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Calcium in PDB 5la2: The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans

Protein crystallography data

The structure of The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans, PDB code: 5la2 was solved by A.Basle, A.Labourel, F.Cuskin, A.Jackson, L.Crouch, A.Rogowski, H.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.43 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.273, 123.176, 125.380, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 19.9

Calcium Binding Sites:

The binding sites of Calcium atom in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans (pdb code 5la2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans, PDB code: 5la2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5la2

Go back to Calcium Binding Sites List in 5la2
Calcium binding site 1 out of 6 in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:18.6
occ:1.00
 OD1 A:ASN509 2.3 15.7 1.0
O A:TYR420 2.3 15.3 1.0
OE1 A:GLU377 2.4 15.7 1.0
O A:ASN509 2.4 14.9 1.0
OE1 A:GLU379 2.5 16.7 1.0
O A:HOH908 2.5 21.2 1.0
OE2 A:GLU379 2.7 19.1 1.0
CD A:GLU379 2.9 18.4 1.0
C A:ASN509 3.4 15.2 1.0
C A:TYR420 3.5 14.6 1.0
CG A:ASN509 3.5 16.3 1.0
CD A:GLU377 3.5 15.3 1.0
CA A:ASN509 3.9 14.1 1.0
N A:TYR420 4.0 15.9 1.0
CB A:GLU377 4.1 15.3 1.0
CA A:TYR420 4.3 14.6 1.0
CG A:GLU377 4.3 15.5 1.0
CB A:ASN509 4.3 15.7 1.0
N A:ALA378 4.4 12.8 1.0
OE2 A:GLU377 4.4 18.2 1.0
N A:ASN421 4.4 15.3 1.0
ND2 A:ASN509 4.5 18.5 1.0
CG A:GLU379 4.5 18.1 1.0
N A:TRP510 4.5 14.2 1.0
CA A:GLU377 4.5 13.8 1.0
CA A:ASN421 4.5 15.7 1.0
O A:HOH1094 4.6 32.6 1.0
CB A:TRP510 4.7 12.9 1.0
O A:HOH789 4.7 31.8 1.0
CD1 A:TRP510 4.8 14.9 1.0
O A:HOH759 4.8 29.3 1.0
CB A:TYR420 4.8 15.6 1.0
C A:GLU377 4.9 12.0 1.0
CA A:TRP510 4.9 13.4 1.0
O A:GLY418 5.0 20.0 1.0
N A:GLU379 5.0 12.7 1.0

Calcium binding site 2 out of 6 in 5la2

Go back to Calcium Binding Sites List in 5la2
Calcium binding site 2 out of 6 in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca608

b:18.6
occ:1.00
 OD1 A:ASP394 2.3 21.3 1.0
OD2 A:ASP392 2.3 16.9 1.0
O A:VAL396 2.3 18.3 1.0
O A:GLY407 2.3 17.8 1.0
O A:ASP394 2.4 17.5 1.0
OD1 A:ASP409 2.4 18.0 1.0
OD2 A:ASP409 3.0 18.3 1.0
CG A:ASP409 3.0 16.2 1.0
CG A:ASP392 3.2 18.2 1.0
C A:ASP394 3.4 17.6 1.0
CG A:ASP394 3.5 22.5 1.0
C A:GLY407 3.5 15.8 1.0
C A:VAL396 3.5 18.1 1.0
OD1 A:ASP392 4.0 17.7 1.0
CA A:ASP394 4.0 19.3 1.0
N A:ASP394 4.1 19.1 1.0
CB A:ASP392 4.1 16.0 1.0
CA A:GLY407 4.2 18.4 1.0
CB A:ASP394 4.2 20.9 1.0
CA A:CA609 4.3 18.8 1.0
N A:VAL396 4.3 20.8 1.0
N A:ASN397 4.4 19.7 1.0
CA A:ASN397 4.4 18.7 1.0
O A:HOH760 4.4 29.5 1.0
N A:ASP409 4.4 15.7 1.0
C A:SER395 4.4 22.0 1.0
N A:SER395 4.4 19.6 1.0
OD2 A:ASP394 4.4 25.7 1.0
CB A:ASP409 4.4 15.3 1.0
CA A:VAL396 4.5 21.9 1.0
C A:VAL408 4.5 15.3 1.0
N A:VAL408 4.6 15.2 1.0
CG1 A:VAL396 4.6 22.9 1.0
N A:VAL398 4.6 19.4 1.0
CG1 A:VAL398 4.7 32.8 1.0
O A:HOH859 4.7 19.9 1.0
CA A:SER395 4.7 22.9 1.0
CA A:VAL408 4.8 13.7 1.0
CA A:ASP409 4.8 15.5 1.0
O A:SER395 4.8 22.9 1.0
O A:VAL408 5.0 17.7 1.0

