Sodium in PDB 8qnf: Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Protein crystallography data
The structure of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase, PDB code: 8qnf
was solved by
M.Karanth,
S.Schmelz,
J.Kirkpatrick,
J.Krausze,
A.Scrima,
T.Carlomagno,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.94 /
1.65
|
Space group
|
F 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.65,
160.06,
163.9,
90,
90,
90
|
R / Rfree (%)
|
17.7 /
19.7
|
Other elements in 8qnf:
The structure of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
(pdb code 8qnf). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase, PDB code: 8qnf:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 8qnf
Go back to
Sodium Binding Sites List in 8qnf
Sodium binding site 1 out
of 7 in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na614
b:33.7
occ:1.00
|
HG23
|
A:VAL190
|
2.6
|
27.8
|
1.0
|
HG21
|
A:THR206
|
2.6
|
29.9
|
1.0
|
OE2
|
A:GLU173
|
2.8
|
30.4
|
1.0
|
OG1
|
A:THR206
|
2.8
|
25.7
|
1.0
|
HB3
|
A:LEU186
|
2.9
|
30.9
|
1.0
|
O
|
A:LEU186
|
3.1
|
25.8
|
1.0
|
HG1
|
A:THR206
|
3.3
|
31.0
|
1.0
|
HD22
|
A:LEU186
|
3.3
|
33.1
|
1.0
|
HA
|
A:LEU186
|
3.3
|
30.9
|
1.0
|
HB
|
A:THR206
|
3.3
|
27.4
|
1.0
|
CB
|
A:THR206
|
3.4
|
22.7
|
1.0
|
CG2
|
A:THR206
|
3.4
|
24.8
|
1.0
|
CG2
|
A:VAL190
|
3.4
|
23.0
|
1.0
|
HE
|
A:ARG189
|
3.5
|
33.6
|
1.0
|
CD
|
A:GLU173
|
3.5
|
24.3
|
1.0
|
HB3
|
A:ARG189
|
3.5
|
31.2
|
1.0
|
HG21
|
A:VAL190
|
3.5
|
27.8
|
1.0
|
HG22
|
A:VAL190
|
3.7
|
27.8
|
1.0
|
C
|
A:LEU186
|
3.7
|
24.2
|
1.0
|
CB
|
A:LEU186
|
3.7
|
25.6
|
1.0
|
CA
|
A:LEU186
|
3.8
|
25.6
|
1.0
|
HD12
|
A:ILE218
|
3.8
|
32.4
|
1.0
|
HH21
|
A:ARG189
|
3.8
|
33.8
|
1.0
|
HG3
|
A:GLU173
|
3.9
|
30.1
|
1.0
|
HG2
|
A:ARG189
|
3.9
|
31.2
|
1.0
|
H
|
A:VAL190
|
3.9
|
29.0
|
1.0
|
HG23
|
A:THR206
|
4.0
|
29.9
|
1.0
|
NE
|
A:ARG189
|
4.0
|
27.9
|
1.0
|
HG22
|
A:THR206
|
4.0
|
29.9
|
1.0
|
HG2
|
A:GLU173
|
4.0
|
30.1
|
1.0
|
CG
|
A:GLU173
|
4.1
|
25.0
|
1.0
|
CD2
|
A:LEU186
|
4.2
|
27.4
|
1.0
|
NH2
|
A:ARG189
|
4.2
|
28.1
|
1.0
|
OE1
|
A:GLU173
|
4.2
|
27.6
|
1.0
|
O
|
A:HOH760
|
4.3
|
30.6
|
1.0
|
CZ
|
A:ARG189
|
4.4
|
33.1
|
1.0
|
CB
|
A:ARG189
|
4.4
|
25.9
|
1.0
|
HD13
|
A:ILE218
|
4.4
|
32.4
|
1.0
|
HB2
|
A:LEU186
|
4.4
|
30.9
|
1.0
|
HD23
|
A:LEU186
|
4.4
|
33.1
|
1.0
|
N
|
A:VAL190
|
4.5
|
24.0
|
1.0
|
CG
|
A:ARG189
