Zinc in PDB 5l43: Structure of K26-Dcp

The structure of Structure of K26-Dcp, PDB code: 5l43 was solved by G.Masuyer, K.R.Acharya, G.J.Kramer, B.O.Bachmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.81 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.470, 66.936, 101.786, 97.34, 90.86, 117.31
R / Rfree (%)	17.7 / 20

The structure of Structure of K26-Dcp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Structure of K26-Dcp (pdb code 5l43). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of K26-Dcp, PDB code: 5l43:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of K26-Dcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of K26-Dcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:20.6 occ:1.00 OE1 A:GLU492 1.9 12.5 1.0 O1 A:SO41004 2.1 33.6 1.0 NE2 A:HIS467 2.2 11.6 1.0 CE1 A:HIS463 2.2 12.8 1.0 O4 A:SO41004 2.7 31.9 1.0 CD A:GLU492 2.7 12.6 1.0 OE2 A:GLU492 2.8 14.2 1.0 S A:SO41004 2.9 33.9 1.0 NE2 A:HIS463 2.9 13.0 1.0 CE1 A:HIS467 3.1 12.0 1.0 CD2 A:HIS467 3.2 11.6 1.0 ND1 A:HIS463 3.3 12.8 1.0 OG A:SER495 3.6 13.4 1.0 O3 A:SO41004 3.8 36.9 1.0 CB A:SER495 4.0 13.1 1.0 O2 A:SO41004 4.0 36.5 1.0 CD2 A:HIS463 4.2 12.0 1.0 CE2 A:TYR606 4.2 13.1 1.0 CG A:GLU492 4.2 12.8 1.0 ND1 A:HIS467 4.2 11.8 1.0 OH A:TYR606 4.3 13.7 1.0 CG A:HIS467 4.3 11.1 1.0 CG A:HIS463 4.4 12.1 1.0 OE2 A:GLU464 4.5 15.7 1.0 OH A:TYR599 4.6 22.6 1.0 CZ A:TYR606 4.7 13.4 1.0 OE1 A:GLU464 4.8 13.0 1.0 CB A:GLU492 4.8 12.7 1.0 CA A:GLU492 5.0 12.7 1.0 CD A:GLU464 5.0 12.8 1.0

Zinc binding site 2 out of 2 in the Structure of K26-Dcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of K26-Dcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:20.7 occ:1.00 OE1 B:GLU492 1.9 13.7 1.0 O3 B:SO41004 2.1 32.0 1.0 NE2 B:HIS463 2.2 12.1 1.0 NE2 B:HIS467 2.2 11.9 1.0 CD B:GLU492 2.7 13.4 1.0 O1 B:SO41004 2.7 34.1 1.0 OE2 B:GLU492 2.8 14.7 1.0 S B:SO41004 2.9 32.1 1.0 CE1 B:HIS463 3.1 11.9 1.0 CE1 B:HIS467 3.1 12.3 1.0 CD2 B:HIS463 3.2 11.8 1.0 CD2 B:HIS467 3.2 11.6 1.0 OG B:SER495 3.5 11.6 1.0 O2 B:SO41004 3.8 39.9 1.0 CB B:SER495 3.9 11.2 1.0 O4 B:SO41004 4.1 35.2 1.0 CE1 B:TYR606 4.1 12.7 1.0 CG B:GLU492 4.2 13.0 1.0 ND1 B:HIS463 4.2 11.5 1.0 ND1 B:HIS467 4.2 12.2 1.0 OH B:TYR606 4.2 12.9 1.0 CG B:HIS463 4.3 11.1 1.0 CG B:HIS467 4.3 11.5 1.0 OE2 B:GLU464 4.5 15.8 1.0 CZ B:TYR606 4.7 12.7 1.0 OH B:TYR599 4.7 21.1 1.0 OE1 B:GLU464 4.8 13.9 1.0 CB B:GLU492 4.8 12.5 1.0 CD B:GLU464 5.0 13.2 1.0 CA B:GLU492 5.0 12.0 1.0

G.Masuyer, G.E.Cozier, G.J.Kramer, B.O.Bachmann, K.R.Acharya. Crystal Structure of A Peptidyl-Dipeptidase K-26-Dcp From Actinomycete in Complex with Its Natural Inhibitor. Febs J. V. 283 4357 2016.
ISSN: ISSN 1742-4658
PubMed: 27754586
DOI: 10.1111/FEBS.13928