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Sodium in PDB 2y8k: Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase.

Protein crystallography data

The structure of Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase., PDB code: 2y8k was solved by S.J.Firbank, M.A.Correia, K.Mazumder, J.L.Bras, Y.Zhu, R.J.Lewis, W.S.York, C.M.Fontes, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.58 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.120, 75.550, 105.970, 90.00, 90.00, 90.00
R / Rfree (%) 14.581 / 16.627

Other elements in 2y8k:

The structure of Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase. also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase. (pdb code 2y8k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase., PDB code: 2y8k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2y8k

Go back to Sodium Binding Sites List in 2y8k
Sodium binding site 1 out of 4 in the Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1527

b:16.6
occ:1.00
O A:GLY407 2.2 14.8 1.0
O A:VAL396 2.3 18.6 1.0
OD1 A:ASP409 2.4 16.3 1.0
O A:ASP394 2.4 21.2 1.0
OD2 A:ASP392 2.4 16.2 1.0
CG A:ASP392 3.1 15.9 1.0
CG A:ASP409 3.2 14.8 1.0
CB A:ASP394 3.2 22.2 1.0
C A:ASP394 3.3 21.9 1.0
C A:VAL396 3.3 19.9 1.0
OD2 A:ASP409 3.4 18.0 1.0
C A:GLY407 3.4 15.5 1.0
CA A:ASP394 3.7 22.0 1.0
CB A:ASP392 3.8 15.7 1.0
OD1 A:ASP392 3.8 14.8 1.0
N A:ASN397 4.0 18.5 1.0
N A:ASP394 4.0 20.4 1.0
CA A:ASN397 4.0 18.3 1.0
CA A:GLY407 4.1 16.2 1.0
N A:VAL396 4.1 21.5 1.0
N A:ASP409 4.3 14.6 1.0
N A:VAL398 4.3 19.4 1.0
CA A:VAL396 4.4 21.3 1.0
C A:SER395 4.4 22.6 1.0
C A:VAL408 4.4 14.7 1.0
N A:SER395 4.4 23.0 1.0
N A:VAL408 4.4 14.5 1.0
CB A:ASP409 4.5 15.0 1.0
CG A:ASP394 4.6 25.4 1.0
CA A:CA1526 4.6 17.4 1.0
CA A:VAL408 4.6 14.3 1.0
CA A:ASP409 4.7 14.9 1.0
CG1 A:VAL398 4.7 20.8 1.0
C A:ASN397 4.7 19.5 1.0
O A:HOH2509 4.7 20.9 1.0
O A:SER395 4.7 23.1 1.0
CA A:SER395 4.8 23.9 1.0
O A:VAL408 4.8 15.8 1.0
OD2 A:ASP394 5.0 24.8 1.0

Sodium binding site 2 out of 4 in 2y8k

Go back to Sodium Binding Sites List in 2y8k
Sodium binding site 2 out of 4 in the Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1528

b:15.6
occ:1.00
O A:TYR420 2.3 17.6 1.0
OD1 A:ASN509 2.4 16.8 1.0
OE1 A:GLU379 2.4 17.6 1.0
OE1 A:GLU377 2.4 18.8 1.0
O A:ASN509 2.4 14.7 1.0
O A:HOH2492 2.6 27.2 1.0
CD A:GLU379 3.1 18.2 1.0
OE2 A:GLU379 3.1 21.9 1.0
C A:ASN509 3.4 14.2 1.0
C A:TYR420 3.5 17.1 1.0
CG A:ASN509 3.5 16.2 1.0
CD A:GLU377 3.6 19.6 1.0
CA A:ASN509 3.8 15.1 1.0
CB A:GLU377 4.1 14.8 1.0
N A:TYR420 4.1 19.6 1.0
N A:ALA378 4.2 13.4 1.0
CG A:GLU377 4.3 16.3 1.0
CB A:ASN509 4.3 15.8 1.0
CA A:TYR420 4.3 18.7 1.0
N A:ASN421 4.4 16.5 1.0
CA A:GLU377 4.4 14.7 1.0
N A:TRP510 4.5 14.1 1.0
CA A:ASN421 4.5 16.0 1.0
OE2 A:GLU377 4.5 23.1 1.0
ND2 A:ASN509 4.6 16.0 1.0
CG A:GLU379 4.6 17.0 1.0
O A:HOH2488 4.7 42.1 1.0
CB A:TRP510 4.7 14.6 1.0
CB A:TYR420 4.7 18.8 1.0
C A:GLU377 4.7 14.2 1.0
N A:GLU379 4.9 13.7 1.0
CA A:TRP510 4.9 14.2 1.0
CD1 A:TRP510 4.9 17.0 1.0