|
4.5
|
25.9
|
1.0
|
HB3
|
A:ALA175
|
4.5
|
35.3
|
1.0
|
CD1
|
A:ILE218
|
4.5
|
26.9
|
1.0
|
CG
|
A:LEU186
|
4.5
|
28.5
|
1.0
|
HD13
|
A:LEU186
|
4.6
|
32.0
|
1.0
|
CB
|
A:VAL190
|
4.6
|
23.9
|
1.0
|
HB
|
A:VAL190
|
4.6
|
28.9
|
1.0
|
HB
|
A:ILE218
|
4.7
|
27.9
|
1.0
|
HH22
|
A:ARG189
|
4.8
|
33.8
|
1.0
|
HG21
|
A:ILE218
|
4.8
|
27.0
|
1.0
|
CA
|
A:THR206
|
4.9
|
24.7
|
1.0
|
O
|
A:HOH893
|
4.9
|
27.4
|
1.0
|
CD
|
A:ARG189
|
4.9
|
35.6
|
1.0
|
N
|
A:VAL187
|
4.9
|
24.8
|
1.0
|
HD21
|
A:LEU186
|
4.9
|
33.1
|
1.0
|
HB2
|
A:ARG189
|
5.0
|
31.2
|
1.0
|
|
Sodium binding site 2 out
of 7 in 8qnf
Go back to
Sodium Binding Sites List in 8qnf
Sodium binding site 2 out
of 7 in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na615
b:36.8
occ:1.00
|
H
|
A:ARG124
|
2.1
|
27.9
|
0.5
|
H
|
A:ARG124
|
2.1
|
27.9
|
0.5
|
O
|
A:ARG457
|
2.7
|
31.4
|
1.0
|
OE2
|
A:GLU459
|
2.8
|
36.0
|
1.0
|
HA
|
A:VAL123
|
2.8
|
28.4
|
0.5
|
HA
|
A:VAL123
|
2.8
|
28.2
|
0.5
|
HG3
|
A:ARG124
|
2.9
|
35.0
|
1.0
|
N
|
A:ARG124
|
2.9
|
23.1
|
1.0
|
HG3
|
A:GLU459
|
3.1
|
40.3
|
1.0
|
HB2
|
A:ARG124
|
3.1
|
33.0
|
1.0
|
HG23
|
A:VAL123
|
3.2
|
31.0
|
0.5
|
HB3
|
A:ARG457
|
3.4
|
37.2
|
1.0
|
HG13
|
A:VAL123
|
3.4
|
30.4
|
0.5
|
H
|
A:ARG457
|
3.4
|
32.9
|
1.0
|
CG
|
A:ARG124
|
3.6
|
29.0
|
1.0
|
CB
|
A:ARG124
|
3.6
|
27.4
|
1.0
|
CA
|
A:VAL123
|
3.6
|
23.5
|
0.5
|
O
|
A:HOH910
|
3.6
|
47.5
|
1.0
|
C
|
A:ARG457
|
3.7
|
29.3
|
1.0
|
CA
|
A:VAL123
|
3.7
|
23.4
|
0.5
|
CD
|
A:GLU459
|
3.7
|
39.8
|
1.0
|
C
|
A:VAL123
|
3.8
|
22.1
|
0.5
|
C
|
A:VAL123
|
3.8
|
22.1
|
0.5
|
HG2
|
A:ARG457
|
3.8
|
55.0
|
1.0
|
HD2
|
A:ARG124
|
3.8
|
35.9
|
1.0
|
CG
|
A:GLU459
|
3.8
|
33.5
|
1.0
|
CA
|
A:ARG124
|
3.8
|
24.8
|
1.0
|
N
|
A:ARG457
|
4.0
|
27.3
|
1.0
|
CG2
|
A:VAL123
|
4.0
|
25.7
|
0.5
|
CB
|
A:ARG457
|
4.1
|
30.9
|
1.0
|
HE
|
A:ARG124
|
4.1
|
39.1
|
1.0
|
CA
|
A:ARG457
|
4.1
|
27.3
|
1.0
|
CD
|
A:ARG124
|
4.1
|
29.8
|
1.0
|
CG1
|
A:VAL123
|
4.1
|
25.2
|
0.5
|
HG22
|
A:VAL123
|
4.2
|
31.0
|
0.5
|
HG12
|
A:VAL123
|
4.2
|
30.4
|
0.5
|
O
|
A:ARG124
|
4.2
|
28.4
|
1.0
|
O
|
A:PHE122
|
4.3
|
25.3
|
1.0
|
CG
|
A:ARG457
|
4.4
|
45.7
|
1.0
|
HG2
|
A:ARG124
|
4.4
|
35.0
|
1.0
|
CB
|
A:VAL123
|
4.4
|
26.0
|
0.5
|
HG2
|
A:GLU459
|
4.4
|
40.3
|
1.0
|
H
|
A:GLU459
|
4.5
|
30.6
|
0.6
|
H
|
A:GLU459
|
4.5
|
30.6
|
0.4
|
NE
|
A:ARG124
|
4.5
|
32.4
|
1.0
|
HB2
|
A:GLU459
|
