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Potassium in PDB 6q8m: GH10 Endo-Xylanase

Enzymatic activity of GH10 Endo-Xylanase

All present enzymatic activity of GH10 Endo-Xylanase:
3.2.1.8;

Protein crystallography data

The structure of GH10 Endo-Xylanase, PDB code: 6q8m was solved by G.J.Davies, R.J.Rowland, L.Wu, O.Moroz, E.Blagova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.09 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.342, 74.073, 213.902, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17

Potassium Binding Sites:

The binding sites of Potassium atom in the GH10 Endo-Xylanase (pdb code 6q8m). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the GH10 Endo-Xylanase, PDB code: 6q8m:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6q8m

Go back to Potassium Binding Sites List in 6q8m
Potassium binding site 1 out of 4 in the GH10 Endo-Xylanase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of GH10 Endo-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K518

b:18.0
occ:1.00
 O1 A:EDO506 2.6 19.7 1.0
O A:TYR306 2.6 15.0 1.0
O A:HOH659 2.7 33.8 1.0
O A:HOH915 2.7 25.8 1.0
OE2 A:GLU45 2.8 15.8 1.0
O A:HOH893 2.8 31.3 1.0
O2 A:EDO506 3.2 30.1 1.0
C1 A:EDO506 3.6 21.0 1.0
C A:TYR306 3.8 13.2 1.0
C2 A:EDO506 3.9 24.9 1.0
CD A:GLU45 4.0 14.2 1.0
CB A:TYR306 4.2 14.2 1.0
OD2 A:ASP301 4.2 14.3 1.0
O A:HOH780 4.3 11.9 1.0
O A:HOH975 4.3 42.5 1.0
CA A:TYR306 4.3 13.2 1.0
O A:HOH812 4.5 33.1 1.0
OE1 A:GLU45 4.7 14.4 1.0
CB A:ASP42 4.7 13.5 1.0
N A:TRP308 4.8 10.8 1.0
C A:SER307 4.8 12.5 1.0
N A:SER307 4.8 12.1 1.0
CG A:GLU45 4.9 15.4 1.0
OD2 A:ASP42 4.9 18.2 1.0

Potassium binding site 2 out of 4 in 6q8m

Go back to Potassium Binding Sites List in 6q8m
Potassium binding site 2 out of 4 in the GH10 Endo-Xylanase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of GH10 Endo-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K519

b:15.7
occ:1.00
 O A:THR291 2.6 13.1 1.0
O A:CYS288 2.7 14.3 1.0
O A:HOH678 2.7 22.8 1.0
O A:CYS294 2.7 14.7 1.0
O A:HOH839 3.0 25.7 1.0
O A:HOH846 3.3 33.7 1.0
CD2 A:LEU34 3.4 21.3 1.0
O A:VAL289 3.6 15.6 1.0
C A:THR291 3.6 14.0 1.0
C A:CYS294 3.8 13.2 1.0
C A:CYS288 3.8 13.3 1.0
C A:VAL289 4.0 14.3 1.0
N A:CYS294 4.1 11.6 1.0
CB A:CYS294 4.2 13.0 1.0
CA A:VAL289 4.2 13.9 1.0
CA A:CYS294 4.2 11.9 1.0
N A:THR291 4.3 13.3 1.0
O A:HOH734 4.4 28.3 1.0
N A:VAL289 4.5 13.3 1.0
N A:THR292 4.5 14.4 1.0
CA A:THR291 4.5 12.7 1.0
N A:GLY293 4.6 17.0 1.0
CA A:THR292 4.6 15.6 1.0
CG A:LEU34 4.7 17.7 1.0
SG A:CYS288 4.9 24.0 1.0
N A:GLN290 4.9 12.4 0.5
C A:GLN290 4.9 13.8 0.5
N A:GLN290 4.9 13.0 0.5
C A:THR292 5.0 15.7 1.0
CA A:CYS288 5.0 14.2 1.0
N A:VAL295 5.0 11.7 1.0

