Sodium in PDB 7uda: Structure of the Estg
Protein crystallography data
The structure of Structure of the Estg, PDB code: 7uda
was solved by
Z.Chen,
S.B.Gabelli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.62 /
2.47
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.321,
110.321,
55.918,
90,
90,
90
|
R / Rfree (%)
|
18 /
21.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of the Estg
(pdb code 7uda). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Structure of the Estg, PDB code: 7uda:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7uda
Go back to
Sodium Binding Sites List in 7uda
Sodium binding site 1 out
of 4 in the Structure of the Estg
![](/pictures/NA/pdb/ud/7uda-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/ud/7uda-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 Structure of the Estg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na602
b:62.1
occ:1.00
|
O
|
A:SER204
|
2.5
|
47.4
|
1.0
|
O
|
A:LEU206
|
2.7
|
41.3
|
1.0
|
N
|
A:ARG137
|
3.1
|
52.8
|
1.0
|
N
|
A:LEU206
|
3.2
|
42.5
|
1.0
|
C
|
A:SER204
|
3.3
|
46.9
|
1.0
|
C
|
A:GLY205
|
3.3
|
45.5
|
1.0
|
C
|
A:LEU206
|
3.4
|
44.0
|
1.0
|
CA
|
A:LEU136
|
3.5
|
49.0
|
1.0
|
CA
|
A:GLY205
|
3.6
|
46.8
|
1.0
|
O
|
A:ASN135
|
3.7
|
57.5
|
1.0
|
C
|
A:LEU136
|
3.8
|
49.9
|
1.0
|
N
|
A:GLY205
|
3.8
|
43.1
|
1.0
|
CD2
|
A:LEU136
|
3.9
|
47.0
|
1.0
|
CA
|
A:LEU206
|
3.9
|
42.4
|
1.0
|
NH2
|
A:ARG137
|
3.9
|
110.8
|
1.0
|
O
|
A:GLY205
|
3.9
|
47.0
|
1.0
|
NE
|
A:ARG137
|
4.0
|
96.0
|
1.0
|
O
|
A:ARG137
|
4.0
|
45.7
|
1.0
|
O
|
A:VAL203
|
4.0
|
40.8
|
1.0
|
CB
|
A:ARG137
|
4.1
|
55.6
|
1.0
|
CA
|
A:ARG137
|
4.1
|
49.0
|
1.0
|
N
|
A:PRO207
|
4.4
|
48.1
|
1.0
|
N
|
A:LEU136
|
4.4
|
49.6
|
1.0
|
CZ
|
A:ARG137
|
4.4
|
98.4
|
1.0
|
C
|
A:ASN135
|
4.4
|
53.0
|
1.0
|
CA
|
A:SER204
|
4.4
|
45.4
|
1.0
|
CB
|
A:LEU136
|
4.5
|
48.0
|
1.0
|
C
|
A:ARG137
|
4.6
|
44.9
|
1.0
|
O
|
A:HOH701
|
4.7
|
37.4
|
1.0
|
CA
|
A:PRO207
|
4.7
|
48.9
|
1.0
|
CG
|
A:LEU136
|
4.7
|
45.4
|
1.0
|
C
|
A:VAL203
|
5.0
|
41.6
|
1.0
|
O
|
A:LEU136
|
5.0
|
50.6
|
1.0
|
CD
|
A:ARG137
|
5.0
|
75.2
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7uda
Go back to
Sodium Binding Sites List in 7uda
Sodium binding site 2 out
of 4 in the Structure of the Estg