Calcium binding site 3 out of 6 in 5la2

Go back to Calcium Binding Sites List in 5la2
Calcium binding site 3 out of 6 in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca609

b:18.8
occ:1.00
 OD2 A:ASP409 2.3 18.3 1.0
O A:TRP424 2.4 17.8 1.0
O A:HOH859 2.4 19.9 1.0
OD1 A:ASP392 2.5 17.7 1.0
O A:HOH836 2.5 14.8 1.0
OE2 A:GLU429 2.5 15.5 1.0
OE1 A:GLU429 2.6 15.7 1.0
OD2 A:ASP392 2.8 16.9 1.0
CD A:GLU429 2.9 15.4 1.0
CG A:ASP392 2.9 18.2 1.0
CG A:ASP409 3.5 16.2 1.0
C A:TRP424 3.6 16.8 1.0
O A:HOH975 4.1 15.6 1.0
CB A:ASP409 4.2 15.3 1.0
O A:HOH760 4.2 29.5 1.0
O A:GLY423 4.2 18.1 1.0
CA A:CA608 4.3 18.6 1.0
CA A:ILE425 4.3 16.3 1.0
CB A:TRP424 4.3 18.6 1.0
CB A:ASP392 4.4 16.0 1.0
N A:ILE425 4.4 16.8 1.0
OD1 A:ASP409 4.4 18.0 1.0
CG A:GLU429 4.4 15.4 1.0
N A:ASP409 4.5 15.7 1.0
N A:SER426 4.5 17.4 1.0
OG A:SER426 4.6 27.1 1.0
OG1 A:THR393 4.6 20.1 1.0
CA A:TRP424 4.6 17.0 1.0
O A:HOH813 4.6 14.8 1.0
N A:THR393 4.7 17.5 1.0
OD1 A:ASP394 4.7 21.3 1.0
CA A:ASP392 4.8 15.0 1.0
C A:ILE425 4.9 18.3 1.0
O A:GLY407 4.9 17.8 1.0

Calcium binding site 4 out of 6 in 5la2

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Calcium binding site 4 out of 6 in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca607

b:19.4
occ:1.00
 OE1 B:GLU377 2.3 16.5 1.0
O B:TYR420 2.3 14.2 1.0
OD1 B:ASN509 2.3 15.6 1.0
O B:ASN509 2.4 13.5 1.0
OE1 B:GLU379 2.4 14.3 1.0
O B:HOH991 2.5 23.4 1.0
OE2 B:GLU379 2.7 20.8 1.0
CD B:GLU379 2.9 15.9 1.0
C B:ASN509 3.3 14.4 1.0
CD B:GLU377 3.4 16.3 1.0
C B:TYR420 3.5 15.7 1.0
CG B:ASN509 3.6 16.3 1.0
CA B:ASN509 3.9 14.3 1.0
N B:TYR420 4.1 16.0 1.0
CB B:GLU377 4.1 15.1 1.0
CG B:GLU377 4.2 15.4 1.0
CA B:TYR420 4.3 15.2 1.0
CB B:ASN509 4.3 16.0 1.0
OE2 B:GLU377 4.3 18.6 1.0
N B:ALA378 4.4 13.4 1.0
N B:TRP510 4.4 13.6 1.0
CG B:GLU379 4.4 15.6 1.0
N B:ASN421 4.5 15.7 1.0
O B:HOH960 4.5 41.7 1.0
CA B:GLU377 4.5 14.1 1.0
CA B:ASN421 4.5 15.4 1.0
ND2 B:ASN509 4.6 16.6 1.0
CB B:TRP510 4.6 14.8 1.0
O B:HOH1088 4.7 43.0 1.0
CD1 B:TRP510 4.8 15.3 1.0
O B:HOH715 4.8 27.4 1.0
CB B:TYR420 4.8 17.3 1.0
CA B:TRP510 4.9 12.9 1.0
C B:GLU377 4.9 15.0 1.0
N B:GLU379 5.0 16.9 1.0

