Barium in PDB 6kam: Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor

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

Resolution Low / High (Å)	45.69 / 2.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.571, 119.240, 254.646, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.9

The structure of Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor 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, Cdp-Ribtol, and Sugar Acceptor (pdb code 6kam). 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, Cdp-Ribtol, and Sugar Acceptor, PDB code: 6kam:
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, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba506 b:0.2 occ:1.00 O2A A:CDP504 2.6 91.4 1.0 OD1 A:ASP362 2.6 69.0 1.0 O3B A:CDP504 2.7 95.1 1.0 OD1 A:ASP360 2.9 69.7 1.0 PA A:CDP504 3.2 91.5 1.0 OD2 A:ASP364 3.3 76.7 1.0 OD2 A:ASP360 3.3 71.2 1.0 O5' A:CDP504 3.4 87.6 1.0 O3A A:CDP504 3.4 94.5 1.0 CG A:ASP360 3.5 68.0 1.0 PB A:CDP504 3.6 95.9 1.0 CG A:ASP362 3.8 66.0 1.0 O A:ASP362 4.1 60.5 1.0 C5' A:CDP504 4.3 84.4 1.0 OD2 A:ASP362 4.4 67.4 1.0 C4' A:CDP504 4.4 82.0 1.0 CG A:ASP364 4.5 74.5 1.0 O1B A:CDP504 4.5 96.9 1.0 N A:ASP362 4.6 63.5 1.0 C A:ASP362 4.6 59.4 1.0 CA A:GLY345 4.6 60.0 1.0 N A:GLY345 4.6 63.5 1.0 O1A A:CDP504 4.7 97.2 1.0 O3' A:CDP504 4.7 80.3 1.0 CZ A:TYR361 4.8 82.2 1.0 O2B A:CDP504 4.8 98.8 1.0 CB A:ASP362 4.8 63.1 1.0 CE2 A:TYR361 4.9 79.5 1.0 C3' A:CDP504 4.9 81.1 1.0 CA A:ASP362 4.9 61.4 1.0 CB A:ASP360 4.9 63.5 1.0

Barium binding site 2 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba505 b:0.8 occ:1.00 O2A B:CDP503 2.5 56.6 1.0 OD1 B:ASP362 2.5 53.1 1.0 OD2 B:ASP364 2.6 65.6 1.0 O1B B:CDP503 2.8 64.6 1.0 OD2 B:ASP360 3.3 65.8 1.0 OD1 B:ASP360 3.4 64.9 1.0 O B:ASP362 3.4 51.5 1.0 CG B:ASP360 3.7 63.5 1.0 CG B:ASP362 3.7 54.6 1.0 PA B:CDP503 3.8 59.3 1.0 CG B:ASP364 3.8 63.8 1.0 C B:ASP362 4.0 52.5 1.0 PB B:CDP503 4.0 68.1 1.0 O3A B:CDP503 4.2 64.0 1.0 N B:GLY345 4.2 46.0 1.0 O5' B:CDP503 4.3 59.4 1.0 CA B:GLY345 4.4 42.0 1.0 OD1 B:ASP364 4.4 66.5 1.0 OD2 B:ASP362 4.4 57.5 1.0 N B:ASP362 4.5 57.2 1.0 CA B:ASP362 4.6 55.9 1.0 N B:VAL363 4.7 52.2 1.0 CB B:ASP362 4.8 55.5 1.0 N B:SER346 4.8 44.1 1.0 CB B:ASP364 4.8 60.3 1.0 N B:ASP364 4.8 54.2 1.0 C B:GLY345 4.9 42.2 1.0 CA B:VAL363 4.9 52.4 1.0 OG B:SER346 4.9 53.1 1.0 C4' B:CDP503 4.9 55.7 1.0 O3B B:CDP503 4.9 66.7 1.0 O2B B:CDP503 5.0 77.2 1.0 O1A B:CDP503 5.0 59.7 1.0 C B:VAL363 5.0 54.1 1.0

Barium binding site 3 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ba506 b:0.7 occ:1.00 OD1 C:ASP362 2.6 73.8 1.0 OD2 C:ASP364 2.6 72.0 1.0 O3B C:CDP504 2.7 97.4 1.0 O2A C:CDP504 2.7 98.7 1.0 OD2 C:ASP360 3.2 61.5 1.0 PA C:CDP504 3.4 94.2 1.0 O5' C:CDP504 3.4 88.3 1.0 OD1 C:ASP360 3.5 58.7 1.0 O3A C:CDP504 3.7 98.3 1.0 PB C:CDP504 3.7 99.3 1.0 CG C:ASP360 3.8 58.7 1.0 O C:ASP362 3.8 62.0 1.0 CG C:ASP362 3.8 71.9 1.0 CG C:ASP364 3.9 71.1 1.0 N C:GLY345 4.3 65.2 1.0 C C:ASP362 4.3 61.9 1.0 OD2 C:ASP362 4.4 75.9 1.0 C5' C:CDP504 4.6 81.9 1.0 CA C:GLY345 4.6 63.5 1.0 O2B C:CDP504 4.7 100.0 1.0 OD1 C:ASP364 4.7 73.5 1.0 CB C:ASP364 4.7 69.6 1.0 N C:ASP362 4.8 61.3 1.0 C5 C:RB0505 4.8 99.4 1.0 O1A C:CDP504 4.8 95.6 1.0 O1B C:CDP504 4.8 99.8 1.0 C4' C:CDP504 4.9 78.0 1.0 CA C:ASP362 4.9 62.8 1.0 CB C:ASP362 5.0 67.2 1.0 N C:ASP364 5.0 66.2 1.0 N C:VAL363 5.0 61.4 1.0

Barium binding site 4 out of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor


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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ D:Ba506 b:0.5 occ:1.00 OD1 D:ASP362 2.6 82.2 1.0 OD2 D:ASP364 2.6 69.5 1.0 O1B D:CDP504 2.7 77.5 1.0 O2A D:CDP504 2.7 64.4 1.0 OD2 D:ASP360 3.0 67.0 1.0 OD1 D:ASP360 3.5 68.6 1.0 CG D:ASP360 3.6 66.4 1.0 O D:ASP362 3.6 66.7 1.0 CG D:ASP362 3.8 79.5 1.0 PA D:CDP504 3.8 68.2 1.0 CG D:ASP364 3.9 69.7 1.0 O5' D:CDP504 3.9 67.1 1.0 PB D:CDP504 4.0 77.4 1.0 N D:GLY345 4.1 57.1 1.0 CA D:GLY345 4.1 53.3 1.0 C D:ASP362 4.2 67.4 1.0 O3A D:CDP504 4.2 76.3 1.0 OD2 D:ASP362 4.4 83.2 1.0 N D:SER346 4.5 52.1 1.0 C D:GLY345 4.6 52.2 1.0 OD1 D:ASP364 4.7 72.8 1.0 O2B D:CDP504 4.7 82.3 1.0 N D:ASP362 4.7 68.7 1.0 O D:HOH644 4.7 53.3 1.0 CB D:ASP364 4.8 65.9 1.0 C5' D:CDP504 4.8 63.4 1.0 CA D:ASP362 4.8 70.2 1.0 N D:VAL363 4.8 64.7 1.0 C4' D:CDP504 4.8 60.4 1.0 CB D:ASP362 4.9 74.5 1.0 OG D:SER346 4.9 51.0 1.0 N D:ASP364 4.9 62.3 1.0 O D:HOH627 5.0 65.4 1.0 CA D:VAL363 5.0 60.9 1.0

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