Sodium in PDB 3zx3: Crystal Structure and Domain Rotation of NTPDASE1 CD39
Enzymatic activity of Crystal Structure and Domain Rotation of NTPDASE1 CD39
All present enzymatic activity of Crystal Structure and Domain Rotation of NTPDASE1 CD39:
3.6.1.5;
Protein crystallography data
The structure of Crystal Structure and Domain Rotation of NTPDASE1 CD39, PDB code: 3zx3
was solved by
M.Zebisch,
P.Schaefer,
N.Straeter,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
146.62 /
1.70
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
163.133,
81.136,
165.465,
90.00,
117.61,
90.00
|
R / Rfree (%)
|
17.6 /
23.3
|
Other elements in 3zx3:
The structure of Crystal Structure and Domain Rotation of NTPDASE1 CD39 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure and Domain Rotation of NTPDASE1 CD39
(pdb code 3zx3). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Crystal Structure and Domain Rotation of NTPDASE1 CD39, PDB code: 3zx3:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 3zx3
Go back to
Sodium Binding Sites List in 3zx3
Sodium binding site 1 out
of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na521
b:51.8
occ:1.00
|
OD1
|
B:ASN429
|
2.4
|
64.9
|
1.0
|
O
|
B:GLN426
|
2.5
|
52.7
|
1.0
|
O
|
B:ALA343
|
2.6
|
38.3
|
1.0
|
O
|
B:GLY427
|
2.7
|
43.1
|
1.0
|
O
|
B:CYS342
|
3.2
|
44.9
|
1.0
|
CG
|
B:ASN429
|
3.5
|
59.4
|
1.0
|
C
|
B:GLY427
|
3.5
|
41.2
|
1.0
|
C
|
B:ALA343
|
3.6
|
37.5
|
1.0
|
C
|
B:GLN426
|
3.7
|
47.6
|
1.0
|
CA
|
B:ALA343
|
3.9
|
37.6
|
1.0
|
ND2
|
B:ASN429
|
3.9
|
58.2
|
1.0
|
CA
|
B:GLY427
|
4.0
|
40.3
|
1.0
|
C
|
B:CYS342
|
4.2
|
41.2
|
1.0
|
O
|
B:HOH2152
|
4.2
|
50.1
|
1.0
|
OXT
|
B:ACY512
|
4.3
|
57.3
|
1.0
|
N
|
B:GLY427
|
4.3
|
41.8
|
1.0
|
ND2
|
B:ASN334
|
4.3
|
54.0
|
1.0
|
N
|
B:ASN429
|
4.5
|
41.4
|
1.0
|
N
|
B:ALA343
|
4.5
|
37.1
|
1.0
|
O
|
B:HOH2123
|
4.6
|
59.4
|
1.0
|
N
|
B:TYR428
|
4.6
|
38.9
|
1.0
|
CB
|
B:ASN429
|
4.7
|
56.8
|
1.0
|
N
|
B:PHE344
|
4.8
|
33.1
|
1.0
|
CA
|
B:GLN426
|
4.9
|
44.5
|
1.0
|
CA
|
B:ASN429
|
4.9
|
48.3
|
1.0
|
|
Sodium binding site 2 out
of 5 in 3zx3
Go back to
Sodium Binding Sites List in 3zx3
Sodium binding site 2 out
of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na521
b:52.5
occ:1.00
|
O
|
C:PHE332
|
2.5
|
36.8
|
1.0
|
O
|
C:LEU329
|
2.6
|
38.6
|
1.0
|
O
|
C:HOH2136
|
2.7
|
55.1
|
1.0
|
O
|
C:HOH2137
|
2.9
|
43.5
|
1.0
|
C
|
C:LEU329