Calcium binding site 5 out of 6 in 5la2

Go back to Calcium Binding Sites List in 5la2
Calcium binding site 5 out of 6 in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca608

b:17.2
occ:1.00
 OD2 B:ASP409 2.2 18.3 1.0
O B:TRP424 2.3 17.1 1.0
O B:HOH858 2.4 19.9 1.0
OD1 B:ASP392 2.4 16.0 1.0
OE2 B:GLU429 2.4 16.5 1.0
O B:HOH836 2.5 15.8 1.0
OE1 B:GLU429 2.5 18.5 1.0
CD B:GLU429 2.8 16.4 1.0
OD2 B:ASP392 2.9 17.4 1.0
CG B:ASP392 3.0 16.1 1.0
CG B:ASP409 3.4 18.7 1.0
C B:TRP424 3.5 18.1 1.0
O B:HOH823 4.0 16.8 1.0
CB B:ASP409 4.2 19.0 1.0
O B:GLY423 4.2 20.9 1.0
CB B:TRP424 4.3 19.9 1.0
O B:HOH920 4.3 29.1 1.0
CA B:CA609 4.3 18.6 1.0
CB B:ASP392 4.3 15.0 1.0
CA B:ILE425 4.4 17.1 1.0
N B:ILE425 4.4 16.1 1.0
CG B:GLU429 4.4 16.6 1.0
OD1 B:ASP409 4.4 17.4 1.0
OG B:SER426 4.4 24.0 1.0
N B:SER426 4.5 17.9 1.0
CA B:TRP424 4.5 20.1 1.0
N B:ASP409 4.5 16.3 1.0
O B:HOH889 4.6 16.8 1.0
N B:THR393 4.6 16.4 1.0
OG1 B:THR393 4.7 19.8 1.0
CA B:ASP392 4.7 14.4 1.0
OD1 B:ASP394 4.8 22.7 1.0
C B:ILE425 4.9 18.0 1.0
O B:GLY407 4.9 13.8 1.0
CB B:SER426 4.9 22.4 1.0

Calcium binding site 6 out of 6 in 5la2

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Calcium binding site 6 out of 6 in the The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Mechanism By Which Arabinoxylanases Can Recognise Highly Decorated Xylans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca609

b:18.6
occ:1.00
 OD1 B:ASP394 2.2 22.7 1.0
OD2 B:ASP392 2.3 17.4 1.0
OD1 B:ASP409 2.3 17.4 1.0
O B:VAL396 2.3 19.4 1.0
O B:GLY407 2.4 13.8 1.0
O B:ASP394 2.4 17.8 1.0
CG B:ASP409 3.0 18.7 1.0
OD2 B:ASP409 3.0 18.3 1.0
CG B:ASP392 3.2 16.1 1.0
C B:ASP394 3.4 17.9 1.0
CG B:ASP394 3.5 24.3 1.0
C B:GLY407 3.5 16.4 1.0
C B:VAL396 3.6 22.2 1.0
OD1 B:ASP392 3.9 16.0 1.0
CA B:ASP394 4.0 19.7 1.0
CB B:ASP392 4.1 15.0 1.0
N B:ASP394 4.1 18.8 1.0
CA B:GLY407 4.1 20.5 1.0
CB B:ASP394 4.2 22.1 1.0
CA B:CA608 4.3 17.2 1.0
CB B:ASP409 4.4 19.0 1.0
N B:VAL396 4.4 23.0 1.0
N B:ASP409 4.4 16.3 1.0
OD2 B:ASP394 4.4 24.2 1.0
N B:ASN397 4.4 22.9 1.0
CA B:ASN397 4.4 21.6 1.0
N B:SER395 4.4 18.1 1.0
C B:SER395 4.5 22.8 1.0
C B:VAL408 4.5 17.0 1.0
O B:HOH920 4.6 29.1 1.0
N B:VAL408 4.6 14.1 1.0
CA B:VAL396 4.6 24.5 1.0
N B:VAL398 4.6 16.9 1.0
O B:HOH858 4.7 19.9 1.0
CA B:SER395 4.7 20.3 1.0
CA B:VAL408 4.7 15.4 1.0
CG1 B:VAL396 4.8 27.3 1.0
CA B:ASP409 4.8 16.4 1.0
CG2 B:VAL398 4.8 24.8 1.0
O B:SER395 4.9 23.6 1.0
O B:VAL408 4.9 20.4 1.0

Reference:

A.Labourel, L.I.Crouch, J.L.Bras, A.Jackson, A.Rogowski, J.Gray, M.P.Yadav, B.Henrissat, C.M.Fontes, H.J.Gilbert, S.Najmudin, A.Basle, F.Cuskin. The Mechanism By Which Arabinoxylanases Can Recognize Highly Decorated Xylans. J.Biol.Chem. V. 291 22149 2016.
ISSN: ESSN 1083-351X
PubMed: 27531750
DOI: 10.1074/JBC.M116.743948
Page generated: Mon Jul 15 07:27:10 2024

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