Zinc in PDB 5t67: X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product

The structure of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product, PDB code: 5t67 was solved by H.M.Holden, J.B.Thoden, G.T.Dow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.088, 108.893, 142.783, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.9

The structure of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product (pdb code 5t67). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product, PDB code: 5t67:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.5 occ:1.00 SG A:CYS57 2.2 13.8 1.0 SG A:CYS54 2.3 18.1 1.0 SG A:CYS16 2.3 18.2 1.0 SG A:CYS13 2.5 15.4 1.0 CB A:CYS54 3.1 14.8 1.0 CB A:CYS13 3.1 18.3 1.0 CB A:CYS57 3.2 15.1 1.0 CB A:CYS16 3.4 17.0 1.0 N A:CYS16 3.8 16.6 1.0 N A:CYS57 3.8 18.5 1.0 CA A:CYS57 4.0 15.7 1.0 CA A:CYS16 4.1 19.7 1.0 CA A:CYS54 4.6 15.6 1.0 CA A:CYS13 4.6 19.6 1.0 O A:HOH923 4.7 28.6 1.0 C A:CYS57 4.7 13.7 1.0 N A:GLY58 4.7 13.3 1.0 CB A:VAL15 4.7 15.8 1.0 C A:CYS16 4.7 22.1 1.0 CB A:ALA56 4.8 23.4 1.0 N A:GLY17 4.8 22.3 1.0 N A:ASP18 4.8 22.9 1.0 C A:VAL15 4.8 20.9 1.0 C A:ALA56 4.9 19.5 1.0 NE2 A:GLN61 4.9 16.1 1.0 CB A:MET59 5.0 11.4 1.0 CB A:ASP18 5.0 25.0 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:22.1 occ:1.00 SG B:CYS57 2.2 19.5 1.0 SG B:CYS16 2.2 23.5 1.0 SG B:CYS54 2.4 19.5 1.0 SG B:CYS13 2.4 19.2 1.0 CB B:CYS54 3.1 22.5 1.0 CB B:CYS13 3.2 19.3 1.0 CB B:CYS57 3.3 22.4 1.0 CB B:CYS16 3.4 24.0 1.0 N B:CYS57 3.7 22.5 1.0 N B:CYS16 3.8 22.0 1.0 CA B:CYS57 4.0 22.8 1.0 CA B:CYS16 4.1 22.7 1.0 CA B:CYS54 4.5 22.0 1.0 CA B:CYS13 4.6 22.0 1.0 CB B:VAL15 4.6 23.9 1.0 N B:GLY17 4.7 26.0 1.0 C B:CYS16 4.7 24.2 1.0 C B:CYS57 4.7 20.4 1.0 CB B:ALA56 4.8 27.6 1.0 N B:ASP18 4.8 22.5 1.0 C B:VAL15 4.8 23.1 1.0 C B:ALA56 4.8 28.1 1.0 CB B:ASP18 4.8 24.7 1.0 N B:GLY58 4.9 20.5 1.0 CB B:MET59 5.0 16.6 1.0

G.T.Dow, J.B.Thoden, H.M.Holden. Structural Studies on KIJD1, A Sugar C-3'-Methyltransferase. Protein Sci. V. 25 2282 2016.
ISSN: ESSN 1469-896X
PubMed: 27595766
DOI: 10.1002/PRO.3034