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Sodium in PDB 7dfo: Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose

Enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose

All present enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose, PDB code: 7dfo was solved by Z.Fujimoto, N.Kishine, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.06 / 2.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 142.709, 142.709, 72.454, 90, 90, 120
R / Rfree (%) 16.5 / 21.8

Other elements in 7dfo:

The structure of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose also contains other interesting chemical elements:

Chlorine (Cl) 43 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose (pdb code 7dfo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose, PDB code: 7dfo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 7dfo

Go back to Sodium Binding Sites List in 7dfo
Sodium binding site 1 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:38.3
occ:1.00
 O A:HOH565 2.3 33.6 1.0
O A:HOH614 2.3 33.6 1.0
O A:GLY162 2.3 25.6 1.0
O A:HOH563 2.4 39.6 1.0
O A:HOH590 2.5 48.0 1.0
O A:HOH607 3.1 40.9 1.0
C A:GLY162 3.5 27.3 1.0
CA A:MET163 4.2 24.9 1.0
N A:MET163 4.2 24.6 1.0
O A:HOH513 4.3 30.4 1.0
O A:HOH611 4.4 41.5 1.0
O A:HOH616 4.4 27.4 1.0
O A:HOH589 4.4 20.5 1.0
NE2 A:GLN118 4.5 29.9 1.0
N A:GLN164 4.5 26.1 1.0
OH A:TYR136 4.6 27.8 1.0
CA A:GLY162 4.7 27.6 1.0
C A:MET163 4.9 26.1 1.0

Sodium binding site 2 out of 13 in 7dfo

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Sodium binding site 2 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:40.7
occ:1.00
 O B:SER70 2.0 42.7 1.0
C B:SER70 3.2 42.9 1.0
N B:SER182 3.3 24.7 1.0
O B:HOH442 3.8 38.5 1.0
CA B:SER181 3.8 28.1 1.0
CB B:SER70 3.8 38.1 1.0
C B:SER181 3.9 27.7 1.0
CB B:SER182 4.0 26.3 1.0
OG B:SER182 4.1 26.9 1.0
N B:GLY71 4.2 38.0 1.0
CA B:SER70 4.2 41.4 1.0
CB B:SER181 4.2 28.0 1.0
CA B:SER182 4.2 26.7 1.0
CA B:GLY71 4.3 35.9 1.0
O B:SER182 4.4 29.2 1.0
O B:HOH416 4.6 36.5 1.0
C B:SER182 4.8 27.2 1.0
O B:GLN180 4.9 29.6 1.0
O B:SER181 5.0 28.8 1.0

Sodium binding site 3 out of 13 in 7dfo

Go back to Sodium Binding Sites List in 7dfo
Sodium binding site 3 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na307

b:43.3
occ:1.00
 O C:HOH412 2.1 37.6 1.0
O C:GLY24 2.2 42.0 1.0
O C:ASN43 2.4 31.2 1.0
OD1 C:ASN43 2.5 39.9 1.0
CG C:ASN43 3.3 41.3 1.0
C C:GLY24 3.3 40.9 1.0
C C:ASN43 3.4 29.6 1.0
CA C:GLY25 3.7 36.4 1.0
CB C:ASN43 3.8 35.8 1.0
O C:CYS44 3.9 28.0 1.0
N C:GLY25 3.9 37.1 1.0
C C:CYS44 4.2 29.6 1.0
CA C:ASN43 4.2 31.1 1.0
ND2 C:ASN43 4.3 42.6 1.0
N C:CYS44 4.4 30.8 1.0
CA C:GLY24 4.5 45.3 1.0
CA C:CYS44 4.6 30.6 1.0
N C:GLY45 4.7 29.2 1.0
O C:HOH493 4.8 36.8 1.0

Sodium binding site 4 out of 13 in 7dfo

Go back to Sodium Binding Sites List in 7dfo
Sodium binding site 4 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:45.5
occ:1.00
 O D:HOH471 2.1 35.9 1.0
O D:GLY65 2.3 31.7 1.0
O D:THR145 2.3 37.2 1.0
C D:GLY65 3.5 30.4 1.0
C D:THR145 3.5 35.0 1.0
N D:GLY65 3.5 31.2 1.0
CG2 D:THR145 3.9 41.3 1.0
CB D:THR145 3.9 38.2 1.0
CA D:GLY65 4.0 29.5 1.0
CA D:THR145 4.3 36.3 1.0
N D:GLY146 4.5 33.0 1.0
CA D:GLY146 4.6 34.2 1.0
C D:SER64 4.6 31.1 1.0
N D:SER66 4.6 29.5 1.0
CA D:SER64 4.8 32.2 1.0
O D:HOH488 4.9 36.2 1.0
O D:HOH467 5.0 27.2 1.0

Sodium binding site 5 out of 13 in 7dfo

Go back to Sodium Binding Sites List in 7dfo
Sodium binding site 5 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na305

b:42.2
occ:1.00
 O D:ASN83 2.5 28.0 1.0
OG D:SER167 3.2 35.6 1.0
N D:SER167 3.6 30.7 1.0
C D:ASN83 3.6 29.2 1.0
O D:SER82 3.7 25.8 1.0
CA D:GLY166 3.8 31.4 1.0
CB D:ASN83 3.9 34.0 1.0
C D:GLY166 4.0 31.3 1.0
CB D:SER167 4.3 33.1 1.0
CA D:ASN83 4.3 30.2 1.0
CA D:SER167 4.4 29.8 1.0
N D:PRO84 4.6 25.9 1.0
C D:SER82 4.7 26.3 1.0
O D:HOH405 4.7 42.2 1.0
CD D:PRO84 4.8 27.8 1.0
N D:ASN83 4.9 29.1 1.0
O D:GLY166 5.0 29.1 1.0