4.5
|
35.1
|
1.0
|
CB
|
A:VAL123
|
4.5
|
26.1
|
0.5
|
HB3
|
A:ARG124
|
4.5
|
33.0
|
1.0
|
C
|
A:ARG124
|
4.5
|
30.3
|
1.0
|
HA
|
A:ARG124
|
4.6
|
30.0
|
1.0
|
HG22
|
A:VAL123
|
4.6
|
32.2
|
0.5
|
N
|
A:VAL123
|
4.7
|
22.6
|
0.5
|
N
|
A:VAL123
|
4.7
|
22.6
|
0.5
|
HB
|
A:VAL123
|
4.7
|
31.4
|
0.5
|
HG3
|
A:ARG457
|
4.7
|
55.0
|
1.0
|
HA
|
A:ILE458
|
4.8
|
33.4
|
0.6
|
CB
|
A:GLU459
|
4.8
|
29.1
|
1.0
|
N
|
A:ILE458
|
4.8
|
27.0
|
0.6
|
N
|
A:ILE458
|
4.8
|
27.2
|
0.4
|
HG21
|
A:VAL123
|
4.8
|
31.0
|
0.5
|
HA
|
A:ILE458
|
4.8
|
33.5
|
0.4
|
N
|
A:GLU459
|
4.8
|
25.4
|
1.0
|
HE2
|
A:PHE122
|
4.9
|
38.0
|
1.0
|
OE1
|
A:GLU459
|
4.9
|
36.4
|
1.0
|
HD2
|
A:PHE122
|
4.9
|
34.6
|
1.0
|
C
|
A:PHE122
|
4.9
|
22.4
|
1.0
|
HB2
|
A:ARG457
|
4.9
|
37.2
|
1.0
|
HG11
|
A:VAL123
|
5.0
|
30.4
|
0.5
|
O
|
A:VAL123
|
5.0
|
22.8
|
0.5
|
O
|
A:VAL123
|
5.0
|
23.4
|
0.5
|
|
Sodium binding site 3 out
of 7 in 8qnf
Go back to
Sodium Binding Sites List in 8qnf
Sodium binding site 3 out
of 7 in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na616
b:33.2
occ:1.00
|
HE
|
A:ARG366
|
2.4
|
30.1
|
1.0
|
HD2
|
A:ARG366
|
2.7
|
31.7
|
1.0
|
OD2
|
A:ASP227
|
2.8
|
29.6
|
1.0
|
O
|
A:HOH966
|
2.8
|
26.3
|
1.0
|
OG
|
A:SER364
|
2.9
|
29.3
|
1.0
|
HG12
|
A:VAL379
|
3.0
|
37.7
|
0.3
|
O
|
A:PHE378
|
3.1
|
27.0
|
1.0
|
HG
|
A:SER364
|
3.1
|
35.4
|
1.0
|
NE
|
A:ARG366
|
3.1
|
25.0
|
1.0
|
HG3
|
A:ARG366
|
3.1
|
32.1
|
1.0
|
HG13
|
A:VAL379
|
3.2
|
37.7
|
0.3
|
HG13
|
A:VAL379
|
3.2
|
33.5
|
0.1
|
CD
|
A:ARG366
|
3.2
|
26.3
|
1.0
|
HB2
|
A:PHE378
|
3.3
|
30.1
|
1.0
|
HG23
|
A:VAL379
|
3.3
|
36.1
|
0.5
|
HG22
|
A:VAL379
|
3.3
|
36.1
|
0.5
|
HA
|
A:SER364
|
3.4
|
29.3
|
1.0
|
HB2
|
A:SER364
|
3.4
|
38.1
|
1.0
|
CG
|
A:ASP227
|
3.4
|
29.5
|
1.0
|
HB3
|
A:ALA229
|
3.5
|
28.6
|
1.0
|
CG1
|
A:VAL379
|
3.5
|
31.2
|
0.3
|
CB
|
A:SER364
|
3.6
|
31.6
|
1.0
|
CG
|
A:ARG366
|
3.7
|
26.6
|
1.0
|
CG2
|
A:VAL379
|
3.8
|
30.0
|
0.5
|
HG11
|
A:VAL379
|
3.9
|
37.7
|
0.3
|
HB2
|
A:ALA229
|
3.9
|
28.6
|
1.0
|
HB2
|
A:ASP227
|
3.9
|
30.0
|
1.0
|
HG22
|
A:VAL379
|
3.9
|
33.0
|
0.1
|
C
|
A:PHE378
|
3.9
|
26.4
|
1.0
|
H
|
A:LEU365
|
4.0
|
35.6
|
1.0
|
CA
|
A:SER364
|
4.0
|
24.2
|
1.0
|
OD1
|
A:ASP227
|
4.0
|
25.5
|
1.0
|
CB
|
A:PHE378
|
4.1
|
25.0
|
1.0
|
H
|
A:ALA229
|
4.1
|
29.2
|
1.0
|
O
|
A:HOH794
|
4.1
|
44.8
|
1.0
|
CG1
|
A:VAL379
|
4.1
|
27.8
|
0.1
|
CB
|
A:ALA229
