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Nickel 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:

Potassium (K) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of SZ348 in Complex with Cyclopentene Oxide, PDB code: 5yng:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5yng

Go back to Nickel Binding Sites List in 5yng
Nickel 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 Nickel with other atoms in the Ni 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:Ni202

b:96.4
occ:1.00
CD2 A:HIS-2 3.3 58.0 0.8
NE2 A:HIS-2 3.9 63.8 0.8
CD2 A:HIS-3 4.0 67.2 1.0
CB A:HIS-3 4.0 62.8 1.0
N A:HIS-2 4.0 59.9 0.8
CA A:HIS-3 4.1 64.1 1.0
CG A:HIS-2 4.3 62.0 0.8
CG A:HIS-3 4.3 69.4 1.0
CE1 A:HIS0 4.4 59.2 0.8
C A:HIS-3 4.6 64.4 1.0
NE2 A:HIS0 4.8 57.5 0.8
CB A:HIS-2 4.9 58.1 0.8

Nickel binding site 2 out of 2 in 5yng

Go back to Nickel Binding Sites List in 5yng
Nickel 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 Nickel with other atoms in the Ni 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:Ni203

b:0.3
occ:1.00
CE1 A:HIS-3 3.8 62.9 1.0
NE2 A:HIS-3 4.2 66.5 1.0
ND1 A:HIS-3 5.0 67.0 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: Wed Dec 16 01:50:17 2020

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