![](/pictures/NA/pdb/ud/7uda-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/ud/7uda-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 Structure of the Estg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na603
b:53.9
occ:1.00
|
OE2
|
A:GLU102
|
2.4
|
55.3
|
1.0
|
O
|
A:TRP403
|
2.8
|
42.0
|
1.0
|
O
|
A:GLY416
|
3.1
|
40.2
|
1.0
|
CD
|
A:GLU102
|
3.2
|
48.0
|
1.0
|
OE1
|
A:GLU102
|
3.3
|
44.1
|
1.0
|
SD
|
A:MET417
|
3.4
|
45.1
|
1.0
|
C
|
A:TRP403
|
3.5
|
40.4
|
1.0
|
CG1
|
A:VAL415
|
3.5
|
46.1
|
1.0
|
N
|
A:TRP403
|
3.7
|
38.9
|
1.0
|
N
|
A:GLY416
|
3.8
|
39.3
|
1.0
|
CE
|
A:MET417
|
3.8
|
46.6
|
1.0
|
C
|
A:GLY416
|
3.9
|
39.9
|
1.0
|
CB
|
A:THR402
|
4.0
|
37.9
|
1.0
|
CG
|
A:MET417
|
4.1
|
46.6
|
1.0
|
CB
|
A:PHE404
|
4.2
|
35.3
|
1.0
|
CA
|
A:TRP403
|
4.2
|
40.4
|
1.0
|
CA
|
A:VAL415
|
4.3
|
42.9
|
1.0
|
N
|
A:PHE404
|
4.3
|
33.5
|
1.0
|
CB
|
A:VAL415
|
4.4
|
42.8
|
1.0
|
C
|
A:VAL415
|
4.4
|
40.9
|
1.0
|
C
|
A:THR402
|
4.4
|
42.2
|
1.0
|
CA
|
A:GLY416
|
4.4
|
39.6
|
1.0
|
CA
|
A:THR402
|
4.6
|
39.2
|
1.0
|
CD2
|
A:PHE310
|
4.6
|
38.3
|
1.0
|
OG1
|
A:THR402
|
4.7
|
36.4
|
1.0
|
CA
|
A:PHE404
|
4.7
|
35.2
|
1.0
|
CG
|
A:GLU102
|
4.7
|
44.9
|
1.0
|
N
|
A:MET417
|
4.7
|
39.1
|
1.0
|
CG2
|
A:THR402
|
4.8
|
38.1
|
1.0
|
CG
|
A:PHE310
|
4.8
|
36.5
|
1.0
|
CG2
|
A:VAL415
|
4.9
|
42.0
|
1.0
|
CA
|
A:MET417
|
5.0
|
42.7
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7uda
Go back to
Sodium Binding Sites List in 7uda
Sodium binding site 3 out
of 4 in the Structure of the Estg
![](/pictures/NA/pdb/ud/7uda-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/ud/7uda-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 Structure of the Estg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:61.6
occ:1.00
|
OD1
|
A:ASP407
|
2.7
|
35.8
|
1.0
|
O
|
A:PRO391
|
2.7
|
50.8
|
1.0
|
N
|
A:THR393
|
3.1
|
36.8
|
1.0
|
N
|
A:ALA409
|
3.2
|
44.1
|
1.0
|
OG1
|
A:THR393
|
3.2
|
40.0
|
1.0
|
CD
|
A:PRO408
|
3.3
|
43.9
|
1.0
|
N
|
A:PRO408
|
3.3
|
45.0
|
1.0
|
C
|
A:GLY392
|
3.3
|
39.4
|
1.0
|
O
|
A:GLY390
|
3.4
|
56.5
|
1.0
|
C
|
A:PRO391
|
3.5
|
46.5
|
1.0
|
C
|
A:ASP407
|
3.5
|
41.0
|
1.0
|
CB
|
A:ALA409
|
3.6
|
41.0
|
1.0
|
CA
|
A:THR393
|
3.6
|
39.8
|
1.0
|
CA
|
A:ASP407
|
3.6
|
37.8
|
1.0
|
CG
|
A:ASP407
|
3.7
|
34.2
|
1.0
|
O
|
A:GLY392
|
3.7
|
44.1
|
1.0
|
C
|
A:GLY390
|
3.8
|
52.9
|
1.0
|
CA
|
A:GLY392
|
3.8
|
41.0
|
1.0
|
CA
|
A:ALA409
|
3.9
|
42.9
|
1.0
|
N
|
A:GLY392
