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Potassium in PDB 2b5w: Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei

Enzymatic activity of Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei

All present enzymatic activity of Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei:
1.1.1.47;

Protein crystallography data

The structure of Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei, PDB code: 2b5w was solved by K.L.Britton, P.J.Baker, M.Fisher, S.Ruzheinikov, D.J.Gilmour, M.-J.Bonete, J.Ferrer, C.Pire, J.Esclapez, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 60.534, 109.255, 151.893, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.6

Other elements in 2b5w:

The structure of Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei (pdb code 2b5w). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei, PDB code: 2b5w:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 2b5w

Go back to Potassium Binding Sites List in 2b5w
Potassium binding site 1 out of 5 in the Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei


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 D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K901

b:23.2
occ:1.00
O A:THR347 2.7 23.8 1.0
O A:ASP344 2.8 23.0 1.0
C A:ASP344 3.8 25.7 1.0
C A:THR347 3.9 18.5 1.0
NH2 A:ARG208 4.3 20.7 1.0
CA A:ASP345 4.3 23.5 1.0
N A:ASP345 4.5 21.7 1.0
O A:ASP345 4.6 23.2 1.0
CB A:THR347 4.6 27.1 1.0
C A:ASP345 4.6 24.3 1.0
CA A:THR347 4.6 19.3 1.0
N A:THR347 4.6 20.3 1.0
N A:ASP344 4.6 29.2 1.0
C A:ASP343 4.7 37.8 1.0
CA A:ASP344 4.8 27.0 1.0
N A:ILE348 4.8 17.3 1.0
CA A:ILE348 4.9 16.8 1.0
O A:ASP343 4.9 0.3 1.0

Potassium binding site 2 out of 5 in 2b5w

Go back to Potassium Binding Sites List in 2b5w
Potassium binding site 2 out of 5 in the Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei


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 D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K902

b:23.4
occ:1.00
O A:PRO173 2.7 20.7 1.0
O A:LYS197 2.7 21.2 1.0
OD1 A:ASP172 2.7 27.3 1.0
O A:GLY198 2.9 21.5 1.0
C A:GLY198 3.6 21.3 1.0
C A:PRO173 3.8 18.4 1.0
CG A:ASP172 3.8 29.6 1.0
C A:LYS197 3.9 20.6 1.0
CA A:GLY198 4.1 20.7 1.0
OD2 A:ASP172 4.3 32.8 1.0
C A:ASP172 4.4 21.3 1.0
N A:PRO173 4.4 18.4 1.0
N A:TYR199 4.4 17.1 1.0
N A:GLY198 4.5 20.4 1.0
OG A:SER174 4.5 31.0 1.0
O A:ASP172 4.6 23.3 1.0
N A:SER174 4.6 18.5 1.0
CA A:SER174 4.6 19.1 1.0
CA A:PRO173 4.7 19.9 1.0
CD A:PRO173 4.9 20.2 1.0
CA A:TYR199 4.9 18.8 1.0
CA A:ASP172 5.0 20.9 1.0

Potassium binding site 3 out of 5 in 2b5w

Go back to Potassium Binding Sites List in 2b5w
Potassium binding site 3 out of 5 in the Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K903

b:26.8
occ:1.00
OG1 A:THR315 2.8 16.6 1.0
CB A:THR315 3.9 17.1 1.0
CG2 A:THR315 4.1 19.9 1.0
NZ A:LYS318 4.3 29.9 1.0
CA A:THR315 4.4 14.6 1.0
OE2 A:GLU156 4.5 21.2 1.0
OE1 A:GLU156 4.7 18.7 1.0
CA A:ASP195 4.8 17.0 1.0
O A:VAL194 4.8 21.2 1.0

Potassium binding site 4 out of 5 in 2b5w

Go back to Potassium Binding Sites List in 2b5w
Potassium binding site 4 out of 5 in the Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K904

b:34.8
occ:1.00
O A:TYR240 2.7 26.2 1.0
O A:PRO237 2.7 26.9 1.0
O A:ASP238 3.0 28.1 1.0
C A:ASP238 3.6 29.2 1.0
C A:TYR240 3.6 24.4 1.0
C A:PRO237 3.9 21.1 1.0
CA A:ASP238 4.0 31.7 1.0
N A:TYR240 4.3 25.3 1.0
N A:GLU241 4.4 23.4 1.0
CA A:GLU241 4.4 22.5 1.0
N A:ASP238 4.4 24.7 1.0
C A:VAL239 4.5 27.6 1.0
CA A:TYR240 4.5 21.7 1.0
N A:VAL239 4.5 26.5 1.0
O A:VAL239 4.7 26.7 1.0

Potassium binding site 5 out of 5 in 2b5w

Go back to Potassium Binding Sites List in 2b5w
Potassium binding site 5 out of 5 in the Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of D38C Glucose Dehydrogenase Mutant From Haloferax Mediterranei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K905

b:39.3
occ:1.00
O2X A:NAP701 4.5 21.9 1.0
O3X A:NAP701 4.6 23.1 1.0
OD1 A:ASP345 4.8 24.7 1.0
P2B A:NAP701 4.9 22.4 1.0
O1X A:NAP701 4.9 22.3 1.0

Reference:

K.L.Britton, P.J.Baker, M.Fisher, S.Ruzheinikov, D.J.Gilmour, M.-J.Bonete, J.Ferrer, C.Pire, J.Esclapez, D.W.Rice. Analysis of Protein Solvent Interactions in Glucose Dehydrogenase From the Extreme Halophile Haloferax Mediterranei. Proc.Natl.Acad.Sci.Usa V. 103 4846 2006.
ISSN: ISSN 0027-8424
PubMed: 16551747
DOI: 10.1073/PNAS.0508854103
Page generated: Sun Dec 13 23:08:59 2020

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