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Potassium in PDB 5ykp: Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin

Enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin

All present enzymatic activity of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin:
3.4.11.18;

Protein crystallography data

The structure of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin, PDB code: 5ykp was solved by T.Arya, V.Pillalamarri, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.75 / 1.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.713, 77.398, 47.489, 90.00, 91.62, 90.00
R / Rfree (%) 17.5 / 21.2

Other elements in 5ykp:

The structure of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin also contains other interesting chemical elements:

Cobalt (Co) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin (pdb code 5ykp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin, PDB code: 5ykp:

Potassium binding site 1 out of 1 in 5ykp

Go back to Potassium Binding Sites List in 5ykp
Potassium binding site 1 out of 1 in the Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human Methionine Aminopeptidase Type 1B (F309M Mutant) in Complex with Ovalicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:22.6
occ:1.00
 O A:VAL209 2.5 20.5 1.0
O A:SER363 2.7 22.1 1.0
O A:HOH683 2.8 19.9 1.0
O A:ASN207 2.8 24.2 1.0
O A:SER205 2.9 19.0 1.0
N A:ASN207 3.6 20.7 1.0
C A:SER205 3.6 20.5 1.0
C A:ASN207 3.7 22.2 1.0
C A:VAL206 3.7 19.1 1.0
C A:SER363 3.7 20.2 1.0
C A:VAL209 3.7 22.0 1.0
O A:VAL206 4.1 21.3 1.0
CA A:ASN207 4.1 22.7 1.0
CB A:SER205 4.1 20.4 1.0
N A:VAL206 4.2 21.5 1.0
CA A:VAL206 4.3 19.6 1.0
N A:VAL209 4.3 22.4 1.0
O A:HOH566 4.5 20.6 1.0
N A:SER363 4.5 22.3 1.0
CA A:SER205 4.5 17.9 1.0
CA A:VAL209 4.5 19.5 1.0
CA A:SER363 4.5 22.5 1.0
N A:ALA364 4.6 20.9 1.0
CG1 A:ILE225 4.6 21.8 1.0
CB A:SER363 4.7 22.2 1.0
CA A:ALA364 4.7 20.8 1.0
CD1 A:ILE225 4.7 24.1 1.0
N A:GLU208 4.7 21.8 1.0
N A:ILE210 4.7 20.9 1.0
O A:ILE225 4.8 19.2 1.0
N A:ASN227 4.8 19.2 1.0
CB A:VAL209 4.9 19.1 1.0
CB A:ASN227 4.9 18.6 1.0
O A:HOH596 4.9 19.2 1.0
C A:GLU208 4.9 21.1 1.0

Reference:

V.Pillalamarri, T.Arya, N.Haque, S.C.Bala, A.K.Marapaka, A.Addlagatta. Discovery of Natural Product Ovalicin Sensitive Type 1 Methionine Aminopeptidases: Molecular and Structural Basis. Biochem. J. V. 476 991 2019.
ISSN: ESSN 1470-8728
PubMed: 30837307
DOI: 10.1042/BCJ20180874
Page generated: Sat Aug 9 10:17:59 2025

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