Sodium in PDB 1m65: Ycdx Protein
Protein crystallography data
The structure of Ycdx Protein, PDB code: 1m65
was solved by
A.Teplyakov,
G.Obmolova,
P.P.Khil,
R.D.Camerini-Otero,
G.L.Gilliland,
Structure 2 Function Project (S2F),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
1.57
|
Space group
|
P 3 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.230,
77.230,
79.990,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.7 /
20.8
|
Other elements in 1m65:
The structure of Ycdx Protein also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Ycdx Protein
(pdb code 1m65). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Ycdx Protein, PDB code: 1m65:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 1m65
Go back to
Sodium Binding Sites List in 1m65
Sodium binding site 1 out
of 3 in the Ycdx Protein
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Ycdx Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:15.7
occ:1.00
|
O
|
A:HOH562
|
2.0
|
26.4
|
1.0
|
OD1
|
A:ASP192
|
2.1
|
20.3
|
1.0
|
NE2
|
A:HIS9
|
2.2
|
15.1
|
1.0
|
OE1
|
A:GLU73
|
2.3
|
17.3
|
1.0
|
NE2
|
A:HIS7
|
2.4
|
20.4
|
1.0
|
CG
|
A:ASP192
|
3.0
|
22.6
|
1.0
|
CE1
|
A:HIS9
|
3.0
|
16.1
|
1.0
|
CE1
|
A:HIS7
|
3.2
|
18.4
|
1.0
|
CD2
|
A:HIS9
|
3.3
|
14.9
|
1.0
|
OD2
|
A:ASP192
|
3.3
|
26.1
|
1.0
|
CD
|
A:GLU73
|
3.3
|
21.2
|
1.0
|
CD2
|
A:HIS7
|
3.4
|
22.7
|
1.0
|
NA
|
A:NA302
|
3.4
|
17.9
|
1.0
|
OE2
|
A:GLU73
|
3.8
|
20.6
|
1.0
|
CE1
|
A:HIS40
|
3.8
|
22.9
|
1.0
|
CE1
|
A:HIS194
|
4.0
|
18.8
|
1.0
|
ND1
|
A:HIS9
|
4.2
|
13.6
|
1.0
|
NE2
|
A:HIS40
|
4.3
|
13.1
|
1.0
|
ND1
|
A:HIS7
|
4.3
|
17.8
|
1.0
|
CB
|
A:ASP192
|
4.3
|
18.9
|
1.0
|
CG
|
A:HIS9
|
4.3
|
13.8
|
1.0
|
O
|
A:HOH572
|
4.3
|
27.8
|
1.0
|
CG
|
A:HIS7
|
4.4
|
16.4
|
1.0
|
ZN
|
A:ZN300
|
4.5
|
20.0
|
1.0
|
NE2
|
A:HIS194
|
4.5
|
16.9
|
1.0
|
CG
|
A:GLU73
|
4.5
|
14.7
|
1.0
|
CA
|
A:ASP192
|
4.7
|
16.3
|
1.0
|
ND1
|
A:HIS40
|
4.7
|
16.3
|
1.0
|
CB
|
A:GLU73
|
4.8
|
13.4
|
1.0
|
|
Sodium binding site 2 out
of 3 in 1m65
Go back to
Sodium Binding Sites List in 1m65
Sodium binding site 2 out
of 3 in the Ycdx Protein
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Ycdx Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:17.9
occ:1.00
|
O
|
A:HOH562
|
1.7
|
26.4
|
1.0
|
NE2
|
A:HIS101
|
2.2
|
27.7
