Sodium in PDB 8vg9: Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)

Protein crystallography data

The structure of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A), PDB code: 8vg9 was solved by M.M.Vacilotto, E.A.Araujo, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.05 / 1.37
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.62, 55.019, 63.329, 90, 95.16, 90
R / Rfree (%) 14 / 16.4

Other elements in 8vg9:

The structure of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) (pdb code 8vg9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A), PDB code: 8vg9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8vg9

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Sodium binding site 1 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:14.9
occ:1.00
 O A:TRP284 2.8 8.1 1.0
O A:THR246 2.8 8.4 1.0
NH1 A:ARG64 3.0 8.4 1.0
CD A:ARG64 3.2 7.5 1.0
CG A:GLU247 3.4 7.8 1.0
CB A:GLU247 3.4 7.6 1.0
CB A:MET32 3.5 8.3 0.0
CA A:GLU247 3.6 7.7 1.0
C A:TRP284 3.6 7.6 1.0
CB A:MET32 3.7 7.8 1.0
CA A:TRP285 3.8 6.9 1.0
CG1 A:VAL283 3.9 9.7 1.0
C A:THR246 3.9 7.5 1.0
CZ A:ARG64 3.9 7.5 1.0
NE A:ARG64 4.0 7.7 1.0
N A:TRP285 4.0 8.4 1.0
CE3 A:TRP285 4.0 8.3 1.0
O A:VAL283 4.2 8.7 1.0
SD A:MET32 4.2 9.4 1.0
N A:GLU247 4.2 6.8 1.0
N A:MET32 4.2 8.2 1.0
N A:MET32 4.3 8.2 0.0
CB A:ARG64 4.3 7.6 1.0
CG A:MET32 4.3 9.0 0.0
CA A:MET32 4.3 7.7 0.0
CG A:ARG64 4.3 6.8 1.0
CA A:MET32 4.4 7.3 1.0
CG A:MET32 4.4 9.3 1.0
CD A:GLU247 4.4 8.3 1.0
OE1 A:GLU247 4.5 8.2 1.0
C A:VAL283 4.6 8.2 1.0
SD A:MET32 4.6 8.6 0.0
C A:TRP285 4.6 7.5 1.0
CB A:VAL283 4.7 8.1 1.0
CZ3 A:TRP285 4.7 8.5 1.0
O A:TRP285 4.8 8.4 1.0
C A:GLY31 4.8 8.3 1.0
CB A:TRP285 4.8 8.4 1.0
C A:GLU247 4.8 8.1 1.0
CA A:TRP284 4.9 8.5 1.0
N A:TRP284 4.9 8.2 1.0
CD2 A:TRP285 5.0 8.2 1.0

Sodium binding site 2 out of 8 in 8vg9

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Sodium binding site 2 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:20.1
occ:1.00
 N A:GLU262 3.0 10.6 1.0
C A:TRP260 3.3 10.9 1.0
N A:PRO261 3.3 11.7 1.0
O A:TRP260 3.3 12.3 1.0
CB A:GLU262 3.4 10.9 1.0
CD A:PRO261 3.4 11.9 1.0
CG2 A:THR259 3.6 12.3 1.0
CA A:GLU262 3.7 10.1 1.0
N A:TRP260 3.9 11.1 1.0
C A:PRO261 4.0 10.7 1.0
CA A:TRP260 4.0 10.9 1.0
CA A:PRO261 4.2 10.9 1.0
CG A:PRO261 4.2 12.5 1.0
O A:HOH662 4.3 24.9 1.0
C A:THR259 4.4 10.7 1.0
O A:HOH1021 4.6 27.5 1.0
CG A:GLU262 4.6 12.8 1.0
O A:THR259 4.8 11.5 1.0
O A:HOH643 4.9 30.3 1.0
CB A:THR259 4.9 12.6 1.0
CB A:PRO261 4.9 11.6 1.0

