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Sodium in PDB 6fkx: Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome

Enzymatic activity of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome

All present enzymatic activity of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome:
3.1.1.72;

Protein crystallography data

The structure of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome, PDB code: 6fkx was solved by F.A.Adesioye, T.P.Makhalanyane, S.Vikram, B.T.Sewell, W.Schubert, D.A.Cowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.23 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.680, 116.820, 159.420, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 22

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome (pdb code 6fkx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome, PDB code: 6fkx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6fkx

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Sodium binding site 1 out of 6 in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:35.2
occ:1.00
 O A:MET171 2.4 23.5 1.0
O A:LEU169 2.5 19.9 1.0
O A:VAL174 2.6 23.5 1.0
C A:MET171 3.4 27.0 1.0
C A:ALA170 3.7 24.4 1.0
C A:LEU169 3.7 17.8 1.0
C A:VAL174 3.7 24.3 1.0
CG A:PRO176 3.8 36.2 1.0
N A:MET171 3.8 26.8 1.0
O A:ALA170 3.9 22.6 1.0
CA A:ALA170 4.0 22.3 1.0
CD A:PRO176 4.1 28.0 1.0
O A:HOH758 4.2 33.4 1.0
CA A:MET171 4.2 24.9 1.0
N A:ASP172 4.3 36.6 1.0
N A:ALA170 4.3 17.3 1.0
N A:VAL174 4.3 24.8 1.0
CA A:VAL174 4.4 19.6 1.0
CA A:ASP172 4.4 46.9 1.0
CB A:VAL174 4.4 23.3 1.0
N A:PRO176 4.4 26.4 1.0
C A:ASP172 4.5 38.9 1.0
O A:ASP172 4.6 35.8 1.0
CB A:PRO176 4.6 28.6 1.0
O A:HOH681 4.7 40.2 1.0
N A:ASP175 4.8 21.4 1.0
CA A:LEU169 4.8 11.8 1.0
CG1 A:VAL174 4.9 20.0 1.0
CA A:PRO176 4.9 20.3 1.0
C A:ASP175 5.0 22.0 1.0
O A:VAL168 5.0 29.4 1.0

Sodium binding site 2 out of 6 in 6fkx

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Sodium binding site 2 out of 6 in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:26.6
occ:1.00
 O B:VAL174 2.3 17.9 1.0
O B:MET171 2.3 22.4 1.0
O B:LEU169 2.4 18.1 1.0
O B:HOH720 2.6 41.3 1.0
O B:HOH512 2.8 44.8 1.0
C B:VAL174 3.4 13.6 1.0
C B:MET171 3.5 22.6 1.0
C B:LEU169 3.5 24.3 1.0
N B:MET171 3.8 13.6 1.0
C B:ALA170 3.8 23.0 1.0
CD B:PRO176 3.9 20.5 1.0
N B:VAL174 4.0 25.6 1.0
CA B:VAL174 4.1 21.0 1.0
CB B:VAL174 4.1 15.1 1.0
O B:ALA170 4.2 25.5 1.0
CA B:ALA170 4.2 25.9 1.0
CA B:MET171 4.2 19.6 1.0
N B:ALA170 4.3 24.6 1.0
O B:ASP172 4.3 28.4 1.0
N B:PRO176 4.4 20.8 1.0
C B:ASP172 4.5 27.0 1.0
N B:ASP172 4.5 23.4 1.0
CG B:PRO176 4.5 22.0 1.0
CA B:LEU169 4.5 17.5 1.0
N B:ASP175 4.5 10.8 1.0
O B:VAL168 4.6 25.9 1.0
CA B:ASP172 4.6 24.1 1.0
O B:HOH799 4.6 40.9 1.0
CG1 B:VAL174 4.7 13.7 1.0
CB B:PRO176 4.8 22.2 1.0
CA B:ASP175 4.8 17.9 1.0
C B:ASP175 4.9 21.7 1.0
CB B:MET171 5.0 18.6 1.0

Sodium binding site 3 out of 6 in 6fkx

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Sodium binding site 3 out of 6 in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:31.9
occ:1.00
 O D:LEU169 2.3 21.1 1.0
O D:MET171 2.4 23.4 1.0
O D:VAL174 2.5 16.4 1.0
O D:HOH531 2.8 31.6 1.0
C D:MET171 3.4 19.4 1.0
C D:LEU169 3.5 19.9 1.0
C D:VAL174 3.7 14.1 1.0
C D:ALA170 3.7 22.0 1.0
N D:MET171 3.8 18.6 1.0
CD D:PRO176 3.8 25.4 1.0
CA D:ALA170 4.0 16.8 1.0
O D:ALA170 4.0 24.7 1.0
N D:ALA170 4.1 19.8 1.0
CA D:MET171 4.2 13.8 1.0
N D:VAL174 4.2 21.9 1.0
CA D:VAL174 4.3 18.1 1.0
CB D:VAL174 4.3 13.3 1.0
CG D:PRO176 4.3 23.9 1.0
N D:ASP172 4.3 18.9 1.0
N D:PRO176 4.4 29.0 1.0
CA D:ASP172 4.4 31.1 1.0
CB D:PRO176 4.5 17.4 1.0
CA D:LEU169 4.6 13.0 1.0
C D:ASP172 4.6 23.5 1.0
O D:ASP172 4.6 26.9 1.0
O D:VAL168 4.7 19.1 1.0
N D:ASP175 4.7 13.9 1.0
CG1 D:VAL174 4.8 14.2 1.0
O D:HOH780 4.9 39.9 1.0
CA D:PRO176 4.9 22.1 1.0
C D:ASP175 4.9 23.7 1.0
CA D:ASP175 5.0 12.8 1.0

