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Sodium in PDB 5cxp: X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum

Protein crystallography data

The structure of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum, PDB code: 5cxp was solved by F.J.St John, E.Pozharski, J.C.Hurlbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.77
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.483, 91.866, 141.251, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21

Other elements in 5cxp:

The structure of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum (pdb code 5cxp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum, PDB code: 5cxp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5cxp

Go back to Sodium Binding Sites List in 5cxp
Sodium binding site 1 out of 7 in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:17.4
occ:1.00
 O A:SER291 2.4 11.1 1.0
O A:ILE294 2.4 14.0 1.0
O A:HOH786 2.4 14.2 1.0
O A:HOH981 2.4 17.7 1.0
O A:HOH728 2.4 15.4 1.0
O A:HOH938 2.4 15.6 1.0
C A:ILE294 3.5 14.9 1.0
C A:SER291 3.6 11.2 1.0
NA A:NA603 3.6 19.6 1.0
OD2 A:ASP45 3.7 14.2 1.0
O A:HOH931 3.9 26.2 1.0
CA A:GLY295 4.0 17.4 1.0
O A:HOH1053 4.1 25.6 1.0
N A:GLY295 4.2 15.0 1.0
OG A:SER291 4.3 12.5 1.0
N A:ILE294 4.4 12.6 1.0
CA A:SER291 4.4 11.0 1.0
C A:LYS292 4.4 11.7 1.0
O A:GLY43 4.4 10.8 1.0
O A:LYS292 4.5 11.7 1.0
O A:HOH1080 4.5 33.5 1.0
N A:LYS292 4.5 10.8 1.0
CA A:ILE294 4.5 13.0 1.0
O A:HOH1047 4.6 24.5 1.0
O A:HOH1144 4.6 16.1 1.0
C A:GLY295 4.6 20.5 1.0
CA A:LYS292 4.6 11.4 1.0
CG A:ASP45 4.8 15.3 1.0
N A:PHE293 4.8 11.4 1.0
O A:GLY295 4.9 19.8 1.0
CB A:SER291 5.0 10.9 1.0
C A:PHE293 5.0 12.8 1.0

Sodium binding site 2 out of 7 in 5cxp

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Sodium binding site 2 out of 7 in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:32.3
occ:1.00
 O A:HOH739 2.4 20.0 1.0
O A:HOH988 2.4 20.0 1.0
O A:HOH960 2.6 16.1 1.0
O A:HOH1070 2.6 34.2 1.0
O A:HOH814 3.9 27.6 1.0
O A:ALA145 3.9 13.4 1.0
NA A:NA606 3.9 31.2 1.0
OD2 A:ASP147 4.0 23.3 0.5
O A:HOH890 4.2 6.7 0.5
N A:ASN103 4.4 13.4 1.0
CL A:CL608 4.4 17.1 1.0
O A:GLY101 4.6 12.5 1.0
O A:HOH1087 4.6 43.3 1.0
CA A:ALA102 4.7 14.1 1.0
CG A:ASP147 4.8 17.8 0.5
OD1 A:ASP147 4.9 15.6 0.5
O A:HOH716 4.9 45.5 1.0

Sodium binding site 3 out of 7 in 5cxp

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Sodium binding site 3 out of 7 in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:19.6
occ:1.00
 O A:HOH779 2.2 27.8 1.0
O A:HOH1080 2.4 33.5 1.0
O A:HOH966 2.4 22.7 1.0
O A:HOH981 2.4 17.7 1.0
OD2 A:ASP45 2.5 14.2 1.0
O A:HOH786 2.9 14.2 1.0
CG A:ASP45 3.3 15.3 1.0
CB A:ASP45 3.4 13.2 1.0
O A:HOH842 3.5 40.1 1.0
NA A:NA601 3.6 17.4 1.0
NA A:NA604 3.6 26.1 1.0
OD1 A:ASN296 3.8 30.5 1.0
O A:HOH1053 4.0 25.6 1.0
O A:HOH728 4.1 15.4 1.0
O A:HOH800 4.4 18.4 1.0
O A:HOH1047 4.5 24.5 1.0
O A:GLY79 4.5 15.0 1.0
OD1 A:ASP45 4.5 16.9 1.0
O A:HOH925 4.6 15.0 1.0
O A:HOH902 4.7 19.0 1.0
O A:HOH1056 4.7 35.4 1.0
O A:HOH1144 4.7 16.1 1.0
O A:GLY43 4.8 10.8 1.0
O A:HOH938 4.9 15.6 1.0
CA A:ASP45 4.9 11.9 1.0
CG A:ASN296 4.9 27.1 1.0
O A:HOH989 4.9 28.5 1.0

Sodium binding site 4 out of 7 in 5cxp

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Sodium binding site 4 out of 7 in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:26.1
occ:1.00
 O A:HOH1053 2.1 25.6 1.0
O A:HOH989 2.4 28.5 1.0
O A:ARG18 2.5 15.9 1.0
OD2 A:ASP45 2.5 14.2 1.0
O A:HOH925 2.5 15.0 1.0
O A:HOH779 2.8 27.8 1.0
CG A:ASP45 3.2 15.3 1.0
C A:ARG18 3.5 13.3 1.0
OD1 A:ASP45 3.6 16.9 1.0
NA A:NA603 3.6 19.6 1.0
O A:HOH981 3.7 17.7 1.0
O A:HOH1026 3.7 36.7 1.0
OD1 A:ASN296 3.9 30.5 1.0
CA A:GLY19 4.0 10.8 1.0
O A:HOH800 4.0 18.4 1.0
O A:HOH768 4.0 31.6 1.0
O A:HOH728 4.0 15.4 1.0
N A:GLY19 4.1 11.1 1.0
CB A:ASP45 4.2 13.2 1.0
O A:HOH931 4.2 26.2 1.0
CA A:ARG18 4.6 14.1 1.0
O A:ASP45 4.9 10.2 1.0

