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Magnesium in PDB 7qbm: Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602

Enzymatic activity of Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602

All present enzymatic activity of Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602:
3.4.22.38;

Protein crystallography data

The structure of Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602, PDB code: 7qbm was solved by J.Benysek, M.Busa, M.Mares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 1.88
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.283, 103.283, 55.464, 90, 90, 90
R / Rfree (%) 19 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602 (pdb code 7qbm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602, PDB code: 7qbm:

Magnesium binding site 1 out of 1 in 7qbm

Go back to Magnesium Binding Sites List in 7qbm
Magnesium binding site 1 out of 1 in the Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Activation Intermediate of Cathepsin K in Complex with the 3-Cyano-3-Aza-Beta-Amino Acid Inhibitor GU2602 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg402

b:36.4
occ:1.00
 O P:HOH550 2.2 31.3 0.5
O A:HOH516 2.3 30.7 1.0
O P:HOH538 2.3 37.7 1.0
OG P:SER68 2.4 31.4 1.0
OG1 A:THR140 2.4 26.7 1.0
O A:HOH545 2.5 54.1 1.0
OE2 P:GLU69 3.2 43.6 0.5
CB P:SER68 3.3 30.7 1.0
CB A:THR140 3.7 24.9 1.0
N A:THR140 3.7 24.7 1.0
CD P:GLU69 4.0 40.9 0.5
OE1 P:GLU69 4.1 34.3 0.5
O A:HOH428 4.1 28.8 1.0
CA A:THR140 4.2 24.0 1.0
O A:HOH438 4.2 36.8 0.5
N P:SER68 4.2 30.0 1.0
CA P:SER68 4.3 33.5 1.0
O A:SER138 4.6 24.8 1.0
C A:LEU139 4.7 25.7 1.0
CG2 A:THR140 4.8 23.2 1.0
CA A:LEU139 4.9 26.0 1.0
N P:GLU69 5.0 41.7 1.0

Reference:

J.Benysek, M.Busa, P.Rubesova, J.Fanfrlik, M.Lepsik, J.Brynda, Z.Matouskova, U.Bartz, M.Horn, M.Gutschow, M.Mares. Highly Potent Inhibitors of Cathepsin K with A Differently Positioned Cyanohydrazide Warhead: Structural Analysis of Binding Mode to Mature and Zymogen-Like Enzymes. J Enzyme Inhib Med Chem V. 37 515 2022.
ISSN: ESSN 1475-6374
PubMed: 35144520
DOI: 10.1080/14756366.2021.2024527
Page generated: Thu Oct 3 05:05:18 2024

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