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:
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
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_01_stereo.jpg) 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
Go back to
Sodium Binding Sites List in 5cxp
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
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_02_stereo.jpg) 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
Go back to
Sodium Binding Sites List in 5cxp
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
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_03_stereo.jpg) 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
Go back to
Sodium Binding Sites List in 5cxp
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
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_04_stereo.jpg) 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
Go back to
Sodium Binding Sites List in 5cxp
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
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_05.jpg) Mono view
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_05_stereo.jpg) 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
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_06.jpg) Mono view
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_06_stereo.jpg) 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
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_07.jpg) Mono view
![](/pictures/NA/pdb/cx/5cxp-NA-sphere_07_stereo.jpg) 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
|
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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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