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Sodium in PDB 3mmd: Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose

Enzymatic activity of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose

All present enzymatic activity of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose, PDB code: 3mmd was solved by V.Solomon, G.Zolotnitsky, H.Feinberg, O.Tabachnikov, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.241, 61.856, 89.066, 90.00, 119.20, 90.00
R / Rfree (%) 21.4 / 23.6

Other elements in 3mmd:

The structure of Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose (pdb code 3mmd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose, PDB code: 3mmd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3mmd

Go back to Sodium Binding Sites List in 3mmd
Sodium binding site 1 out of 3 in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose


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 the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:13.4
occ:1.00
 O A:HOH556 2.2 25.1 1.0
OD1 A:ASP297 2.3 24.0 1.0
O A:ALA374 2.3 18.9 1.0
O A:LYS379 2.4 28.0 1.0
O A:HOH520 2.5 22.8 1.0
O A:HOH584 2.5 26.5 1.0
OD1 A:ASP377 2.5 26.5 1.0
CG A:ASP297 3.5 23.8 1.0
C A:ALA374 3.5 18.7 1.0
CG A:ASP377 3.5 25.4 1.0
C A:LYS379 3.5 29.4 1.0
OD2 A:ASP377 3.7 27.0 1.0
CE A:LYS301 3.9 19.1 0.4
CB A:ASP297 4.2 21.0 1.0
OXT A:LYS379 4.3 30.8 1.0
N A:LYS379 4.3 28.8 1.0
CA A:ALA374 4.3 17.1 1.0
OD2 A:ASP297 4.4 25.8 1.0
O A:HOH688 4.4 32.0 1.0
CA A:ASP297 4.4 20.4 1.0
CA A:ILE375 4.4 18.1 1.0
N A:ILE375 4.4 18.3 1.0
O A:HOH598 4.4 29.9 1.0
CA A:LYS379 4.5 28.5 1.0
O A:ASP297 4.5 21.4 1.0
O A:ASP377 4.6 24.2 1.0
CG A:LYS301 4.6 17.9 0.4
NZ A:LYS301 4.8 18.7 0.4
C A:ASP377 4.9 25.2 1.0
CD A:LYS301 4.9 19.1 0.4
CB A:ASP377 4.9 25.1 1.0
C A:ASP297 4.9 19.8 1.0
CB A:ALA374 5.0 17.9 1.0

Sodium binding site 2 out of 3 in 3mmd

Go back to Sodium Binding Sites List in 3mmd
Sodium binding site 2 out of 3 in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose


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 the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:17.3
occ:1.00
 CL A:CL420 2.1 45.2 1.0
O A:HOH579 2.1 27.1 1.0
NE2 A:HIS322 2.1 23.9 1.0
OE1 A:GLU58 2.2 19.0 1.0
OE2 A:GLU58 2.5 18.1 1.0
CE1 A:HIS322 2.5 24.9 1.0
CD A:GLU58 2.6 19.0 1.0
CD2 A:HIS322 3.4 22.8 1.0
O3B A:XYP451 3.8 23.7 1.0
ND1 A:HIS322 3.8 23.9 1.0
OE2 A:GLU35 3.8 19.1 1.0
CG A:GLU58 4.0 16.1 1.0
O A:HOH680 4.0 26.6 1.0
CG A:GLU35 4.1 14.9 1.0
O A:HOH521 4.2 18.9 1.0
CG A:HIS322 4.2 22.1 1.0
O A:HOH749 4.3 41.8 1.0
CD A:GLU35 4.4 17.5 1.0
ND2 A:ASN59 4.4 18.0 1.0
CB A:GLU58 4.8 16.4 1.0
O4B A:XYP451 4.8 27.7 1.0
O A:HOH551 4.9 21.4 1.0
C3B A:XYP451 5.0 27.9 1.0

Sodium binding site 3 out of 3 in 3mmd

Go back to Sodium Binding Sites List in 3mmd
Sodium binding site 3 out of 3 in the Crystal Structure of the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose


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 the W241A Mutant of Xylanase From Geobacillus Stearothermophilus T-6 (XT6) Complexed with Hydrolyzed Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:20.2
occ:1.00
 OD2 A:ASP282 2.1 23.4 1.0
O A:HOH685 2.1 31.0 1.0
OD1 A:ASP282 2.6 23.0 1.0
CG A:ASP282 2.7 21.0 1.0
O A:HOH557 3.6 25.6 1.0
O A:HOH806 3.8 29.2 1.0
O A:HOH790 4.1 44.1 1.0
CB A:ASP282 4.1 20.9 1.0
O A:HOH581 4.2 40.9 1.0
N A:ASP282 4.6 20.7 1.0
CD2 A:TYR281 4.6 22.6 1.0
CA A:ASP282 4.7 21.4 1.0
CB A:TYR281 4.8 21.1 1.0

Reference:

V.Solomon, G.Zolotnitsky, H.Feinberg, O.Tabachnikov, Y.Shoham, G.Shoham. Structural-Based Rational Mutagenesis of Xylanases From G.Stearothermophilus To Be Published.
Page generated: Mon Oct 7 11:31:34 2024

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