 OD2 B:ASP362 4.5 43.1 1.0 CA B:ASP362 4.5 38.3 1.0 C4' B:CDP504 4.6 39.5 1.0 CB B:ASP360 4.6 42.0 1.0 C5' B:CDP504 4.7 40.9 1.0 CB B:ASP362 4.7 34.4 1.0 C B:GLY345 4.8 30.2 1.0 N B:VAL363 4.8 41.1 1.0 O B:HOH657 4.8 36.3 1.0 N B:SER346 4.8 33.1 1.0 O B:HOH624 4.9 28.9 1.0 OD1 B:ASP364 4.9 53.1 1.0 N B:TYR361 5.0 34.7 1.0 O3' B:CDP504 5.0 36.2 1.0 O1A B:CDP504 5.0 42.4 1.0

Barium binding site 3 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ba506 b:0.5 occ:1.00 OD2 C:ASP364 2.7 55.4 1.0 O2A C:CDP504 2.7 65.0 1.0 OD1 C:ASP362 2.7 54.2 1.0 OD2 C:ASP360 2.8 56.5 1.0 O C:HOH602 2.8 65.7 1.0 O3B C:CDP504 3.2 66.1 1.0 O C:ASP362 3.3 45.4 1.0 CG C:ASP360 3.4 50.9 1.0 OD1 C:ASP360 3.5 53.3 1.0 PA C:CDP504 3.9 61.4 1.0 CG C:ASP364 3.9 53.5 1.0 CA C:GLY345 3.9 47.6 1.0 O5' C:CDP504 4.0 61.7 1.0 C C:ASP362 4.0 46.7 1.0 CG C:ASP362 4.0 53.8 1.0 N C:GLY345 4.0 51.3 1.0 O C:HOH647 4.4 36.6 1.0 N C:SER346 4.4 46.5 1.0 C C:GLY345 4.4 45.5 1.0 PB C:CDP504 4.5 66.0 1.0 OG C:SER346 4.5 48.4 1.0 N C:VAL363 4.6 48.5 1.0 O3A C:CDP504 4.6 64.1 1.0 N C:ASP362 4.6 40.5 1.0 N C:ASP364 4.6 47.0 1.0 CA C:VAL363 4.7 47.1 1.0 O C:HOH657 4.7 36.2 1.0 OD2 C:ASP362 4.7 58.5 1.0 CA C:ASP362 4.7 43.8 1.0 OD1 C:ASP364 4.7 54.7 1.0 CB C:ASP364 4.8 51.9 1.0 CB C:ASP360 4.8 42.3 1.0 C5' C:CDP504 4.9 54.0 1.0 C4' C:CDP504 4.9 53.7 1.0 C C:VAL363 4.9 47.0 1.0 CB C:ASP362 5.0 47.8 1.0

Barium binding site 4 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Ba506 b:0.8 occ:1.00 O2A D:CDP504 2.6 43.7 1.0 OD1 D:ASP362 2.6 0.0 1.0 OD1 D:ASP360 2.7 57.9 1.0 O1B D:CDP504 2.8 47.1 1.0 OD2 D:ASP360 2.9 47.5 1.0 CG D:ASP360 3.1 51.1 1.0 OD2 D:ASP364 3.4 51.5 1.0 CG D:ASP362 3.4 0.7 1.0 PA D:CDP504 3.5 45.5 1.0 O5' D:CDP504 3.6 47.7 1.0 OD2 D:ASP362 3.7 0.2 1.0 PB D:CDP504 3.8 50.0 1.0 O3A D:CDP504 3.9 51.0 1.0 O D:ASP362 4.3 52.5 1.0 O3B D:CDP504 4.4 57.1 1.0 C4' D:CDP504 4.4 42.9 1.0 N D:ASP362 4.5 58.7 1.0 C5' D:CDP504 4.5 43.7 1.0 CB D:ASP362 4.5 0.8 1.0 CG D:ASP364 4.6 51.1 1.0 CA D:GLY345 4.6 39.4 1.0 CB D:ASP360 4.6 43.7 1.0 C D:ASP362 4.6 63.2 1.0 N D:GLY345 4.7 41.7 1.0 CA D:ASP362 4.8 75.0 1.0 O3' D:CDP504 4.8 41.5 1.0 O1A D:CDP504 4.8 49.3 1.0 C3' D:CDP504 4.9 43.9 1.0 N D:TYR361 4.9 38.8 1.0

N.Kuwabara, R.Imae, H.Manya, T.Tanaka, M.Mizuno, H.Tsumoto, M.Kanagawa, K.Kobayashi, T.Toda, T.Senda, T.Endo, R.Kato. Crystal Structures of Fukutin-Related Protein (Fkrp), A Ribitol-Phosphate Transferase Related to Muscular Dystrophy. Nat Commun V. 11 303 2020.
ISSN: ESSN 2041-1723
PubMed: 31949166
DOI: 10.1038/S41467-019-14220-Z