Sodium binding site 6 out of 13 in 7dfo

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Sodium binding site 6 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na306

b:41.6
occ:1.00
 OD1 D:ASN55 2.1 42.0 1.0
OG D:SER54 2.4 26.0 1.0
O D:HOH487 2.7 33.8 1.0
CG D:ASN55 3.1 35.6 1.0
N D:ASN55 3.5 26.8 1.0
CB D:ASN55 3.6 31.7 1.0
CB D:SER54 3.6 25.0 1.0
O C:HOH432 3.9 39.5 1.0
C D:SER54 3.9 25.4 1.0
CA D:SER54 4.1 26.9 1.0
CA D:ASN55 4.1 27.9 1.0
ND2 D:ASN55 4.3 39.2 1.0
N D:SER54 4.4 25.7 1.0
O D:HOH481 4.5 26.3 1.0
O D:HOH497 4.5 38.6 1.0
O D:SER54 4.6 23.2 1.0

Sodium binding site 7 out of 13 in 7dfo

Go back to Sodium Binding Sites List in 7dfo
Sodium binding site 7 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na307

b:42.3
occ:1.00
 O D:SER70 2.1 39.6 1.0
O D:HOH460 2.4 51.1 1.0
C D:SER70 3.2 38.7 1.0
N D:SER182 3.4 29.4 1.0
CA D:SER181 3.7 29.7 1.0
OG D:SER70 3.8 48.7 1.0
C D:SER181 3.9 29.7 1.0
N D:GLY71 4.0 33.0 1.0
CA D:GLY71 4.0 31.1 1.0
OG D:SER182 4.1 29.0 1.0
CB D:SER181 4.1 31.6 1.0
CB D:SER182 4.1 29.9 1.0
O D:HOH501 4.2 47.8 1.0
CB D:SER70 4.2 40.0 1.0
CA D:SER70 4.3 38.3 1.0
CA D:SER182 4.3 29.4 1.0
O D:SER182 4.5 30.4 1.0
O D:HOH440 4.6 37.0 1.0
O D:GLN180 4.8 34.5 1.0
C D:SER182 4.9 30.0 1.0
N D:SER181 5.0 30.0 1.0
O D:SER181 5.0 26.7 1.0

Sodium binding site 8 out of 13 in 7dfo

Go back to Sodium Binding Sites List in 7dfo
Sodium binding site 8 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na306

b:44.2
occ:1.00
 O E:HOH441 2.2 26.6 1.0
O E:HOH440 2.2 39.4 1.0
O E:GLY162 2.4 36.7 1.0
O E:HOH457 2.7 48.5 1.0
C E:GLY162 3.6 32.3 1.0
CA E:MET163 4.1 30.4 1.0
N E:MET163 4.3 29.8 1.0
NE2 E:GLN118 4.3 39.6 1.0
CL E:CL303 4.3 41.5 1.0
N E:GLN164 4.4 31.1 1.0
O E:HOH499 4.4 31.4 1.0
O E:HOH411 4.5 36.8 1.0
OH E:TYR136 4.5 32.8 1.0
CA E:GLY162 4.8 34.3 1.0
C E:MET163 4.8 30.6 1.0
O E:HOH417 4.8 30.8 1.0

Sodium binding site 9 out of 13 in 7dfo

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Sodium binding site 9 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:44.4
occ:1.00
 O F:SER70 2.2 44.5 1.0
O F:HOH408 3.3 34.8 1.0
C F:SER70 3.3 47.1 1.0
N F:SER182 3.4 29.3 1.0
CA F:SER181 3.9 31.8 1.0
CB F:SER70 4.0 47.5 1.0
C F:SER181 4.0 31.4 1.0
OG F:SER182 4.1 31.5 1.0
CB F:SER181 4.2 32.8 1.0
CB F:SER182 4.2 31.3 1.0
N F:GLY71 4.2 46.7 1.0
CA F:SER70 4.3 48.1 1.0
CA F:GLY71 4.3 45.8 1.0
CA F:SER182 4.4 29.0 1.0
O F:SER182 4.7 33.3 1.0
O F:HOH434 4.9 46.8 1.0
O F:GLN180 4.9 32.0 1.0
C F:SER182 5.0 32.2 1.0

Sodium binding site 10 out of 13 in 7dfo

Go back to Sodium Binding Sites List in 7dfo
Sodium binding site 10 out of 13 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with 4-O-Methyl-Alpha-D- Glucuronopyranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na311

b:50.3
occ:1.00
 O I:ALA1 2.4 42.7 1.0
C I:ALA1 3.5 51.1 1.0
O I:HOH458 3.8 43.7 1.0
CG2 I:VAL3 4.2 39.6 1.0
N I:ALA1 4.4 51.7 1.0
N I:THR2 4.4 44.3 1.0
CA I:ALA1 4.5 50.5 1.0
CA I:THR2 4.5 40.8 1.0
N I:VAL3 4.7 35.5 1.0
CB I:ALA1 4.9 49.8 1.0
C I:THR2 5.0 37.7 1.0

Reference:

Z.Fujimoto, K.Naomi, K.Teramoto, S.Tsutsui, S.Kaneko. Structure-Based Substrate Specificity of GH11 Xylanase From Streptomyces Olivaceoviridis E-86 To Be Published.
Page generated: Tue Oct 8 16:34:51 2024

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