Zinc in PDB 3ndi: X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosylmethionine and Dtmp

The structure of X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosylmethionine and Dtmp, PDB code: 3ndi 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)	50.00 / 1.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.963, 114.385, 37.782, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.2

The binding sites of Zinc atom in the X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosylmethionine and Dtmp (pdb code 3ndi). 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- Adenosylmethionine and Dtmp, PDB code: 3ndi:

Zinc binding site 1 out of 1 in the X-Ray Structure of A C-3'-Methyltransferase in Complex with S- Adenosylmethionine and Dtmp


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- Adenosylmethionine and Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn415 b:10.8 occ:1.00 SG A:CYS13 2.3 10.6 1.0 SG A:CYS16 2.3 13.2 1.0 SG A:CYS54 2.3 10.7 1.0 SG A:CYS57 2.4 12.5 1.0 CB A:CYS13 3.2 11.3 1.0 CB A:CYS54 3.2 7.2 1.0 CB A:CYS57 3.3 13.9 1.0 CB A:CYS16 3.5 8.4 1.0 N A:CYS16 3.8 10.0 1.0 N A:CYS57 3.8 13.9 1.0 CA A:CYS57 4.1 13.4 1.0 CA A:CYS16 4.1 11.3 1.0 CB A:VAL15 4.4 9.0 1.0 N A:GLY18 4.4 13.0 1.0 CA A:CYS54 4.6 8.2 1.0 CA A:CYS13 4.6 10.1 1.0 C A:CYS16 4.7 13.9 1.0 C A:CYS57 4.7 12.4 1.0 N A:GLY17 4.7 11.7 1.0 C A:VAL15 4.7 12.2 1.0 CB A:SER56 4.8 13.0 1.0 CA A:GLY18 4.8 12.3 1.0 C A:SER56 4.8 13.9 1.0 N A:GLU58 4.8 7.3 1.0 CB A:MET59 4.8 9.0 1.0 CG1 A:VAL15 4.9 8.5 1.0 N A:SER56 4.9 14.5 1.0 CA A:VAL15 4.9 8.2 1.0 N A:VAL15 4.9 8.8 1.0 N A:MET59 5.0 7.5 1.0 NE2 A:GLN61 5.0 5.2 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