|
4.0
|
45.1
|
1.0
|
CA
|
A:PRO408
|
4.0
|
46.9
|
1.0
|
CB
|
A:THR393
|
4.0
|
44.5
|
1.0
|
C
|
A:PRO408
|
4.1
|
47.5
|
1.0
|
CG
|
A:PRO408
|
4.1
|
41.7
|
1.0
|
CA
|
A:GLY390
|
4.2
|
46.5
|
1.0
|
CB
|
A:ASP407
|
4.2
|
36.6
|
1.0
|
CB
|
A:PRO408
|
4.2
|
42.0
|
1.0
|
O
|
A:ASP407
|
4.3
|
45.7
|
1.0
|
N
|
A:PRO391
|
4.4
|
57.6
|
1.0
|
OD2
|
A:ASP407
|
4.6
|
37.4
|
1.0
|
CA
|
A:PRO391
|
4.6
|
50.6
|
1.0
|
N
|
A:GLY390
|
4.7
|
42.0
|
1.0
|
N
|
A:ASN410
|
4.8
|
43.8
|
1.0
|
O
|
A:ILE406
|
4.9
|
34.2
|
1.0
|
N
|
A:ASP407
|
4.9
|
35.7
|
1.0
|
C
|
A:ALA409
|
4.9
|
43.3
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7uda
Go back to
Sodium Binding Sites List in 7uda
Sodium binding site 4 out
of 4 in the Structure of the Estg
![](/pictures/NA/pdb/ud/7uda-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/ud/7uda-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 Structure of the Estg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na605
b:59.7
occ:1.00
|
OE1
|
A:GLN315
|
2.6
|
35.9
|
1.0
|
N
|
A:GLY73
|
3.0
|
51.3
|
1.0
|
CD1
|
A:LEU318
|
3.4
|
37.1
|
1.0
|
CD
|
A:GLN315
|
3.5
|
39.9
|
1.0
|
O
|
A:ASN411
|
3.5
|
44.5
|
1.0
|
N
|
A:HIS72
|
3.6
|
52.9
|
1.0
|
CA
|
A:GLY73
|
3.6
|
52.5
|
1.0
|
C
|
A:ARG71
|
3.6
|
50.4
|
1.0
|
CA
|
A:ARG71
|
3.7
|
48.1
|
1.0
|
N
|
A:ARG71
|
3.7
|
48.3
|
1.0
|
NE2
|
A:GLN315
|
3.7
|
39.2
|
1.0
|
C
|
A:ALA70
|
3.7
|
42.3
|
1.0
|
O
|
A:ALA70
|
3.8
|
45.9
|
1.0
|
CB
|
A:ALA70
|
4.0
|
42.5
|
1.0
|
CE2
|
A:PHE413
|
4.1
|
46.2
|
1.0
|
C
|
A:HIS72
|
4.1
|
56.1
|
1.0
|
CD2
|
A:PHE413
|
4.1
|
41.8
|
1.0
|
O
|
A:ARG71
|
4.2
|
53.3
|
1.0
|
C
|
A:GLY73
|
4.3
|
49.1
|
1.0
|
CA
|
A:HIS72
|
4.4
|
56.0
|
1.0
|
N
|
A:ARG74
|
4.4
|
54.4
|
1.0
|
CA
|
A:ALA70
|
4.4
|
44.4
|
1.0
|
CA
|
A:LEU412
|
4.5
|
46.7
|
1.0
|
C
|
A:ASN411
|
4.5
|
45.9
|
1.0
|
CG
|
A:LEU318
|
4.8
|
38.6
|
1.0
|
CG
|
A:GLN315
|
4.9
|
41.5
|
1.0
|
N
|
A:PHE413
|
4.9
|
40.6
|
1.0
|
N
|
A:LEU412
|
5.0
|
44.7
|
1.0
|
C
|
A:LEU412
|
5.0
|
46.0
|
1.0
|
|
Reference:
A.K.Daitch,
B.C.Orsburn,
Z.Chen,
L.Alvarez,
C.D.Eberhard,
K.Sundararajan,
R.Zeinert,
D.F.Kreitler,
J.Jakoncic,
P.Chien,
F.Cava,
S.B.Gabelli,
E.D.Goley.
Estg Is A Novel Esterase Required For Cell Envelope Integrity in Caulobacter. Curr.Biol. 2022.
ISSN: ISSN 0960-9822
PubMed: 36516849
DOI: 10.1016/J.CUB.2022.11.037
Page generated: Fri Apr 7 16:39:18 2023
|