Zinc in PDB 5kd8: BT_4244 Metallopeptidase in Complex with Tn Antigen.

The structure of BT_4244 Metallopeptidase in Complex with Tn Antigen., PDB code: 5kd8 was solved by I.Noach, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.72 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.450, 88.230, 98.650, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.2

The structure of BT_4244 Metallopeptidase in Complex with Tn Antigen. also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the BT_4244 Metallopeptidase in Complex with Tn Antigen. (pdb code 5kd8). 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 BT_4244 Metallopeptidase in Complex with Tn Antigen., PDB code: 5kd8:

Zinc binding site 1 out of 1 in the BT_4244 Metallopeptidase in Complex with Tn Antigen.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BT_4244 Metallopeptidase in Complex with Tn Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:49.0 occ:1.00 OE1 A:GLU591 1.9 37.5 1.0 NE2 A:HIS574 1.9 35.5 1.0 O A:TNR902 2.1 69.7 1.0 NE2 A:HIS578 2.1 45.0 1.0 CD A:GLU591 2.6 36.1 1.0 OE2 A:GLU591 2.7 45.6 1.0 CE1 A:HIS574 2.9 39.6 1.0 CD2 A:HIS574 2.9 39.2 1.0 CE1 A:HIS578 3.0 41.3 1.0 C A:TNR902 3.1 73.8 1.0 CD2 A:HIS578 3.1 42.6 1.0 OXT A:TNR902 3.4 78.7 1.0 OE2 A:GLU575 3.9 59.0 1.0 ND1 A:HIS574 4.0 39.4 1.0 CG A:HIS574 4.0 38.0 1.0 CG A:GLU591 4.1 34.9 1.0 ND1 A:HIS578 4.1 41.5 1.0 ND2 A:ASN594 4.2 41.4 1.0 CG A:HIS578 4.2 42.8 1.0 CA A:TNR902 4.4 71.0 1.0 CD A:GLU575 4.6 60.6 1.0 CB A:GLU591 4.7 35.0 1.0 CB A:TNR902 4.7 67.1 1.0 OH A:TYR723 4.8 65.1 1.0 OE1 A:GLU575 4.8 74.1 1.0 CA A:GLU591 4.8 31.8 1.0 C8 A:TNR902 4.9 56.9 1.0 O1 A:TNR902 4.9 67.7 1.0 O A:HIS574 4.9 51.1 1.0

I.Noach, E.Ficko-Blean, B.Pluvinage, C.Stuart, M.L.Jenkins, D.Brochu, N.Buenbrazo, W.Wakarchuk, J.E.Burke, M.Gilbert, A.B.Boraston. Recognition of Protein-Linked Glycans As A Determinant of Peptidase Activity. Proc. Natl. Acad. Sci. V. 114 E679 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28096352
DOI: 10.1073/PNAS.1615141114