Sodium binding site 3 out of 8 in 8vg9

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Sodium binding site 3 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:14.8
occ:1.00
 O A:HOH1007 2.7 12.4 1.0
O A:VAL67 2.8 9.0 1.0
N A:TRP96 2.9 8.0 1.0
N A:GLU97 3.0 9.2 1.0
CE1 A:PHE66 3.4 8.8 1.0
O A:HOH725 3.4 10.1 1.0
CD A:PRO69 3.5 10.4 1.0
CA A:TRP96 3.5 8.2 1.0
O A:GLU97 3.5 9.1 1.0
CB A:TRP96 3.5 9.8 1.0
CG A:PRO69 3.7 13.2 1.0
CZ A:PHE66 3.7 9.8 1.0
C A:TRP96 3.7 7.6 1.0
C A:PRO95 3.9 7.4 1.0
C A:VAL67 4.0 8.6 1.0
CA A:PRO95 4.0 8.1 1.0
CA A:GLU97 4.0 9.4 1.0
N A:PRO69 4.1 10.0 1.0
C A:GLU97 4.2 10.2 1.0
CD1 A:PHE66 4.3 9.1 1.0
CB A:GLU97 4.4 10.8 1.0
CA A:ASN68 4.5 9.1 1.0
C A:ASN68 4.5 9.9 1.0
O A:HOH1039 4.6 16.1 1.0
CB A:PRO95 4.6 9.4 1.0
CG A:TRP96 4.6 8.6 1.0
N A:ASN68 4.7 8.6 1.0
CE3 A:TRP96 4.7 8.7 1.0
CG A:GLU97 4.7 11.1 1.0
CE2 A:PHE66 4.8 9.2 1.0
CB A:PRO69 4.8 11.7 1.0
CA A:PRO69 4.8 10.7 1.0
O A:TRP96 4.9 8.6 1.0
CA A:VAL67 5.0 8.1 1.0

Sodium binding site 4 out of 8 in 8vg9

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Sodium binding site 4 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:29.4
occ:1.00
 O A:HOH642 3.1 27.5 1.0
O A:ALA103 3.5 17.4 1.0
C A:ALA103 3.8 13.8 1.0
O A:LEU102 3.9 14.6 1.0
ND2 A:ASN118 3.9 13.1 1.0
CB A:GLU104 4.0 12.9 1.0
CG A:PRO115 4.0 16.9 1.0
C A:LEU102 4.1 12.7 1.0
N A:GLU104 4.1 10.2 1.0
O A:ASN101 4.3 16.2 1.0
CA A:GLU104 4.3 10.3 1.0
N A:ALA103 4.3 12.2 1.0
CD A:PRO115 4.5 12.3 1.0
CA A:ALA103 4.6 12.9 1.0
OE1 A:GLU104 4.7 13.2 1.0
CA A:LEU102 4.7 12.0 1.0
CG A:GLU104 4.9 12.7 1.0
C A:ASN101 5.0 14.9 1.0

Sodium binding site 5 out of 8 in 8vg9

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Sodium binding site 5 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:32.6
occ:1.00
 O A:TYR23 2.7 13.4 1.0
OG1 A:THR25 2.9 17.2 1.0
N A:THR25 3.3 11.2 1.0
O A:HOH745 3.5 27.5 1.0
C A:GLN24 3.6 9.9 1.0
C A:TYR23 3.9 11.3 1.0
CB A:THR25 3.9 15.2 1.0
CA A:GLN24 3.9 10.1 1.0
CA A:THR25 4.0 12.9 1.0
CG1 A:VAL319 4.2 15.0 1.0
O A:GLN24 4.2 11.8 1.0
N A:GLN24 4.4 10.5 1.0
CG2 A:VAL319 4.7 15.8 1.0
O A:HOH974 4.7 30.1 1.0
OE1 A:GLU22 4.8 31.8 1.0
CB A:VAL319 5.0 11.8 1.0

