Zinc in PDB 5l44: Structure of K-26-Dcp in Complex with the K-26 Tripeptide

The structure of Structure of K-26-Dcp in Complex with the K-26 Tripeptide, PDB code: 5l44 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)	33.00 / 1.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.580, 66.940, 102.000, 97.72, 90.71, 117.37
R / Rfree (%)	18.5 / 21.3

The structure of Structure of K-26-Dcp in Complex with the K-26 Tripeptide also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide (pdb code 5l44). 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 K-26-Dcp in Complex with the K-26 Tripeptide, PDB code: 5l44:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of K-26-Dcp in Complex with the K-26 Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:9.0 occ:1.00 OE1 A:GLU492 2.0 7.0 1.0 OAG A:K261005 2.2 11.0 1.0 NE2 A:HIS463 2.2 5.1 1.0 NE2 A:HIS467 2.2 5.5 1.0 OAJ A:K261005 2.4 9.9 1.0 PBK A:K261005 2.8 10.1 1.0 CD A:GLU492 2.8 7.1 1.0 OE2 A:GLU492 2.9 7.9 1.0 O A:HOH1102 2.9 22.1 1.0 CD2 A:HIS467 3.1 5.6 1.0 CD2 A:HIS463 3.1 5.0 1.0 CE1 A:HIS463 3.2 5.1 1.0 CE1 A:HIS467 3.2 5.7 1.0 OG A:SER495 3.7 6.8 1.0 OAK A:K261005 3.9 8.8 1.0 CB A:SER495 4.0 6.7 1.0 NAY A:K261005 4.0 12.2 1.0 CE1 A:TYR606 4.1 7.5 1.0 CBI A:K261005 4.1 12.2 1.0 OH A:TYR606 4.2 8.0 1.0 CG A:GLU492 4.2 7.0 1.0 CG A:HIS467 4.3 5.5 1.0 CG A:HIS463 4.3 5.1 1.0 ND1 A:HIS463 4.3 5.1 1.0 ND1 A:HIS467 4.3 5.4 1.0 C A:K261005 4.4 12.6 1.0 OH A:TYR599 4.5 11.0 1.0 CB A:K261005 4.7 13.7 1.0 CZ A:TYR606 4.7 7.7 1.0 O A:K261005 4.8 11.3 1.0 OE1 A:GLU464 4.8 11.9 1.0 OE2 A:GLU464 4.8 11.4 1.0 CB A:GLU492 4.9 6.8 1.0

Zinc binding site 2 out of 2 in the Structure of K-26-Dcp in Complex with the K-26 Tripeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of K-26-Dcp in Complex with the K-26 Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:9.1 occ:1.00 OE1 B:GLU492 2.0 6.6 1.0 NE2 B:HIS467 2.0 4.5 1.0 OAG B:K261005 2.2 12.1 1.0 NE2 B:HIS463 2.2 5.5 1.0 OAJ B:K261005 2.4 11.3 1.0 CD B:GLU492 2.8 6.4 1.0 PBK B:K261005 2.8 10.7 1.0 OE2 B:GLU492 2.9 7.0 1.0 CE1 B:HIS467 3.0 4.7 1.0 CD2 B:HIS467 3.0 4.7 1.0 CD2 B:HIS463 3.1 5.5 1.0 CE1 B:HIS463 3.2 5.4 1.0 OG B:SER495 3.6 6.6 1.0 CB B:SER495 3.9 6.5 1.0 O B:HOH1130 4.0 30.0 1.0 OAK B:K261005 4.0 11.0 1.0 NAY B:K261005 4.1 12.3 1.0 ND1 B:HIS467 4.1 4.5 1.0 CBI B:K261005 4.2 12.7 1.0 CG B:HIS467 4.2 4.6 1.0 CE1 B:TYR606 4.2 7.5 1.0 OH B:TYR606 4.3 7.8 1.0 CG B:GLU492 4.3 6.6 1.0 CG B:HIS463 4.3 5.3 1.0 ND1 B:HIS463 4.3 5.5 1.0 C B:K261005 4.4 12.8 1.0 OH B:TYR599 4.5 10.6 1.0 CB B:K261005 4.6 14.0 1.0 OE2 B:GLU464 4.7 9.7 1.0 CZ B:TYR606 4.7 7.8 1.0 O B:K261005 4.7 11.3 1.0 OE1 B:GLU464 4.8 8.8 1.0 CB B:GLU492 4.9 6.3 1.0 CA B:GLU492 5.0 6.4 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