Sodium binding site 4 out of 6 in 6fkx

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Sodium binding site 4 out of 6 in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:18.6
occ:1.00
 O C:MET171 2.3 19.4 1.0
O C:LEU169 2.3 17.6 1.0
O C:VAL174 2.3 16.9 1.0
O C:HOH691 2.6 25.1 1.0
C C:MET171 3.4 17.1 1.0
C C:LEU169 3.4 9.5 1.0
C C:VAL174 3.4 11.5 1.0
C C:ALA170 3.7 8.6 1.0
N C:MET171 3.7 12.1 1.0
CD C:PRO176 3.8 13.0 1.0
CB C:VAL174 4.0 7.7 1.0
O C:ALA170 4.0 14.9 1.0
CA C:VAL174 4.0 9.0 1.0
N C:VAL174 4.0 8.3 1.0
CA C:ALA170 4.0 14.1 1.0
CA C:MET171 4.1 15.5 1.0
N C:ALA170 4.1 12.7 1.0
N C:PRO176 4.3 14.8 1.0
N C:ASP172 4.4 15.1 1.0
CG C:PRO176 4.4 11.8 1.0
CA C:LEU169 4.5 8.5 1.0
CG1 C:VAL174 4.5 8.2 1.0
O C:ASP172 4.5 17.5 1.0
C C:ASP172 4.5 19.8 1.0
O C:HOH505 4.5 55.0 1.0
N C:ASP175 4.6 7.8 1.0
CB C:PRO176 4.6 12.8 1.0
O C:VAL168 4.6 12.1 1.0
CA C:ASP172 4.6 22.7 1.0
O C:HOH700 4.6 28.1 1.0
C C:ASP175 4.8 14.0 1.0
O C:HOH795 4.8 23.0 1.0
CA C:PRO176 4.8 8.6 1.0
CA C:ASP175 4.8 11.2 1.0
CB C:MET171 4.9 14.0 1.0

Sodium binding site 5 out of 6 in 6fkx

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Sodium binding site 5 out of 6 in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na401

b:31.2
occ:1.00
 O E:LEU169 2.6 18.8 1.0
O E:MET171 2.6 36.7 1.0
O E:VAL174 2.7 17.5 1.0
O E:HOH654 2.9 33.2 1.0
C E:MET171 3.7 30.9 1.0
C E:ALA170 3.7 29.6 1.0
C E:LEU169 3.7 25.1 1.0
C E:VAL174 3.8 14.3 1.0
CD E:PRO176 3.9 20.7 1.0
N E:MET171 3.9 26.5 1.0
O E:ALA170 4.0 34.7 1.0
CA E:ALA170 4.0 21.0 1.0
N E:ALA170 4.3 19.7 1.0
CG E:PRO176 4.4 17.9 1.0
N E:PRO176 4.4 13.7 1.0
CA E:MET171 4.4 26.7 1.0
N E:VAL174 4.5 20.8 1.0
CB E:PRO176 4.5 18.1 1.0
CA E:VAL174 4.5 10.8 1.0
CB E:VAL174 4.6 18.1 1.0
O E:ASP172 4.6 35.4 1.0
N E:ASP172 4.6 28.7 1.0
CA E:ASP172 4.8 30.7 1.0
C E:ASP172 4.8 26.4 1.0
N E:ASP175 4.9 21.1 1.0
CA E:LEU169 4.9 27.1 1.0
CA E:PRO176 4.9 22.4 1.0

Sodium binding site 6 out of 6 in 6fkx

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Sodium binding site 6 out of 6 in the Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of An Acetyl Xylan Esterase From A Desert Metagenome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na401

b:16.9
occ:1.00
 O F:MET171 2.4 15.2 1.0
O F:HOH707 2.4 32.1 1.0
O F:VAL174 2.4 7.3 1.0
O F:LEU169 2.4 23.4 1.0
O F:HOH722 2.5 18.8 1.0
C F:MET171 3.5 16.7 1.0
C F:VAL174 3.5 9.8 1.0
C F:LEU169 3.5 14.9 1.0
C F:ALA170 3.8 17.4 1.0
CD F:PRO176 3.8 9.6 1.0
N F:MET171 3.8 11.1 1.0
O F:ALA170 4.1 22.1 1.0
N F:VAL174 4.1 11.2 1.0
CB F:VAL174 4.1 6.5 1.0
CA F:VAL174 4.1 11.9 1.0
CA F:ALA170 4.1 17.1 1.0
CA F:MET171 4.3 11.2 1.0
N F:ALA170 4.3 10.9 1.0
N F:PRO176 4.3 13.5 1.0
CG F:PRO176 4.3 12.6 1.0
O F:HOH766 4.4 25.5 1.0
N F:ASP172 4.5 21.1 1.0
CB F:PRO176 4.5 13.0 1.0
C F:ASP172 4.5 20.4 1.0
O F:ASP172 4.6 22.7 1.0
CA F:ASP172 4.6 25.4 1.0
CA F:LEU169 4.6 15.4 1.0
CG1 F:VAL174 4.6 11.3 1.0
N F:ASP175 4.6 12.6 1.0
O F:VAL168 4.8 13.1 1.0
CA F:PRO176 4.9 12.6 1.0
C F:ASP175 4.9 8.7 1.0
CA F:ASP175 4.9 11.0 1.0
O F:HOH846 4.9 36.1 1.0

Reference:

F.A.Adesioye, T.P.Makhalanyane, S.Vikram, B.T.Sewell, W.D.Schubert, D.A.Cowan. Structural Characterization and Directed Evolution of A Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family. Appl. Environ. Microbiol. V. 84 2018.
ISSN: ESSN 1098-5336
PubMed: 29453256
DOI: 10.1128/AEM.02695-17
Page generated: Tue Oct 8 08:47:13 2024

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