Sodium binding site 6 out of 8 in 8vg9

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Sodium binding site 6 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:33.6
occ:1.00
 O A:HOH916 2.3 30.9 1.0
O A:ALA89 2.6 13.8 1.0
O A:HOH684 2.9 15.5 1.0
O A:HOH935 3.1 26.5 1.0
C A:ALA89 3.7 11.6 1.0
CB A:ALA85 3.7 16.7 1.0
O A:HOH953 3.8 32.2 1.0
CA A:ALA85 3.9 16.6 1.0
CA A:LYS90 4.1 10.2 1.0
N A:LYS90 4.3 10.1 1.0
O A:ALA85 4.4 16.5 1.0
O A:ASP139 4.4 16.6 1.0
N A:VAL91 4.5 9.4 1.0
CG2 A:VAL91 4.6 10.9 1.0
C A:ALA85 4.6 16.9 1.0
C A:LYS90 4.7 9.4 1.0
N A:ALA89 4.8 13.6 1.0
CA A:ALA89 4.9 12.0 1.0
C A:GLY88 4.9 13.9 1.0

Sodium binding site 7 out of 8 in 8vg9

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Sodium binding site 7 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:15.6
occ:1.00
 O A:PHE66 2.7 8.7 1.0
O A:HOH645 2.7 12.6 1.0
N A:ASN68 2.8 8.6 1.0
CD1 A:TRP74 3.3 10.3 1.0
CB A:ASN68 3.4 11.1 1.0
CE1 A:PHE129 3.5 10.4 1.0
CA A:TRP74 3.6 10.1 1.0
C A:PHE66 3.6 7.9 1.0
CA A:VAL67 3.7 8.1 1.0
C A:VAL67 3.7 8.6 1.0
CA A:ASN68 3.8 9.1 1.0
N A:VAL67 4.1 8.2 1.0
CG A:TRP74 4.1 9.9 1.0
NE1 A:TRP74 4.2 10.2 1.0
O A:TRP74 4.2 10.8 1.0
CZ A:PHE129 4.2 9.1 1.0
CB A:TRP74 4.3 10.6 1.0
CB A:ALA77 4.3 10.6 1.0
O A:HOH735 4.3 11.1 1.0
O A:GLN73 4.3 11.9 1.0
N A:TRP74 4.3 11.1 1.0
C A:TRP74 4.4 10.5 1.0
CD1 A:PHE129 4.4 10.2 1.0
CD2 A:PHE66 4.5 8.8 1.0
C A:GLN73 4.6 10.9 1.0
OE2 A:GLU36 4.7 14.8 1.0
O A:ASN68 4.8 10.8 1.0
CA A:PHE66 4.8 7.5 1.0
C A:ASN68 4.8 9.9 1.0
CB A:PHE66 4.8 7.7 1.0
CG A:ASN68 4.8 10.5 1.0
O A:VAL67 4.9 9.0 1.0
CG A:PHE66 4.9 7.7 1.0

Sodium binding site 8 out of 8 in 8vg9

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Sodium binding site 8 out of 8 in the Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:19.3
occ:1.00
 O A:HOH829 2.8 19.9 1.0
N A:ALA121 3.0 10.4 1.0
O A:SER117 3.0 13.7 1.0
O A:HOH720 3.2 14.4 1.0
CA A:ASN118 3.4 9.8 1.0
N A:THR120 3.4 9.4 1.0
C A:ASN118 3.4 9.4 1.0
CB A:ALA121 3.6 11.0 1.0
CB A:THR120 3.6 10.5 1.0
O A:ASN118 3.7 10.4 1.0
CA A:THR120 3.7 9.7 1.0
C A:THR120 3.8 10.0 1.0
N A:TYR119 3.8 9.4 1.0
CA A:ALA121 3.9 11.0 1.0
O A:HOH861 3.9 17.6 1.0
C A:SER117 3.9 12.1 1.0
N A:ASN118 4.0 11.4 1.0
OG1 A:THR120 4.2 12.5 1.0
C A:TYR119 4.2 9.0 1.0
OD1 A:ASN118 4.4 15.5 1.0
CB A:ASN118 4.5 12.0 1.0
CA A:TYR119 4.7 9.9 1.0
CG2 A:THR120 4.7 12.0 1.0
CG A:ASN118 5.0 12.7 1.0
O A:THR120 5.0 10.9 1.0

Reference:

M.M.Vacilotto, E.A.Araujo, I.Polikarpov. Crystallographic Structure of Ruminococcus Champanellensis Xylanase (RCXYN30A) To Be Published.
Page generated: Sat Feb 8 23:45:24 2025

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