Sodium binding site 3 out of 4 in 2y8k

Go back to Sodium Binding Sites List in 2y8k
Sodium binding site 3 out of 4 in the Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1529

b:32.1
occ:1.00
OD1 A:ASN139 2.2 22.5 1.0
O A:GLY136 2.3 20.4 1.0
O A:HOH2193 2.3 38.9 1.0
O A:HOH2626 2.4 32.0 1.0
O A:HOH2195 2.8 34.7 1.0
CG A:ASN139 3.3 17.7 1.0
C A:GLY136 3.4 18.5 1.0
CA A:ALA137 4.1 19.2 1.0
N A:ALA137 4.2 19.1 1.0
CB A:ASN139 4.2 14.5 1.0
ND2 A:ASN139 4.2 23.1 1.0
C A:ALA137 4.4 19.3 1.0
N A:ASN139 4.4 15.1 1.0
CA A:GLY136 4.5 17.8 1.0
N A:ASN138 4.6 16.2 1.0
O2 A:GOL1524 4.6 24.7 1.0
N A:GLY136 4.8 16.5 1.0
C1 A:GOL1524 4.8 30.8 1.0
CA A:ASN139 4.9 14.3 1.0
O A:ALA137 4.9 20.9 1.0

Sodium binding site 4 out of 4 in 2y8k

Go back to Sodium Binding Sites List in 2y8k
Sodium binding site 4 out of 4 in the Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of CTGH5-CBM6, An Arabinoxylan-Specific Xylanase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1530

b:22.8
occ:1.00
O A:LEU472 2.3 16.5 1.0
O A:HOH2557 2.3 22.7 1.0
O A:HOH2580 2.4 21.5 1.0
O A:HOH2553 2.4 19.8 1.0
O A:HOH2581 2.8 29.5 1.0
C A:LEU472 3.5 18.0 1.0
N A:ALA474 3.9 22.0 1.0
N A:GLY454 4.0 22.9 1.0
O A:HOH2282 4.1 25.5 1.0
O A:HOH2577 4.2 19.5 1.0
C A:PRO473 4.2 21.5 1.0
CA A:PRO473 4.2 20.6 1.0
O A:SER455 4.2 17.9 1.0
O A:HOH2578 4.3 27.0 1.0
N A:PRO473 4.3 18.5 1.0
N A:LEU472 4.3 16.4 1.0
N A:SER455 4.4 21.8 1.0
CA A:LEU472 4.6 16.3 1.0
CB A:ALA474 4.7 22.2 1.0
CA A:GLY454 4.7 23.3 1.0
C A:GLU471 4.7 16.0 1.0
CA A:ALA474 4.7 22.1 1.0
OE1 A:GLU471 4.8 19.3 1.0
OG A:SER455 4.8 23.2 1.0
C A:SER453 4.9 23.0 1.0
CA A:SER453 4.9 23.7 1.0
O A:PRO473 4.9 23.1 1.0
C A:GLY454 4.9 22.2 1.0
CB A:GLU471 5.0 16.4 1.0

Reference:

M.A.Correia, K.Mazumder, J.L.Bras, S.J.Firbank, Y.Zhu, R.J.Lewis, W.S.York, C.M.Fontes, H.J.Gilbert. Structure and Function of An Arabinoxylan-Specific Xylanase. J.Biol.Chem. V. 286 22510 2011.
ISSN: ISSN 0021-9258
PubMed: 21378160
DOI: 10.1074/JBC.M110.217315
Page generated: Tue Dec 15 06:00:20 2020

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