Zinc in PDB 5t6b: X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form

The structure of X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form, PDB code: 5t6b 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 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.707, 82.455, 82.825, 96.05, 110.70, 112.09
R / Rfree (%)	17.6 / 23.4

The binding sites of Zinc atom in the X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form (pdb code 5t6b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form, PDB code: 5t6b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form


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-Methyltransfeerase, Converted to Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:25.1 occ:1.00 SG A:CYS54 2.2 24.0 1.0 SG A:CYS16 2.3 25.2 1.0 SG A:CYS57 2.3 24.0 1.0 SG A:CYS13 2.4 23.4 1.0 CB A:CYS54 3.1 23.1 1.0 CB A:CYS13 3.1 22.9 1.0 CB A:CYS57 3.3 24.3 1.0 CB A:CYS16 3.4 25.4 1.0 N A:CYS16 3.7 30.0 1.0 N A:CYS57 3.8 26.8 1.0 CA A:CYS16 4.1 27.5 1.0 CA A:CYS57 4.1 24.1 1.0 CA A:CYS54 4.5 22.4 1.0 CB A:VAL15 4.5 30.0 1.0 CA A:CYS13 4.6 24.2 1.0 C A:CYS16 4.7 27.9 1.0 N A:GLY17 4.7 27.2 1.0 C A:VAL15 4.8 29.4 1.0 CB A:ALA56 4.8 27.3 1.0 C A:CYS57 4.8 21.5 1.0 N A:ASP18 4.8 27.4 1.0 CB A:ASP18 5.0 27.8 1.0 N A:GLY58 5.0 20.1 1.0 C A:ALA56 5.0 27.8 1.0

Zinc binding site 2 out of 4 in the X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form


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-Methyltransfeerase, Converted to Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:22.3 occ:1.00 SG B:CYS57 2.2 19.5 1.0 SG B:CYS16 2.3 18.8 1.0 SG B:CYS54 2.3 19.7 1.0 SG B:CYS13 2.4 20.5 1.0 CB B:CYS54 3.1 21.0 1.0 CB B:CYS13 3.1 20.9 1.0 CB B:CYS16 3.3 20.1 1.0 CB B:CYS57 3.4 19.0 1.0 N B:CYS57 3.7 21.9 1.0 N B:CYS16 3.7 20.5 1.0 CA B:CYS57 4.1 20.4 1.0 CA B:CYS16 4.1 20.5 1.0 CA B:CYS54 4.6 20.9 1.0 CA B:CYS13 4.6 20.9 1.0 CB B:VAL15 4.7 21.4 1.0 CB B:ALA56 4.7 27.1 1.0 C B:CYS16 4.7 22.2 1.0 C B:VAL15 4.8 22.1 1.0 C B:CYS57 4.8 20.5 1.0 C B:ALA56 4.8 25.2 1.0 N B:GLY17 4.9 24.4 1.0 N B:GLY58 4.9 19.1 1.0 CB B:ASP18 4.9 32.1 1.0

Zinc binding site 3 out of 4 in the X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:21.4 occ:1.00 SG C:CYS57 2.3 20.9 1.0 SG C:CYS16 2.3 20.8 1.0 SG C:CYS54 2.4 19.4 1.0 SG C:CYS13 2.4 19.4 1.0 CB C:CYS13 3.1 24.0 1.0 CB C:CYS54 3.1 21.2 1.0 CB C:CYS57 3.3 22.1 1.0 CB C:CYS16 3.4 22.6 1.0 N C:CYS57 3.7 24.4 1.0 N C:CYS16 3.8 25.1 1.0 CA C:CYS57 4.0 23.0 1.0 CA C:CYS16 4.1 25.0 1.0 CA C:CYS54 4.6 20.5 1.0 CA C:CYS13 4.6 25.3 1.0 CB C:VAL15 4.7 23.3 1.0 C C:CYS16 4.7 26.4 1.0 C C:CYS57 4.7 21.4 1.0 N C:GLY17 4.8 27.0 1.0 N C:GLY58 4.8 21.6 1.0 N C:ASP18 4.8 25.8 1.0 CB C:MET59 4.9 15.1 1.0 C C:VAL15 4.9 25.8 1.0 C C:ALA56 4.9 26.7 1.0 CB C:ALA56 4.9 25.1 1.0 CB C:ASP18 5.0 27.2 1.0

Zinc binding site 4 out of 4 in the X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of the KIJD1 C3-Methyltransfeerase, Converted to Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:34.7 occ:1.00 SG D:CYS57 2.2 27.0 1.0 SG D:CYS13 2.3 29.0 1.0 SG D:CYS54 2.4 31.9 1.0 SG D:CYS16 2.5 38.5 1.0 CB D:CYS54 3.1 32.9 1.0 CB D:CYS13 3.1 30.8 1.0 CB D:CYS16 3.2 37.9 1.0 CB D:CYS57 3.5 28.1 1.0 N D:CYS16 3.8 37.5 1.0 N D:CYS57 3.9 31.7 1.0 CA D:CYS16 4.0 40.4 1.0 CA D:CYS57 4.2 28.2 1.0 CA D:CYS54 4.5 29.8 1.0 CA D:CYS13 4.6 28.6 1.0 C D:CYS16 4.6 42.5 1.0 CB D:VAL15 4.6 33.4 1.0 CB D:ALA56 4.6 37.1 1.0 N D:GLY17 4.7 39.9 1.0 C D:VAL15 4.8 36.7 1.0 C D:CYS57 4.9 27.0 1.0 CB D:MET59 4.9 18.8 1.0 C D:ALA56 5.0 35.5 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