Sodium in PDB 7ugh: Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid
Enzymatic activity of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid
All present enzymatic activity of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid:
4.2.1.11;
Protein crystallography data
The structure of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid, PDB code: 7ugh
was solved by
Seattle Structural Genomics Center For Infectious Disease (Ssgcid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.26 /
1.95
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
96.86,
96.86,
216.64,
90,
90,
90
|
R / Rfree (%)
|
15.3 /
19.1
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid
(pdb code 7ugh). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid, PDB code: 7ugh:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7ugh
Go back to
Sodium Binding Sites List in 7ugh
Sodium binding site 1 out
of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid
![](/pictures/NA/pdb/ug/7ugh-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/ug/7ugh-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 Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na607
b:31.5
occ:1.00
|
OE2
|
A:GLU379
|
2.2
|
30.8
|
1.0
|
OD2
|
A:ASP406
|
2.3
|
30.9
|
1.0
|
OD2
|
A:ASP333
|
2.4
|
33.2
|
1.0
|
O2
|
A:2PG601
|
2.4
|
44.3
|
0.7
|
O
|
A:HOH828
|
2.5
|
31.0
|
1.0
|
O1
|
A:2PG601
|
2.5
|
36.0
|
0.7
|
C1
|
A:2PG601
|
2.8
|
38.9
|
0.7
|
CG
|
A:ASP333
|
3.3
|
35.3
|
1.0
|
CG
|
A:ASP406
|
3.3
|
33.3
|
1.0
|
O
|
A:HOH710
|
3.3
|
38.1
|
1.0
|
CD
|
A:GLU379
|
3.4
|
32.0
|
1.0
|
OD1
|
A:ASP333
|
3.5
|
33.5
|
1.0
|
NZ
|
A:LYS482
|
3.6
|
37.0
|
1.0
|
CB
|
A:ASP406
|
3.8
|
31.6
|
1.0
|
CD2
|
A:LEU429
|
4.1
|
29.9
|
1.0
|
OE1
|
A:GLU379
|
4.2
|
33.1
|
1.0
|
CG
|
A:GLU379
|
4.2
|
31.0
|
1.0
|
OD2
|
A:ASP380
|
4.3
|
34.3
|
1.0
|
NZ
|
A:LYS431
|
4.3
|
35.5
|
1.0
|
C2
|
A:2PG601
|
4.3
|
38.0
|
0.7
|
OD1
|
A:ASP406
|
4.4
|
32.5
|
1.0
|
O
|
A:HOH753
|
4.4
|
46.8
|
1.0
|
CB
|
A:ASP333
|
4.6
|
31.7
|
1.0
|
O
|
A:HOH893
|
4.6
|
50.7
|
1.0
|
O3
|
A:2PG601
|
4.7
|
46.3
|
0.7
|
O1P
|
A:2PG601
|
4.9
|
41.7
|
0.7
|
OE2
|
A:GLU253
|
4.9
|
52.9
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7ugh
Go back to
Sodium Binding Sites List in 7ugh
Sodium binding site 2 out
of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid
![](/pictures/NA/pdb/ug/7ugh-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/ug/7ugh-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 Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na608
b:52.9
occ:1.00
|
O
|
A:GLY242
|
2.3
|
37.6
|
1.0
|
O
|
A:HOH816
|
2.4
|
47.1
|
1.0
|
O
|
A:ALA245
|
2.4
|
46.7
|
1.0
|
O
|
A:HOH780
|
2.5
|
42.2
|
1.0
|
O
|
A:GLY247
|
3.2
|
41.3
|
1.0
|
O
|
A:HOH763
|
3.3
|
41.0
|
1.0
|
C
|
A:GLY242
|
3.4
|
42.3
|
1.0
|
C
|
A:ALA245
|
3.5
|
47.6
|
1.0
|
OE1
|
A:GLN351
|
3.7
|
48.4
|
1.0
|
CA
|
A:GLY242
|
4.2
|
40.6
|
1.0
|
N
|
A:ALA245
|
4.2
|
47.0
|
1.0
|
N
|
A:LYS243
|
4.3
|
47.2
|
1.0
|
C
|
A:GLY247
|
4.4
|
39.0
|
1.0
|
N
|
A:GLY246
|
4.4
|
46.5
|
1.0
|
N
|
A:GLY242
|
4.4
|
36.8
|
1.0
|
O
|
A:LEU249
|
4.4
|
37.4
|
1.0
|
CA
|
A:ALA245
|
4.4
|
47.0
|
1.0
|
C
|
A:GLY246
|
4.4
|
46.0
|
1.0
|
CA
|
A:LYS243
|