|
1.0
|
OE2
|
A:GLU73
|
2.3
|
20.6
|
1.0
|
NE2
|
A:HIS131
|
2.4
|
34.4
|
1.0
|
CE1
|
A:HIS101
|
2.8
|
22.5
|
1.0
|
CD
|
A:GLU73
|
3.0
|
21.2
|
1.0
|
OE1
|
A:GLU73
|
3.0
|
17.3
|
1.0
|
CD2
|
A:HIS131
|
3.3
|
28.2
|
1.0
|
CE1
|
A:HIS131
|
3.4
|
39.0
|
1.0
|
NA
|
A:NA301
|
3.4
|
15.7
|
1.0
|
CD2
|
A:HIS101
|
3.4
|
23.1
|
1.0
|
CE1
|
A:HIS40
|
4.0
|
22.9
|
1.0
|
ND1
|
A:HIS101
|
4.0
|
22.2
|
1.0
|
O
|
A:HOH572
|
4.3
|
27.8
|
1.0
|
OD2
|
A:ASP192
|
4.3
|
26.1
|
1.0
|
CG
|
A:HIS101
|
4.4
|
17.0
|
1.0
|
CG
|
A:GLU73
|
4.4
|
14.7
|
1.0
|
CG
|
A:HIS131
|
4.4
|
23.8
|
1.0
|
OG
|
A:SER130
|
4.5
|
19.2
|
1.0
|
ND1
|
A:HIS131
|
4.5
|
38.0
|
1.0
|
CE1
|
A:HIS7
|
4.6
|
18.4
|
1.0
|
ND1
|
A:HIS40
|
4.6
|
16.3
|
1.0
|
NE2
|
A:HIS7
|
4.7
|
20.4
|
1.0
|
OD1
|
A:ASP192
|
4.8
|
20.3
|
1.0
|
CB
|
A:SER130
|
5.0
|
17.7
|
1.0
|
CG
|
A:ASP192
|
5.0
|
22.6
|
1.0
|
|
Sodium binding site 3 out
of 3 in 1m65
Go back to
Sodium Binding Sites List in 1m65
Sodium binding site 3 out
of 3 in the Ycdx Protein
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Ycdx Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na303
b:32.6
occ:1.00
|
O
|
A:HOH641
|
2.3
|
35.2
|
1.0
|
O
|
A:LEU93
|
2.4
|
17.5
|
1.0
|
O
|
A:HOH599
|
2.5
|
30.1
|
1.0
|
O
|
A:PHE90
|
2.5
|
20.2
|
1.0
|
O
|
A:HOH533
|
2.6
|
21.8
|
1.0
|
O
|
A:HOH592
|
2.7
|
29.4
|
1.0
|
C
|
A:LEU93
|
3.6
|
16.0
|
1.0
|
C
|
A:PHE90
|
3.6
|
19.9
|
1.0
|
O
|
A:HOH530
|
3.9
|
21.1
|
1.0
|
O
|
A:HOH770
|
4.1
|
46.8
|
1.0
|
N
|
A:LEU93
|
4.3
|
13.6
|
1.0
|
O
|
A:HOH673
|
4.4
|
38.2
|
1.0
|
CA
|
A:PHE90
|
4.4
|
19.1
|
1.0
|
CA
|
A:LEU93
|
4.4
|
15.0
|
1.0
|
O
|
A:HOH525
|
4.4
|
19.6
|
1.0
|
N
|
A:ASP94
|
4.6
|
13.5
|
1.0
|
N
|
A:ASP91
|
4.6
|
18.8
|
1.0
|
C
|
A:ASP91
|
4.6
|
18.2
|
1.0
|
CA
|
A:ASP91
|
4.6
|
19.5
|
1.0
|
O
|
A:ASP91
|
4.7
|
20.8
|
1.0
|
CB
|
A:PHE90
|
4.7
|
21.8
|
1.0
|
CA
|
A:ASP94
|
4.7
|
14.6
|
1.0
|
CB
|
A:LEU93
|
4.8
|
13.3
|
1.0
|
O
|
A:HOH796
|
5.0
|
49.6
|
1.0
|
|
Reference:
A.Teplyakov,
G.Obmolova,
P.P.Khil,
A.J.Howard,
R.D.Camerini-Otero,
G.L.Gilliland.
Crystal Structure of the Escherichia Coli Ycdx Protein Reveals A Trinuclear Zinc Active Site Proteins: V. 51 315 2003STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 12661000
DOI: 10.1002/PROT.10352
Page generated: Sun Oct 6 20:19:53 2024
|