Potassium binding site 3 out of 4 in 6q8m

Go back to Potassium Binding Sites List in 6q8m
Potassium binding site 3 out of 4 in the GH10 Endo-Xylanase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of GH10 Endo-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K523

b:14.6
occ:1.00
 O B:TYR306 2.7 12.0 1.0
O1 B:EDO503 2.7 15.6 1.0
OE2 B:GLU45 2.7 12.9 1.0
O2 B:EDO506 2.8 27.8 1.0
O1 B:EDO506 2.8 25.0 1.0
O B:HOH674 3.0 27.0 1.0
O2 B:EDO503 3.1 26.6 1.0
C1 B:EDO506 3.5 30.5 1.0
C2 B:EDO506 3.6 29.0 1.0
O B:HOH863 3.6 31.1 1.0
C1 B:EDO503 3.7 17.7 1.0
C B:TYR306 3.8 10.9 1.0
C2 B:EDO503 3.9 19.4 1.0
CD B:GLU45 3.9 11.5 1.0
OD2 B:ASP301 4.1 12.1 1.0
CB B:TYR306 4.1 10.8 1.0
O B:HOH793 4.3 10.5 1.0
O B:HOH708 4.3 36.1 1.0
CA B:TYR306 4.3 10.5 1.0
OE1 B:GLU45 4.7 12.0 1.0
CB B:ASP42 4.7 12.4 1.0
N B:TRP308 4.8 9.5 1.0
C B:SER307 4.8 9.4 1.0
N B:SER307 4.9 10.1 1.0
CG B:GLU45 4.9 12.6 1.0

Potassium binding site 4 out of 4 in 6q8m

Go back to Potassium Binding Sites List in 6q8m
Potassium binding site 4 out of 4 in the GH10 Endo-Xylanase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of GH10 Endo-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K524

b:15.5
occ:1.00
 O B:THR291 2.6 12.5 1.0
O B:CYS294 2.7 14.0 1.0
O B:HOH651 2.7 29.1 1.0
O B:CYS288 2.7 14.5 1.0
O B:HOH840 2.9 20.9 1.0
O B:HOH875 3.1 34.1 1.0
CD2 B:LEU34 3.5 18.8 1.0
O B:VAL289 3.5 16.6 1.0
C B:THR291 3.7 11.5 1.0
C B:CYS294 3.8 12.1 1.0
C B:CYS288 3.9 14.8 1.0
C B:VAL289 4.0 15.4 1.0
N B:CYS294 4.1 11.3 1.0
CA B:VAL289 4.2 15.2 1.0
CB B:CYS294 4.2 12.7 1.0
N B:THR291 4.3 13.6 1.0
CA B:CYS294 4.3 11.9 1.0
O B:HOH769 4.3 29.7 1.0
N B:GLY293 4.5 14.9 1.0
N B:THR292 4.5 12.5 1.0
N B:VAL289 4.5 14.5 1.0
CA B:THR292 4.5 13.4 1.0
CA B:THR291 4.5 12.5 1.0
O B:HOH1011 4.8 41.2 1.0
CG B:LEU34 4.8 17.1 1.0
C B:THR292 4.8 13.1 1.0
N B:GLN290 4.9 13.7 1.0
SG B:CYS288 4.9 27.1 1.0
N B:VAL295 5.0 11.4 1.0

Reference:

S.P.Schroder, C.De Boer, N.G.S.Mcgregor, R.J.Rowland, O.Moroz, E.Blagova, J.Reijngoud, M.Arentshorst, D.Osborn, M.D.Morant, E.Abbate, M.A.Stringer, K.B.R.M.Krogh, L.Raich, C.Rovira, J.G.Berrin, G.P.Van Wezel, A.F.J.Ram, B.I.Florea, G.A.Van Der Marel, J.D.C.Codee, K.S.Wilson, L.Wu, G.J.Davies, H.S.Overkleeft. Dynamic and Functional Profiling of Xylan-Degrading Enzymes Inaspergillussecretomes Using Activity-Based Probes. Acs Cent.Sci. V. 5 1067 2019.
ISSN: ESSN 2374-7951
PubMed: 31263766
DOI: 10.1021/ACSCENTSCI.9B00221
Page generated: Mon Aug 12 17:18:02 2024

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