|
3.5
|
39.1
|
1.0
|
C
|
C:PHE332
|
3.6
|
35.2
|
1.0
|
CA
|
C:LYS330
|
4.1
|
41.0
|
1.0
|
N
|
C:LYS330
|
4.1
|
36.7
|
1.0
|
OD1
|
C:ASN334
|
4.3
|
40.5
|
1.0
|
N
|
C:PHE332
|
4.4
|
34.7
|
1.0
|
CB
|
C:LEU329
|
4.4
|
35.2
|
1.0
|
CA
|
C:PHE332
|
4.4
|
35.1
|
1.0
|
C
|
C:LYS330
|
4.4
|
38.2
|
1.0
|
CA
|
C:LEU329
|
4.4
|
35.0
|
1.0
|
O
|
C:LYS330
|
4.5
|
40.1
|
1.0
|
O
|
C:HOH2051
|
4.5
|
52.4
|
1.0
|
CB
|
C:PHE332
|
4.5
|
33.1
|
1.0
|
N
|
C:ASN333
|
4.6
|
35.2
|
1.0
|
N
|
C:ASN334
|
4.6
|
37.8
|
1.0
|
CA
|
C:ASN333
|
4.6
|
36.8
|
1.0
|
CD
|
C:LYS330
|
4.7
|
67.1
|
1.0
|
|
Sodium binding site 3 out
of 5 in 3zx3
Go back to
Sodium Binding Sites List in 3zx3
Sodium binding site 3 out
of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na522
b:29.3
occ:1.00
|
O
|
C:HOH2155
|
2.4
|
31.0
|
1.0
|
O
|
C:ALA343
|
2.4
|
27.8
|
1.0
|
OD1
|
C:ASN429
|
2.4
|
26.8
|
1.0
|
O
|
C:GLY427
|
2.5
|
29.0
|
1.0
|
O
|
C:GLN426
|
2.5
|
27.7
|
1.0
|
O
|
C:CYS342
|
2.6
|
26.5
|
1.0
|
C
|
C:GLY427
|
3.3
|
27.2
|
1.0
|
CG
|
C:ASN429
|
3.3
|
27.9
|
1.0
|
C
|
C:ALA343
|
3.3
|
26.5
|
1.0
|
CA
|
C:ALA343
|
3.5
|
26.0
|
1.0
|
C
|
C:CYS342
|
3.6
|
25.9
|
1.0
|
C
|
C:GLN426
|
3.6
|
26.6
|
1.0
|
ND2
|
C:ASN429
|
3.6
|
27.1
|
1.0
|
CA
|
C:GLY427
|
3.6
|
27.2
|
1.0
|
N
|
C:ALA343
|
4.0
|
24.6
|
1.0
|
N
|
C:GLY427
|
4.0
|
26.7
|
1.0
|
O
|
C:HOH2154
|
4.2
|
30.0
|
1.0
|
O
|
C:HOH2186
|
4.4
|
29.4
|
1.0
|
N
|
C:TYR428
|
4.4
|
23.8
|
1.0
|
O
|
C:HOH2187
|
4.4
|
51.7
|
1.0
|
ND2
|
C:ASN334
|
4.4
|
33.7
|
1.0
|
N
|
C:ASN429
|
4.5
|
23.9
|
1.0
|
N
|
C:PHE344
|
4.6
|
28.9
|
1.0
|
CB
|
C:ASN429
|
4.6
|
27.4
|
1.0
|
O
|
C:HOH2142
|
4.7
|
31.3
|
1.0
|
CA
|
C:CYS342
|
4.8
|
25.3
|
1.0
|
CA
|
C:GLN426
|
4.8
|
29.0
|
1.0
|
OXT
|
C:ACY512
|
4.9
|
32.7
|
1.0
|
CA
|
C:ASN429
|
4.9
|
24.4
|
1.0
|
CA
|
C:TYR428
|
4.9
|
25.6
|
1.0
|
C
|
C:TYR428
|
4.9
|
26.2
|
1.0
|
CB
|
C:ALA343
|
4.9
|
25.1
|
1.0
|
N
|
C:CYS342
|
5.0
|
25.9
|
1.0
|
|
Sodium binding site 4 out
of 5 in 3zx3
Go back to
Sodium Binding Sites List in 3zx3
Sodium binding site 4 out
of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na522
b:52.1
occ:1.00
|
O
|
D:HOH2194
|
2.1
|
43.0
|
1.0
|
O
|
D:PHE332
|
2.3
|
40.1
|
1.0
|
O
|
D:HOH2195
|
2.3
|
53.0
|
1.0
|
O
|
D:LEU329
|
2.5
|
36.7
|
1.0
|
O
|
D:HOH2193
|
2.7
|
48.5
|
1.0
|
O
|
D:HOH2197
|
2.8
|
49.5
|
1.0
|
C
|
D:PHE332
|
3.5
|
38.5
|
1.0
|
C
|
D:LEU329
|
3.5
|
