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Potassium in PDB 5yng: Crystal Structure of SZ348 in Complex with Cyclopentene Oxide

Enzymatic activity of Crystal Structure of SZ348 in Complex with Cyclopentene Oxide

All present enzymatic activity of Crystal Structure of SZ348 in Complex with Cyclopentene Oxide:
3.3.2.8;

Protein crystallography data

The structure of Crystal Structure of SZ348 in Complex with Cyclopentene Oxide, PDB code: 5yng was solved by L.Wu, Z.T.Sun, M.T.Reetz, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.46 / 2.50
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 104.159, 104.159, 73.625, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 24.1

Other elements in 5yng:

The structure of Crystal Structure of SZ348 in Complex with Cyclopentene Oxide also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of SZ348 in Complex with Cyclopentene Oxide (pdb code 5yng). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of SZ348 in Complex with Cyclopentene Oxide, PDB code: 5yng:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5yng

Go back to Potassium Binding Sites List in 5yng
Potassium binding site 1 out of 2 in the Crystal Structure of SZ348 in Complex with Cyclopentene Oxide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of SZ348 in Complex with Cyclopentene Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K201

b:61.6
occ:1.00
O A:ALA19 2.6 54.4 1.0
O A:ILE88 2.8 53.6 1.0
O A:ALA16 3.0 69.3 1.0
OD1 B:ASN92 3.0 55.9 1.0
OG A:SER21 3.2 67.9 1.0
CG2 A:ILE88 3.5 47.0 1.0
O A:ALA17 3.6 54.9 1.0
OE1 A:GLU25 3.7 54.4 1.0
CG B:ASN92 3.7 59.5 1.0
C A:ALA19 3.8 60.3 1.0
C A:ILE88 3.8 50.0 1.0
C A:ALA17 3.9 55.5 1.0
CA A:ALA17 4.0 66.8 1.0
ND2 B:ASN92 4.0 62.9 1.0
C A:ALA16 4.1 73.7 1.0
N A:ALA19 4.1 56.7 1.0
CB A:SER21 4.4 59.1 1.0
N A:SER21 4.5 55.2 1.0
CD A:GLU25 4.5 51.9 1.0
N A:ALA17 4.5 74.8 1.0
CA A:ALA19 4.6 60.0 1.0
CA A:ILE88 4.6 50.5 1.0
CB A:ILE88 4.6 50.6 1.0
N A:GLY18 4.7 54.0 1.0
OE2 A:GLU25 4.7 49.2 1.0
N A:GLY89 4.7 48.3 1.0
N A:ILE88 4.7 46.0 1.0
CA A:GLY89 4.8 44.6 1.0
N A:ALA20 4.8 58.2 1.0
C A:GLY18 4.9 56.9 1.0
CB B:SER91 4.9 47.7 1.0
CB B:ASN92 4.9 54.6 1.0
C A:ALA20 4.9 57.0 1.0
CA A:ALA20 5.0 56.1 1.0

Potassium binding site 2 out of 2 in 5yng

Go back to Potassium Binding Sites List in 5yng
Potassium binding site 2 out of 2 in the Crystal Structure of SZ348 in Complex with Cyclopentene Oxide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of SZ348 in Complex with Cyclopentene Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K205

b:47.8
occ:1.00
O B:ALA19 2.6 43.8 1.0
O B:ILE88 2.7 45.0 1.0
OD1 A:ASN92 2.8 49.7 1.0
O B:ALA16 2.8 46.7 1.0
OG B:SER21 3.2 56.2 1.0
O B:ALA17 3.4 43.4 1.0
CG A:ASN92 3.5 50.2 1.0
CG2 B:ILE88 3.6 38.3 1.0
OE1 B:GLU25 3.7 42.7 1.0
C B:ALA17 3.7 42.8 1.0
ND2 A:ASN92 3.7 50.0 1.0
C B:ILE88 3.8 35.9 1.0
CA B:ALA17 3.8 46.2 1.0
C B:ALA19 3.9 47.8 1.0
C B:ALA16 3.9 46.4 1.0
N B:ALA17 4.4 45.8 1.0
N B:ALA19 4.4 47.0 1.0
CB B:SER21 4.5 48.6 1.0
CA B:ILE88 4.5 41.1 1.0
N B:ILE88 4.5 35.6 1.0
N B:SER21 4.5 44.9 1.0
N B:GLY18 4.6 45.4 1.0
CB B:ILE88 4.6 39.8 1.0
CB A:ASN92 4.7 46.6 1.0
CD B:GLU25 4.7 46.5 1.0
C B:GLY18 4.7 47.9 1.0
CA B:ALA19 4.7 43.5 1.0
N B:GLY89 4.7 38.3 1.0
N B:ALA20 4.8 43.8 1.0
CA B:ALA20 4.8 46.9 1.0
C B:ALA20 4.8 44.6 1.0
OE2 B:GLU25 4.9 46.6 1.0
CA B:GLY89 4.9 37.3 1.0

Reference:

Z.Sun, L.Wu, M.Bocola, H.C.S.Chan, R.Lonsdale, X.D.Kong, S.Yuan, J.Zhou, M.T.Reetz. Structural and Computational Insight Into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations. J. Am. Chem. Soc. V. 140 310 2018.
ISSN: ESSN 1520-5126
PubMed: 29232125
DOI: 10.1021/JACS.7B10278
Page generated: Mon Dec 14 00:14:44 2020

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