Sodium in PDB 1tqy: The Actinorhodin Ketosynthase/Chain Length Factor
Protein crystallography data
The structure of The Actinorhodin Ketosynthase/Chain Length Factor, PDB code: 1tqy
was solved by
A.T.Keatinge-Clay,
D.A.Maltby,
K.F.Medzihradszky,
C.Khosla,
R.M.Stroud,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.00
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
262.700,
262.700,
224.030,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.3 /
25.3
|
Other elements in 1tqy:
The structure of The Actinorhodin Ketosynthase/Chain Length Factor also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the The Actinorhodin Ketosynthase/Chain Length Factor
(pdb code 1tqy). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
The Actinorhodin Ketosynthase/Chain Length Factor, PDB code: 1tqy:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 1tqy
Go back to
Sodium Binding Sites List in 1tqy
Sodium binding site 1 out
of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1091
b:39.1
occ:1.00
|
O
|
B:HOH1233
|
1.9
|
31.9
|
1.0
|
O
|
B:PRO13
|
2.3
|
25.0
|
1.0
|
O
|
B:GLN50
|
2.3
|
25.6
|
1.0
|
O
|
B:HOH1112
|
2.3
|
31.7
|
1.0
|
O
|
B:HOH1161
|
3.0
|
38.3
|
1.0
|
C
|
B:PRO13
|
3.3
|
24.3
|
1.0
|
O
|
B:GLY31
|
3.3
|
25.2
|
1.0
|
C
|
B:GLN50
|
3.5
|
27.2
|
1.0
|
CA
|
B:PRO13
|
3.8
|
24.7
|
1.0
|
CA
|
B:GLY31
|
3.8
|
25.9
|
1.0
|
C
|
B:GLY31
|
4.0
|
25.1
|
1.0
|
CB
|
B:PRO13
|
4.1
|
23.8
|
1.0
|
OD2
|
B:ASP52
|
4.1
|
38.2
|
1.0
|
CA
|
B:ILE51
|
4.3
|
28.7
|
1.0
|
O
|
B:HOH1162
|
4.4
|
29.1
|
1.0
|
N
|
B:ILE51
|
4.4
|
27.6
|
1.0
|
N
|
B:ASP52
|
4.4
|
30.0
|
1.0
|
N
|
B:ASN14
|
4.5
|
23.6
|
1.0
|
N
|
B:GLN50
|
4.5
|
27.0
|
1.0
|
O
|
B:HOH1205
|
4.5
|
45.0
|
1.0
|
CA
|
B:GLN50
|
4.5
|
27.4
|
1.0
|
CG
|
B:ASP52
|
4.8
|
35.2
|
1.0
|
C
|
B:ILE51
|
4.8
|
29.0
|
1.0
|
CA
|
B:ASN14
|
4.9
|
25.9
|
1.0
|
O
|
B:HOH1123
|
4.9
|
31.5
|
1.0
|
CB
|
B:GLN50
|
4.9
|
25.9
|
1.0
|
|
Sodium binding site 2 out
of 4 in 1tqy
Go back to
Sodium Binding Sites List in 1tqy
Sodium binding site 2 out
of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na1092
b:38.2
occ:1.00
|
O
|
D:HOH1104
|
2.0
|
25.7
|
1.0
|
O
|
D:HOH1100
|
2.4
|
25.5
|
1.0
|
O
|
D:PRO13
|
2.4
|
17.7
|
1.0
|
O
|
D:GLN50
|
2.5
|
20.1
|
1.0
|
O
|
D:HOH1192
|
2.5
|
38.7
|
1.0
|
O
|
D:GLY31
|
3.2
|
18.4
|
1.0
|
C
|
D:PRO13
|
3.4
|
18.0
|
1.0
|
C
|
D:GLN50
|
3.7
|
21.7
|
1.0
|
CA
|
D:GLY31
|
3.7
|
20.8
|
1.0
|
C
|
D:GLY31
|
3.8
|
20.7
|
1.0
|
CA
|
D:PRO13
|
3.9
|
19.0
|
1.0
|
CB
|
D:PRO13
|
4.1
|
18.4
|
1.0
|
O
|
D:HOH1260
|
4.2
|
43.8
|
1.0
|
OD2
|
D:ASP52
|
4.3
|
32.9
|
1.0
|
O
|
D:HOH1153
|
4.5
|
30.8
|
1.0
|
O
|
D:HOH1225
|
4.5
|
42.2
|
1.0
|
N
|
D:GLN50
|
4.5
|
20.1
|
1.0
|
N
|
D:ASP52
|
4.5
|
23.6
|
1.0
|
N
|
D:ASN14
|
4.5
|
17.5
|
1.0
|
CA
|
D:ILE51
|
4.6
|