4.5
|
50.3
|
1.0
|
CA
|
A:GLY246
|
4.5
|
43.8
|
1.0
|
N
|
A:GLY247
|
4.5
|
44.6
|
1.0
|
C
|
A:LYS243
|
4.6
|
49.2
|
1.0
|
OE1
|
A:GLN250
|
4.8
|
40.8
|
1.0
|
O
|
A:GLY246
|
4.9
|
48.0
|
1.0
|
CD
|
A:GLN351
|
4.9
|
53.8
|
1.0
|
O
|
A:LYS243
|
5.0
|
53.8
|
1.0
|
N
|
A:HIS244
|
5.0
|
51.5
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7ugh
Go back to
Sodium Binding Sites List in 7ugh
Sodium binding site 3 out
of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid
![](/pictures/NA/pdb/ug/7ugh-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/ug/7ugh-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 Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na607
b:32.0
occ:1.00
|
OE2
|
B:GLU379
|
2.2
|
32.1
|
1.0
|
OD2
|
B:ASP406
|
2.2
|
29.7
|
1.0
|
O
|
B:HOH758
|
2.4
|
30.7
|
1.0
|
O1
|
B:2PG602
|
2.4
|
42.5
|
0.8
|
OD2
|
B:ASP333
|
2.4
|
34.5
|
1.0
|
O2
|
B:2PG602
|
2.6
|
37.5
|
0.8
|
C1
|
B:2PG602
|
2.8
|
39.4
|
0.8
|
CG
|
B:ASP406
|
3.3
|
32.0
|
1.0
|
CG
|
B:ASP333
|
3.3
|
36.2
|
1.0
|
CD
|
B:GLU379
|
3.3
|
33.4
|
1.0
|
OD1
|
B:ASP333
|
3.5
|
30.3
|
1.0
|
O
|
B:HOH733
|
3.5
|
37.2
|
1.0
|
NZ
|
B:LYS482
|
3.6
|
35.0
|
1.0
|
CB
|
B:ASP406
|
3.7
|
28.8
|
1.0
|
O
|
B:HOH922
|
3.9
|
42.1
|
1.0
|
CD2
|
B:LEU429
|
4.1
|
28.9
|
1.0
|
OE1
|
B:GLU379
|
4.2
|
30.4
|
1.0
|
NZ
|
B:LYS431
|
4.2
|
34.3
|
1.0
|
CG
|
B:GLU379
|
4.2
|
29.3
|
1.0
|
OD2
|
B:ASP380
|
4.3
|
33.8
|
1.0
|
C2
|
B:2PG602
|
4.3
|
36.1
|
0.8
|
OD1
|
B:ASP406
|
4.3
|
30.3
|
1.0
|
CB
|
B:ASP333
|
4.6
|
33.0
|
1.0
|
OE2
|
B:GLU253
|
4.7
|
57.4
|
1.0
|
O3
|
B:2PG602
|
4.7
|
41.1
|
0.8
|
O
|
B:HOH926
|
4.8
|
50.7
|
1.0
|
O1P
|
B:2PG602
|
4.9
|
38.4
|
0.8
|
|
Sodium binding site 4 out
of 4 in 7ugh
Go back to
Sodium Binding Sites List in 7ugh
Sodium binding site 4 out
of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid
![](/pictures/NA/pdb/ug/7ugh-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/ug/7ugh-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 Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na608
b:53.9
occ:1.00
|
O
|
B:HOH774
|
2.3
|
44.8
|
1.0
|
O
|
B:ALA245
|
2.4
|
46.4
|
1.0
|
O
|
B:HOH844
|
2.4
|
48.6
|
1.0
|
O
|
B:GLY242
|
2.4
|
43.9
|
1.0
|
O
|
B:HOH837
|
2.8
|
45.4
|
1.0
|
O
|
B:GLY247
|
3.2
|
43.6
|
1.0
|
C
|
B:GLY242
|
3.5
|
46.4
|
1.0
|
C
|
B:ALA245
|
3.5
|
48.0
|
1.0
|
OE1
|
B:GLN351
|
4.0
|
50.7
|
1.0
|
CA
|
B:GLY242
|
4.2
|
41.7
|
1.0
|
N
|
B:ALA245
|
4.3
|
48.7
|
1.0
|
O
|
B:LEU249
|
4.3
|
39.3
|
1.0
|
N
|
B:GLY246
|
4.3
|
46.0
|
1.0
|
C
|
B:GLY247
|
4.3
|
46.4
|
1.0
|
C
|
B:GLY246
|
4.3
|
48.0
|
1.0
|
N
|
B:GLY247
|
4.4
|
47.5
|
1.0
|
CA
|
B:GLY246
|
4.4
|
47.2
|
1.0
|
N
|
B:GLY242
|
4.4
|
37.6
|
1.0
|
CA
|
B:ALA245
|
4.4
|
47.6
|
1.0
|
N
|
B:LYS243
|
4.4
|
47.4
|
1.0
|
CA
|
B:LYS243
|
4.7
|
51.0
|
1.0
|
C
|
B:LYS243
|
4.8
|
50.1
|
1.0
|
O
|
B:GLY246
|
4.8
|
46.1
|
1.0
|
OE1
|
B:GLN250
|
4.8
|
44.6
|
1.0
|
CB
|
B:ALA245
|
5.0
|
45.1
|
1.0
|
CA
|
B:GLY247
|
5.0
|
44.9
|
1.0
|
|
Reference:
M.J.Bolejack,
N.D.Debouver,
J.C.Morris,
D.D.Lorimer,
P.S.Horanyi,
T.E.Edwards.
Crystal Structure of Nadp-Linked Putative Oxidoreductase From Klebsiella Pneumoniae To Be Published.
Page generated: Fri Apr 7 16:39:19 2023
|