Zinc 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:

Barium

(Ba)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor, PDB code: 6kam:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:57.5 occ:1.00 SG A:CYS317 2.3 50.3 1.0 SG A:CYS318 2.3 53.7 1.0 SG A:CYS296 2.4 60.2 1.0 SG A:CYS289 2.4 56.8 1.0 N A:CYS318 3.2 56.5 1.0 CB A:CYS289 3.3 56.9 1.0 CB A:CYS317 3.4 51.6 1.0 CB A:CYS296 3.4 58.9 1.0 CB A:CYS318 3.4 54.2 1.0 CA A:CYS318 3.6 56.1 1.0 N A:CYS289 3.6 56.5 1.0 C A:CYS317 3.7 57.7 1.0 N A:CYS296 3.8 58.5 1.0 CB A:PRO315 4.0 53.3 1.0 CA A:CYS289 4.1 57.4 1.0 CA A:CYS317 4.1 56.2 1.0 CA A:CYS296 4.2 58.3 1.0 O A:CYS317 4.5 58.6 1.0 N A:CYS317 4.5 54.6 1.0 CG A:PRO315 4.7 53.5 1.0 C A:GLY288 4.7 57.5 1.0 C A:CYS289 4.9 58.9 1.0 C A:ARG295 4.9 59.9 1.0 O A:PRO315 4.9 55.7 1.0 CA A:GLY288 4.9 57.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:59.4 occ:1.00 SG B:CYS289 2.3 71.8 1.0 SG B:CYS318 2.3 57.0 1.0 SG B:CYS317 2.3 58.1 1.0 SG B:CYS296 2.4 64.1 1.0 N B:CYS318 3.1 51.4 1.0 CB B:CYS289 3.3 69.9 1.0 CB B:CYS296 3.4 62.1 1.0 CB B:CYS318 3.5 52.4 1.0 CB B:CYS317 3.5 59.2 1.0 N B:CYS289 3.5 69.8 1.0 CA B:CYS318 3.5 52.0 1.0 C B:CYS317 3.6 53.9 1.0 N B:CYS296 3.9 66.9 1.0 CA B:CYS289 4.0 69.9 1.0 CB B:PRO315 4.0 53.1 1.0 CA B:CYS317 4.1 57.1 1.0 CA B:CYS296 4.2 64.4 1.0 O B:CYS317 4.3 53.9 1.0 N B:CYS317 4.5 57.6 1.0 C B:GLY288 4.6 67.2 1.0 CG B:PRO315 4.7 51.7 1.0 O B:PRO315 4.8 53.0 1.0 CA B:GLY288 4.8 64.3 1.0 CD1 B:LEU413 4.9 53.4 1.0 C B:ARG295 4.9 70.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:60.8 occ:1.00 SG C:CYS317 2.3 55.6 1.0 SG C:CYS318 2.3 53.2 1.0 SG C:CYS296 2.4 71.1 1.0 SG C:CYS289 2.4 59.1 1.0 N C:CYS318 3.1 59.3 1.0 CB C:CYS296 3.4 65.7 1.0 CB C:CYS289 3.4 58.0 1.0 CB C:CYS318 3.5 53.5 1.0 CB C:CYS317 3.5 57.6 1.0 CA C:CYS318 3.5 58.0 1.0 C C:CYS317 3.6 59.6 1.0 N C:CYS289 3.7 59.8 1.0 N C:CYS296 3.9 64.8 1.0 CB C:PRO315 4.1 55.5 1.0 CA C:CYS317 4.1 58.6 1.0 CA C:CYS289 4.1 60.0 1.0 CA C:CYS296 4.2 65.5 1.0 O C:CYS317 4.3 61.1 1.0 N C:CYS317 4.6 55.8 1.0 CG C:PRO315 4.8 55.5 1.0 C C:GLY288 4.8 59.5 1.0 C C:CYS289 4.9 62.9 1.0 CD1 C:LEU413 4.9 53.6 1.0 C C:ARG295 4.9 65.4 1.0 NE C:ARG275 4.9 57.1 1.0 CA C:GLY288 5.0 58.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn501 b:56.8 occ:1.00 SG D:CYS289 2.3 56.6 1.0 SG D:CYS317 2.3 50.5 1.0 SG D:CYS318 2.3 52.0 1.0 SG D:CYS296 2.4 56.1 1.0 N D:CYS318 3.0 48.7 1.0 CB D:CYS289 3.4 56.9 1.0 CB D:CYS296 3.4 57.4 1.0 CB D:CYS318 3.4 49.1 1.0 CB D:CYS317 3.5 50.8 1.0 CA D:CYS318 3.5 49.1 1.0 C D:CYS317 3.6 51.1 1.0 N D:CYS289 3.7 54.1 1.0 N D:CYS296 3.9 64.3 1.0 CA D:CYS317 4.0 50.8 1.0 CB D:PRO315 4.1 47.9 1.0 CA D:CYS289 4.1 58.1 1.0 CA D:CYS296 4.2 62.2 1.0 O D:CYS317 4.3 54.3 1.0 N D:CYS317 4.4 51.5 1.0 CG D:PRO315 4.7 47.2 1.0 C D:GLY288 4.9 51.6 1.0 O D:PRO315 4.9 50.2 1.0 C D:ARG295 4.9 66.8 1.0 C D:CYS289 4.9 60.3 1.0 CA D:GLY288 5.0 49.3 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