21.8
|
1.0
|
CA
|
D:GLN50
|
4.6
|
21.9
|
1.0
|
N
|
D:ILE51
|
4.6
|
21.6
|
1.0
|
CG
|
D:ASP52
|
4.9
|
28.2
|
1.0
|
O
|
D:HOH1166
|
4.9
|
35.4
|
1.0
|
CA
|
D:ASN14
|
4.9
|
19.3
|
1.0
|
|
Sodium binding site 3 out
of 4 in 1tqy
Go back to
Sodium Binding Sites List in 1tqy
Sodium binding site 3 out
of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na1093
b:45.5
occ:1.00
|
O
|
F:GLN50
|
2.3
|
27.1
|
1.0
|
O
|
F:HOH1112
|
2.3
|
34.5
|
1.0
|
O
|
F:PRO13
|
2.4
|
25.6
|
1.0
|
O
|
F:HOH1135
|
2.4
|
31.6
|
1.0
|
O
|
F:HOH1154
|
2.5
|
42.6
|
1.0
|
O
|
F:GLY31
|
3.1
|
25.2
|
1.0
|
C
|
F:PRO13
|
3.4
|
24.7
|
1.0
|
C
|
F:GLN50
|
3.5
|
27.3
|
1.0
|
CA
|
F:GLY31
|
3.6
|
24.6
|
1.0
|
C
|
F:GLY31
|
3.7
|
24.6
|
1.0
|
CA
|
F:PRO13
|
3.9
|
24.1
|
1.0
|
CB
|
F:PRO13
|
4.1
|
23.3
|
1.0
|
OD2
|
F:ASP52
|
4.2
|
31.8
|
1.0
|
N
|
F:GLN50
|
4.2
|
26.7
|
1.0
|
CA
|
F:GLN50
|
4.4
|
27.4
|
1.0
|
N
|
F:ILE51
|
4.4
|
27.6
|
1.0
|
CA
|
F:ILE51
|
4.5
|
26.6
|
1.0
|
N
|
F:ASP52
|
4.5
|
27.4
|
1.0
|
N
|
F:ASN14
|
4.6
|
23.4
|
1.0
|
O
|
F:HOH1155
|
4.7
|
40.0
|
1.0
|
CG
|
F:ASP52
|
4.8
|
30.2
|
1.0
|
O
|
F:HOH1142
|
4.8
|
33.4
|
1.0
|
CB
|
F:GLN50
|
4.8
|
26.4
|
1.0
|
N
|
F:LEU32
|
4.9
|
25.0
|
1.0
|
O
|
F:HOH1241
|
4.9
|
39.0
|
1.0
|
C
|
F:ILE51
|
5.0
|
26.3
|
1.0
|
|
Sodium binding site 4 out
of 4 in 1tqy
Go back to
Sodium Binding Sites List in 1tqy
Sodium binding site 4 out
of 4 in the The Actinorhodin Ketosynthase/Chain Length Factor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of The Actinorhodin Ketosynthase/Chain Length Factor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na1094
b:36.6
occ:1.00
|
O
|
H:GLN50
|
2.3
|
26.8
|
1.0
|
O
|
H:HOH1125
|
2.4
|
28.1
|
1.0
|
O
|
H:PRO13
|
2.4
|
22.5
|
1.0
|
O
|
H:HOH1176
|
2.5
|
25.1
|
1.0
|
O
|
H:GLY31
|
3.1
|
19.4
|
1.0
|
C
|
H:PRO13
|
3.4
|
19.4
|
1.0
|
C
|
H:GLN50
|
3.6
|
24.6
|
1.0
|
CA
|
H:GLY31
|
3.8
|
19.9
|
1.0
|
C
|
H:GLY31
|
3.8
|
19.5
|
1.0
|
CA
|
H:PRO13
|
3.8
|
18.6
|
1.0
|
OD2
|
H:ASP52
|
4.0
|
31.2
|
1.0
|
CB
|
H:PRO13
|
4.0
|
16.0
|
1.0
|
N
|
H:GLN50
|
4.4
|
21.8
|
1.0
|
N
|
H:ASP52
|
4.4
|
24.3
|
1.0
|
CA
|
H:ILE51
|
4.4
|
24.0
|
1.0
|
N
|
H:ILE51
|
4.5
|
24.3
|
1.0
|
CA
|
H:GLN50
|
4.5
|
24.2
|
1.0
|
N
|
H:ASN14
|
4.5
|
19.7
|
1.0
|
O
|
H:HOH1167
|
4.6
|
32.3
|
1.0
|
CG
|
H:ASP52
|
4.7
|
28.3
|
1.0
|
O
|
H:HOH1141
|
4.8
|
35.3
|
1.0
|
O
|
H:HOH1219
|
4.9
|
33.6
|
1.0
|
C
|
H:ILE51
|
4.9
|
24.5
|
1.0
|
O
|
H:HOH1138
|
4.9
|
34.6
|
1.0
|
CA
|
H:ASN14
|
4.9
|
22.5
|
1.0
|
CB
|
H:GLN50
|
4.9
|
24.4
|
1.0
|
|
Reference:
A.T.Keatinge-Clay,
D.A.Maltby,
K.F.Medzihradszky,
C.Khosla,
R.M.Stroud.
An Antibiotic Factory Caught in Action. Nat.Struct.Mol.Biol. V. 11 888 2004.
ISSN: ISSN 1545-9993
PubMed: 15286722
DOI: 10.1038/NSMB808
Page generated: Sun Oct 6 22:41:46 2024
|