37.5
|
1.0
|
CA
|
D:LYS330
|
3.9
|
40.1
|
1.0
|
C
|
D:LYS330
|
4.1
|
38.9
|
1.0
|
N
|
D:LYS330
|
4.1
|
38.8
|
1.0
|
N
|
D:PHE332
|
4.2
|
35.3
|
1.0
|
O
|
D:LYS330
|
4.2
|
39.5
|
1.0
|
CA
|
D:PHE332
|
4.3
|
36.6
|
1.0
|
N
|
D:ASN333
|
4.4
|
38.0
|
1.0
|
CB
|
D:PHE332
|
4.4
|
34.1
|
1.0
|
CA
|
D:ASN333
|
4.5
|
43.9
|
1.0
|
CA
|
D:LEU329
|
4.5
|
36.5
|
1.0
|
OD1
|
D:ASN334
|
4.5
|
42.0
|
1.0
|
N
|
D:ASN334
|
4.5
|
43.0
|
1.0
|
CB
|
D:LEU329
|
4.5
|
38.5
|
1.0
|
N
|
D:ILE331
|
4.8
|
36.1
|
1.0
|
O
|
D:HOH2202
|
4.9
|
57.2
|
1.0
|
OD1
|
D:ASN333
|
4.9
|
76.3
|
1.0
|
C
|
D:ASN333
|
5.0
|
41.8
|
1.0
|
|
Sodium binding site 5 out
of 5 in 3zx3
Go back to
Sodium Binding Sites List in 3zx3
Sodium binding site 5 out
of 5 in the Crystal Structure and Domain Rotation of NTPDASE1 CD39
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure and Domain Rotation of NTPDASE1 CD39 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na521
b:35.4
occ:1.00
|
O
|
D:GLY427
|
2.4
|
35.6
|
1.0
|
O
|
D:HOH2210
|
2.4
|
38.9
|
1.0
|
OD1
|
D:ASN429
|
2.4
|
36.8
|
1.0
|
O
|
D:CYS342
|
2.5
|
34.7
|
1.0
|
O
|
D:ALA343
|
2.6
|
33.6
|
1.0
|
O
|
D:GLN426
|
2.6
|
39.1
|
1.0
|
C
|
D:GLY427
|
3.2
|
32.7
|
1.0
|
CG
|
D:ASN429
|
3.3
|
35.9
|
1.0
|
C
|
D:ALA343
|
3.4
|
33.4
|
1.0
|
CA
|
D:GLY427
|
3.5
|
32.8
|
1.0
|
C
|
D:CYS342
|
3.5
|
34.7
|
1.0
|
C
|
D:GLN426
|
3.5
|
38.9
|
1.0
|
ND2
|
D:ASN429
|
3.6
|
34.8
|
1.0
|
CA
|
D:ALA343
|
3.6
|
31.8
|
1.0
|
N
|
D:GLY427
|
4.0
|
35.5
|
1.0
|
N
|
D:ALA343
|
4.0
|
33.1
|
1.0
|
O
|
D:HOH2239
|
4.1
|
46.2
|
1.0
|
O
|
D:HOH2209
|
4.2
|
38.5
|
1.0
|
N
|
D:TYR428
|
4.3
|
33.4
|
1.0
|
ND2
|
D:ASN334
|
4.4
|
41.8
|
1.0
|
N
|
D:ASN429
|
4.4
|
34.3
|
1.0
|
O
|
D:HOH2203
|
4.6
|
44.1
|
1.0
|
CB
|
D:ASN429
|
4.6
|
37.4
|
1.0
|
N
|
D:PHE344
|
4.7
|
32.1
|
1.0
|
CA
|
D:CYS342
|
4.8
|
36.7
|
1.0
|
CA
|
D:GLN426
|
4.8
|
39.8
|
1.0
|
OXT
|
D:ACY512
|
4.8
|
35.1
|
1.0
|
CA
|
D:ASN429
|
4.8
|
36.0
|
1.0
|
CA
|
D:TYR428
|
4.8
|
32.9
|
1.0
|
C
|
D:TYR428
|
4.9
|
33.3
|
1.0
|
N
|
D:CYS342
|
5.0
|
37.3
|
1.0
|
CB
|
D:ALA343
|
5.0
|
29.4
|
1.0
|
|
Reference:
M.Zebisch,
M.Krauss,
P.Schafer,
N.Strater.
Crystallographic Evidence For A Domain Motion in Rat Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) 1. J.Mol.Biol. V. 415 288 2012.
ISSN: ISSN 0022-2836
PubMed: 22100451
DOI: 10.1016/J.JMB.2011.10.050
Page generated: Mon Oct 7 14:14:16 2024
|