Zinc in PDB 6kal: Crystal Structure of Fkrp in Complex with Mg Ion and Cmp

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

Resolution Low / High (Å)	48.99 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.583, 118.674, 252.695, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.1

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

Magnesium

(Mg)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp (pdb code 6kal). 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 Mg Ion and Cmp, PDB code: 6kal:
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 Mg Ion and Cmp


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 Mg Ion and Cmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:49.8 occ:1.00 SG A:CYS317 2.3 44.1 1.0 SG A:CYS318 2.3 48.4 1.0 SG A:CYS296 2.3 53.8 1.0 SG A:CYS289 2.3 54.1 1.0 N A:CYS318 3.0 48.2 1.0 CB A:CYS296 3.3 50.1 1.0 CB A:CYS289 3.4 51.1 1.0 CB A:CYS317 3.4 46.1 1.0 CB A:CYS318 3.4 47.1 1.0 CA A:CYS318 3.5 48.1 1.0 C A:CYS317 3.7 48.9 1.0 N A:CYS296 3.8 54.8 1.0 N A:CYS289 3.8 51.2 1.0 CB A:PRO315 3.9 51.1 1.0 CA A:CYS317 4.0 48.0 1.0 CA A:CYS296 4.1 50.6 1.0 CA A:CYS289 4.2 51.5 1.0 O A:CYS317 4.4 51.0 1.0 N A:CYS317 4.5 46.6 1.0 CG A:PRO315 4.5 51.0 1.0 O A:PRO315 4.9 50.0 1.0 C A:ARG295 4.9 56.8 1.0 C A:CYS289 4.9 53.5 1.0 C A:GLY288 4.9 49.8 1.0 O A:CYS289 5.0 55.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 Mg Ion and Cmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:49.0 occ:1.00 SG B:CYS317 2.3 44.8 1.0 SG B:CYS318 2.3 53.5 1.0 SG B:CYS289 2.3 53.7 1.0 SG B:CYS296 2.4 53.7 1.0 N B:CYS318 3.0 48.4 1.0 CB B:CYS289 3.4 59.8 1.0 CB B:CYS296 3.4 50.0 1.0 CB B:CYS317 3.5 45.4 1.0 CB B:CYS318 3.5 49.8 1.0 CA B:CYS318 3.5 48.3 1.0 N B:CYS289 3.6 57.6 1.0 C B:CYS317 3.7 47.7 1.0 N B:CYS296 3.8 53.6 1.0 CB B:PRO315 4.0 46.4 1.0 CA B:CYS289 4.0 60.5 1.0 CA B:CYS317 4.1 46.3 1.0 CA B:CYS296 4.2 49.5 1.0 O B:CYS317 4.4 49.6 1.0 N B:CYS317 4.5 45.0 1.0 CG B:PRO315 4.6 45.8 1.0 C B:GLY288 4.7 55.7 1.0 C B:CYS289 4.8 59.8 1.0 CA B:GLY288 4.8 55.2 1.0 C B:ARG295 4.8 55.5 1.0 O B:CYS289 4.9 60.4 1.0 O B:PRO315 4.9 44.3 1.0 CA B:ARG295 5.0 49.0 1.0 CD1 B:LEU413 5.0 52.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 Mg Ion and Cmp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:57.3 occ:1.00 SG C:CYS317 2.3 51.7 1.0 SG C:CYS289 2.3 56.2 1.0 SG C:CYS318 2.3 47.1 1.0 SG C:CYS296 2.3 54.5 1.0 N C:CYS318 3.1 50.1 1.0 CB C:CYS296 3.4 53.6 1.0 CB C:CYS289 3.4 54.9 1.0 CB C:CYS317 3.4 53.1 1.0 CB C:CYS318 3.5 49.3 1.0 CA C:CYS318 3.5 51.5 1.0 C C:CYS317 3.6 48.4 1.0 N C:CYS289 3.6 49.8 1.0 N C:CYS296 3.8 54.6 1.0 CB C:PRO315 3.9 51.9 1.0 CA C:CYS317 4.0 50.1 1.0 CA C:CYS289 4.1 51.5 1.0 CA C:CYS296 4.2 53.2 1.0 O C:CYS317 4.2 47.3 1.0 N C:CYS317 4.5 48.1 1.0 CG C:PRO315 4.6 51.0 1.0 C C:GLY288 4.7 49.5 1.0 C C:CYS289 4.8 53.2 1.0 C C:ARG295 4.9 54.4 1.0 NE C:ARG275 4.9 55.0 1.0 O C:CYS289 4.9 53.8 1.0 O C:PRO315 4.9 49.0 1.0 CA C:GLY288 4.9 48.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Fkrp in Complex with Mg Ion and Cmp


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 Mg Ion and Cmp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:49.6 occ:1.00 SG D:CYS289 2.3 54.0 1.0 SG D:CYS317 2.3 44.0 1.0 SG D:CYS318 2.3 47.2 1.0 SG D:CYS296 2.4 49.8 1.0 N D:CYS318 3.1 41.7 1.0 CB D:CYS289 3.3 58.2 1.0 CB D:CYS296 3.4 48.9 1.0 CB D:CYS318 3.5 43.8 1.0 CA D:CYS318 3.5 43.2 1.0 CB D:CYS317 3.5 43.1 1.0 C D:CYS317 3.5 41.3 1.0 N D:CYS289 3.7 54.9 1.0 N D:CYS296 3.8 57.9 1.0 CA D:CYS289 4.0 57.9 1.0 CA D:CYS317 4.0 40.9 1.0 O D:CYS317 4.2 43.4 1.0 CA D:CYS296 4.2 52.6 1.0 CB D:PRO315 4.2 39.6 1.0 N D:CYS317 4.5 42.3 1.0 C D:ARG295 4.7 59.2 1.0 O D:CYS289 4.8 57.7 1.0 C D:CYS289 4.8 55.5 1.0 C D:GLY288 4.8 50.2 1.0 CA D:ARG295 4.8 59.3 1.0 O D:PRO315 4.8 43.6 1.0 CG D:PRO315 4.9 38.4 1.0 C D:CYS318 5.0 46.9 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