Zinc in PDB 3ndj: X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Sugar Product

The structure of X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Sugar Product, PDB code: 3ndj was solved by N.A.Bruender, J.B.Thoden, M.Kaur, M.K.Avey, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.944, 114.447, 37.825, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24

The binding sites of Zinc atom in the X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Sugar Product (pdb code 3ndj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Sugar Product, PDB code: 3ndj:

Zinc binding site 1 out of 1 in the X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and 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 A C-3'-Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Sugar Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn416 b:9.6 occ:1.00 SG A:CYS57 2.3 10.8 1.0 SG A:CYS16 2.3 11.1 1.0 SG A:CYS13 2.4 9.3 1.0 SG A:CYS54 2.4 9.7 1.0 CB A:CYS54 3.1 6.9 1.0 CB A:CYS13 3.2 9.4 1.0 CB A:CYS57 3.2 10.4 1.0 CB A:CYS16 3.5 12.9 1.0 N A:CYS57 3.7 10.9 1.0 N A:CYS16 3.8 11.9 1.0 CA A:CYS57 4.0 8.4 1.0 CA A:CYS16 4.1 12.4 1.0 N A:GLY18 4.4 9.5 1.0 CB A:VAL15 4.4 9.1 1.0 CA A:CYS54 4.6 7.0 1.0 CA A:CYS13 4.7 8.0 1.0 CB A:SER56 4.7 16.2 1.0 C A:CYS57 4.7 10.5 1.0 C A:SER56 4.7 13.2 1.0 C A:CYS16 4.7 14.4 1.0 N A:GLY17 4.7 11.4 1.0 C A:VAL15 4.8 11.5 1.0 CA A:GLY18 4.8 10.8 1.0 CB A:MET59 4.8 6.5 1.0 N A:GLU58 4.9 7.8 1.0 N A:SER56 4.9 12.9 1.0 CG1 A:VAL15 4.9 15.5 1.0 CA A:SER56 5.0 11.8 1.0 N A:VAL15 5.0 9.5 1.0

N.A.Bruender, J.B.Thoden, M.Kaur, M.K.Avey, H.M.Holden. Molecular Architecture of A C-3'-Methyltransferase Involved in the Biosynthesis of D-Tetronitrose. Biochemistry V. 49 5891 2010.
ISSN: ISSN 0006-2960
PubMed: 20527922
DOI: 10.1021/BI100782B