Zinc in PDB 5t64: X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah

The structure of X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah, PDB code: 5t64 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.340, 110.894, 143.251, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22

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

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah (pdb code 5t64). 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 C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah, PDB code: 5t64:
Jump to Zinc binding site number: 1; 2;

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


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 C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.6 occ:1.00 SG A:CYS57 2.3 16.8 1.0 SG A:CYS54 2.3 18.5 1.0 SG A:CYS16 2.3 18.7 1.0 SG A:CYS13 2.4 15.0 1.0 CB A:CYS13 3.1 17.8 1.0 CB A:CYS54 3.1 15.9 1.0 CB A:CYS57 3.2 18.2 1.0 CB A:CYS16 3.4 19.0 1.0 N A:CYS57 3.8 19.7 1.0 N A:CYS16 3.9 19.0 1.0 CA A:CYS57 4.0 17.4 1.0 CA A:CYS16 4.2 21.9 1.0 CA A:CYS54 4.6 15.2 1.0 CA A:CYS13 4.6 20.0 1.0 CB A:VAL15 4.7 19.2 1.0 C A:CYS16 4.7 24.0 1.0 C A:CYS57 4.7 16.7 1.0 N A:GLY17 4.8 19.9 1.0 N A:ASP18 4.8 24.8 1.0 CB A:ALA56 4.8 23.5 1.0 N A:GLY58 4.9 15.5 1.0 CB A:MET59 4.9 12.9 1.0 C A:ALA56 4.9 22.7 1.0 C A:VAL15 4.9 20.1 1.0 CB A:ASP18 4.9 23.1 1.0

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


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 C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:17.1 occ:1.00 SG B:CYS57 2.2 17.8 1.0 SG B:CYS16 2.3 19.6 1.0 SG B:CYS54 2.3 17.5 1.0 SG B:CYS13 2.3 16.2 1.0 CB B:CYS13 3.1 17.1 1.0 CB B:CYS54 3.1 15.1 1.0 CB B:CYS57 3.3 19.6 1.0 CB B:CYS16 3.4 22.4 1.0 N B:CYS57 3.7 16.9 1.0 N B:CYS16 3.8 21.5 1.0 CA B:CYS57 4.0 17.8 1.0 CA B:CYS16 4.1 21.1 1.0 CA B:CYS13 4.5 18.2 1.0 CA B:CYS54 4.6 14.6 1.0 C B:CYS16 4.7 20.9 1.0 N B:GLY17 4.7 18.5 1.0 O B:HOH864 4.7 28.8 1.0 CB B:VAL15 4.7 18.9 1.0 C B:CYS57 4.7 16.4 1.0 N B:ASP18 4.8 20.5 1.0 CB B:ALA56 4.8 21.0 1.0 N B:GLY58 4.8 15.5 1.0 C B:VAL15 4.9 21.6 1.0 C B:ALA56 4.9 18.0 1.0 CB B:ASP18 4.9 21.4 1.0 CB B:MET59 4.9 11.0 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