Sodium binding site 5 out of 7 in 5cxp

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Sodium binding site 5 out of 7 in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:31.6
occ:1.00
 O A:HOH1018 2.3 23.9 1.0
O A:HOH770 2.3 40.6 1.0
OG A:SER349 2.4 20.1 0.5
O A:ASN347 2.5 20.3 1.0
O A:HOH929 2.6 40.9 1.0
O A:VAL386 2.7 14.1 1.0
OG A:SER349 3.4 19.6 0.5
CB A:SER349 3.5 18.5 0.5
C A:VAL386 3.6 14.9 1.0
N A:SER349 3.6 16.7 1.0
C A:ASN347 3.7 22.4 1.0
CB A:SER349 3.7 18.5 0.5
O A:HOH724 4.1 23.2 1.0
CA A:ALA387 4.1 17.3 1.0
C A:VAL348 4.2 21.3 1.0
CA A:SER349 4.2 17.1 0.5
N A:ALA387 4.2 16.1 1.0
O A:HOH1073 4.2 28.8 1.0
CA A:SER349 4.3 17.2 0.5
CB A:VAL386 4.3 13.0 1.0
CA A:VAL348 4.4 21.6 1.0
CG1 A:VAL386 4.4 13.8 1.0
OD1 A:ASN347 4.4 28.6 0.4
N A:VAL348 4.5 19.4 1.0
CA A:VAL386 4.6 13.3 1.0
CB A:ASN347 4.6 25.4 0.4
CB A:ASN347 4.6 22.6 0.6
CG A:ASN347 4.6 29.5 0.4
C A:ALA387 4.8 17.6 1.0
CA A:ASN347 4.8 21.7 0.6
CA A:ASN347 4.8 23.1 0.4
N A:ASP388 4.9 17.9 1.0
O A:VAL348 4.9 20.6 1.0

Sodium binding site 6 out of 7 in 5cxp

Go back to Sodium Binding Sites List in 5cxp
Sodium binding site 6 out of 7 in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:31.2
occ:1.00
 O A:HOH988 2.3 20.0 1.0
O A:HOH814 2.3 27.6 1.0
O A:HOH1105 2.7 22.0 1.0
O A:HOH1070 2.9 34.2 1.0
NA A:NA602 3.9 32.3 1.0
O A:HOH739 4.4 20.0 1.0
O A:HOH776 4.6 19.0 1.0
O A:ALA145 4.7 13.4 1.0
OD2 A:ASP147 4.8 23.3 0.5
O A:HOH949 4.8 13.4 1.0
O A:HOH714 4.8 23.7 1.0

Sodium binding site 7 out of 7 in 5cxp

Go back to Sodium Binding Sites List in 5cxp
Sodium binding site 7 out of 7 in the X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of X-Ray Crystallographic Protein Structure of the Glycoside Hydrolase Family 30 Subfamily 8 Xylanase, XYN30A, From Clostridium Acetobutylicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:14.5
occ:1.00
 O10 A:P6G622 2.3 22.4 1.0
O7 A:P6G622 2.4 20.9 1.0
OE2 A:GLU141 2.4 8.8 1.0
OE2 A:GLU230 2.4 9.8 1.0
OE1 A:GLU141 2.5 12.6 1.0
O4 A:P6G622 2.6 15.4 1.0
CD A:GLU141 2.8 10.6 1.0
C6 A:P6G622 3.1 17.6 1.0
C8 A:P6G622 3.3 21.1 1.0
C5 A:P6G622 3.3 17.4 1.0
C9 A:P6G622 3.3 20.9 1.0
C11 A:P6G622 3.3 26.3 1.0
CD A:GLU230 3.4 9.5 1.0
CE2 A:TYR209 3.6 9.0 1.0
OE1 A:GLU230 3.6 9.4 1.0
CZ A:TYR209 3.9 8.8 1.0
OH A:TYR209 3.9 8.8 1.0
C12 A:P6G622 4.1 29.4 1.0
O A:HOH764 4.2 11.7 1.0
CG A:GLU141 4.2 10.1 1.0
CD2 A:TYR209 4.3 8.8 1.0
ND1 A:HIS207 4.3 8.5 0.5
OH A:TYR148 4.3 15.4 1.0
CD2 A:HIS207 4.5 9.7 0.5
ND2 A:ASN140 4.6 10.2 1.0
CE1 A:HIS207 4.7 8.7 0.5
CG A:GLU230 4.7 9.1 1.0
CE1 A:TYR209 4.9 9.2 1.0
O13 A:P6G623 4.9 23.8 0.5
OD1 A:ASN140 5.0 10.8 1.0

Reference:

J.F.St John, D.Dietrich, P.Bologna, J.C.Hurlbert, E.P.Pozharski, C.Crooks. Crystal Structure of A GH30 Xylanase To Be Published.
Page generated: Tue Dec 15 10:47:01 2020

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