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Sodium in PDB 3upw: Pichia Stipitis OYE2.6 Complexed with Nicotinamide

Enzymatic activity of Pichia Stipitis OYE2.6 Complexed with Nicotinamide

All present enzymatic activity of Pichia Stipitis OYE2.6 Complexed with Nicotinamide:
1.6.99.1;

Protein crystallography data

The structure of Pichia Stipitis OYE2.6 Complexed with Nicotinamide, PDB code: 3upw was solved by Y.A.Pompeu, J.D.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.24 / 1.78
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 127.306, 127.306, 123.064, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Pichia Stipitis OYE2.6 Complexed with Nicotinamide (pdb code 3upw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Pichia Stipitis OYE2.6 Complexed with Nicotinamide, PDB code: 3upw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3upw

Go back to Sodium Binding Sites List in 3upw
Sodium binding site 1 out of 4 in the Pichia Stipitis OYE2.6 Complexed with Nicotinamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pichia Stipitis OYE2.6 Complexed with Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:34.6
occ:1.00
O A:HOH791 2.6 40.2 1.0
O A:HOH417 2.7 52.3 1.0
O A:HOH421 2.7 48.3 1.0
O A:HOH755 2.8 26.8 1.0
O A:HOH792 3.2 43.3 1.0
O A:HOH859 3.3 60.9 1.0
O A:HOH848 3.3 33.7 1.0
O1B A:MLA409 3.8 44.9 0.8
O A:HOH684 3.9 32.8 1.0
O A:VAL118 4.2 20.3 1.0
O A:HOH808 4.2 32.4 1.0
O A:HOH515 4.6 28.4 1.0
OE1 A:GLU139 4.6 29.3 1.0
OE1 A:GLN248 4.7 21.2 1.0
C1 A:MLA409 4.7 41.8 0.8
CB A:VAL118 5.0 17.9 1.0

Sodium binding site 2 out of 4 in 3upw

Go back to Sodium Binding Sites List in 3upw
Sodium binding site 2 out of 4 in the Pichia Stipitis OYE2.6 Complexed with Nicotinamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pichia Stipitis OYE2.6 Complexed with Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:28.2
occ:1.00
OD2 A:ASP196 2.7 18.5 1.0
OG A:SER242 2.9 15.2 1.0
O A:HOH505 2.9 18.8 1.0
O A:HOH501 2.9 17.5 1.0
O A:SER242 3.0 15.9 1.0
N A:HIS191 3.6 13.5 1.0
O A:ALA245 3.6 18.0 1.0
CG A:ASP196 3.7 21.0 1.0
CB A:ALA245 3.7 18.2 1.0
O A:HOH516 3.8 14.7 1.0
NE2 A:GLN200 3.9 17.4 1.0
OD1 A:ASP196 4.0 18.8 1.0
C A:SER242 4.0 14.6 1.0
CB A:SER242 4.0 14.6 1.0
N A:GLY192 4.1 14.8 1.0
CA A:HIS191 4.1 15.1 1.0
CG A:MET250 4.1 17.0 1.0
C A:ALA245 4.2 18.9 1.0
CA A:ALA245 4.3 14.8 1.0
N A:ALA245 4.3 15.9 1.0
CB A:MET250 4.3 18.2 1.0
C A:ALA190 4.5 14.5 1.0
C A:HIS191 4.5 16.6 1.0
CA A:SER242 4.6 12.9 1.0
CA A:ALA190 4.9 13.2 1.0
N A:SER242 4.9 13.3 1.0
CB A:ASP196 5.0 12.1 1.0

Sodium binding site 3 out of 4 in 3upw

Go back to Sodium Binding Sites List in 3upw
Sodium binding site 3 out of 4 in the Pichia Stipitis OYE2.6 Complexed with Nicotinamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pichia Stipitis OYE2.6 Complexed with Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na415

b:25.5
occ:1.00
O A:HOH816 2.6 22.4 1.0
O A:HOH747 2.6 22.3 1.0
OD1 A:ASN104 2.6 26.5 1.0
O A:HOH850 3.1 37.7 1.0
CG A:ASN104 3.5 29.1 1.0
O A:HOH795 3.9 49.9 1.0
O A:HOH530 4.0 27.6 1.0
CB A:ASN104 4.1 20.6 1.0
CA A:ASN104 4.1 19.9 1.0
O A:HOH758 4.2 24.5 1.0
ND2 A:ASN104 4.4 24.5 1.0
O A:ASN104 4.5 21.1 1.0
O A:THR58 4.6 21.6 1.0
C A:ASN104 4.7 18.6 1.0
O A:ALA103 4.9 23.0 1.0

Sodium binding site 4 out of 4 in 3upw

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Sodium binding site 4 out of 4 in the Pichia Stipitis OYE2.6 Complexed with Nicotinamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pichia Stipitis OYE2.6 Complexed with Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na416

b:34.1
occ:1.00
O A:ASP335 2.3 23.8 1.0
O A:HOH752 2.5 25.3 1.0
O A:HOH802 2.5 28.5 1.0
OD2 A:ASP338 2.5 21.5 1.0
OG1 A:THR341 3.0 18.2 1.0
CG A:ASP338 3.1 24.9 1.0
C A:ASP335 3.3 21.2 1.0
OD1 A:ASP338 3.4 21.0 1.0
CA A:ASP335 3.8 19.1 1.0
CB A:THR341 3.9 20.7 1.0
CB A:ASP338 4.1 24.6 1.0
CG2 A:THR341 4.3 18.1 1.0
O A:HOH768 4.3 25.4 1.0
O A:HOH849 4.4 41.5 1.0
O A:GLU334 4.4 23.1 1.0
N A:ILE336 4.4 19.7 1.0
OG A:SER309 4.5 21.6 1.0
N A:ASP338 4.5 20.9 1.0
O A:HOH822 4.6 44.1 1.0
CB A:ASP335 4.6 17.4 1.0
CE A:LYS318 4.7 34.2 1.0
CA A:ILE336 4.8 19.6 1.0
NE A:ARG340 4.9 21.5 1.0
O A:HOH667 4.9 44.9 1.0
CA A:ASP338 4.9 23.4 1.0
N A:ALA337 5.0 20.6 1.0
N A:ASP335 5.0 23.1 1.0

Reference:

Y.A.Pompeu, B.Sullivan, A.Z.Walton, J.D.Stewart. Structural and Catalytic Characterization of Pichia Stipitis Oye 2.6, A Useful Biocatalyst For Asymmetric Alkene Reductions Adv.Synth.Catal. 2012.
ISSN: ESSN 1615-4169
DOI: 10.1002/ADSC.201200213
Page generated: Tue Dec 15 06:27:27 2020

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