|
4.1
|
23.7
|
1.0
|
HD3
|
A:ARG366
|
4.1
|
31.7
|
1.0
|
HB3
|
A:PHE378
|
4.2
|
30.1
|
1.0
|
HG21
|
A:VAL379
|
4.2
|
36.1
|
0.5
|
CB
|
A:ASP227
|
4.3
|
24.9
|
1.0
|
HG11
|
A:VAL379
|
4.3
|
33.5
|
0.1
|
O
|
A:HOH1032
|
4.3
|
38.5
|
1.0
|
CZ
|
A:ARG366
|
4.3
|
26.1
|
1.0
|
HB2
|
A:ARG366
|
4.3
|
35.1
|
1.0
|
HH21
|
A:ARG366
|
4.3
|
32.9
|
1.0
|
H
|
A:PHE378
|
4.4
|
29.1
|
1.0
|
HG2
|
A:ARG366
|
4.4
|
32.1
|
1.0
|
H
|
A:ARG366
|
4.4
|
31.0
|
1.0
|
HB3
|
A:SER364
|
4.5
|
38.1
|
1.0
|
CA
|
A:PHE378
|
4.6
|
22.9
|
1.0
|
N
|
A:LEU365
|
4.6
|
29.5
|
1.0
|
HB3
|
A:ASP227
|
4.6
|
30.0
|
1.0
|
CB
|
A:ARG366
|
4.6
|
29.1
|
1.0
|
HG12
|
A:VAL379
|
4.7
|
33.5
|
0.1
|
HB1
|
A:ALA229
|
4.7
|
28.6
|
1.0
|
HA
|
A:VAL379
|
4.7
|
33.2
|
0.5
|
HA
|
A:VAL379
|
4.7
|
33.2
|
0.3
|
NH2
|
A:ARG366
|
4.7
|
27.3
|
1.0
|
HA
|
A:VAL379
|
4.7
|
33.3
|
0.1
|
CG2
|
A:VAL379
|
4.8
|
27.4
|
0.1
|
N
|
A:VAL379
|
4.8
|
27.9
|
0.3
|
N
|
A:VAL379
|
4.8
|
28.0
|
0.1
|
N
|
A:VAL379
|
4.8
|
27.9
|
0.5
|
C
|
A:SER364
|
4.8
|
27.5
|
1.0
|
CB
|
A:VAL379
|
4.8
|
27.4
|
0.3
|
CB
|
A:VAL379
|
4.9
|
26.9
|
0.1
|
N
|
A:ALA229
|
4.9
|
24.2
|
1.0
|
N
|
A:PHE378
|
4.9
|
24.1
|
1.0
|
N
|
A:ARG366
|
5.0
|
25.7
|
1.0
|
|
Sodium binding site 4 out
of 7 in 8qnf
Go back to
Sodium Binding Sites List in 8qnf
Sodium binding site 4 out
of 7 in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na617
b:40.7
occ:1.00
|
HH22
|
A:ARG355
|
2.1
|
34.9
|
0.6
|
OD2
|
A:ASP389
|
2.7
|
39.9
|
1.0
|
NH2
|
A:ARG355
|
2.9
|
28.9
|
0.6
|
HH12
|
A:ARG355
|
3.0
|
40.5
|
0.6
|
HE3
|
A:MET392
|
3.4
|
43.5
|
1.0
|
HE2
|
A:MET392
|
3.4
|
43.5
|
1.0
|
HH21
|
A:ARG355
|
3.4
|
34.9
|
0.6
|
NH1
|
A:ARG355
|
3.6
|
33.6
|
0.6
|
CZ
|
A:ARG355
|
3.7
|
32.8
|
0.6
|
CG
|
A:ASP389
|
3.8
|
36.0
|
1.0
|
CE
|
A:MET392
|
3.8
|
36.1
|
1.0
|
O
|
A:HOH832
|
4.3
|
43.3
|
1.0
|
HE1
|
A:MET392
|
4.3
|
43.5
|
1.0
|
HH21
|
A:ARG355
|
4.4
|
44.1
|
0.4
|
HH11
|
A:ARG355
|
4.4
|
40.5
|
0.6
|
OD1
|
A:ASP389
|
4.4
|
36.0
|
1.0
|
HG2
|
A:MET392
|
4.5
|
37.8
|
1.0
|
HE
|
A:ARG355
|
4.7
|
41.9
|
0.4
|
HB3
|
A:ASP389
|
4.7
|
38.1
|
1.0
|
NE
|
A:ARG355
|
4.9
|
30.9
|
0.6
|
CB
|
A:ASP389
|
4.9
|
31.6
|
1.0
|
HG3
|
A:MET392
|
5.0
|
37.8
|
1.0
|
|
Sodium binding site 5 out
of 7 in 8qnf
Go back to
Sodium Binding Sites List in 8qnf
Sodium binding site 5 out
of 7 in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na618
b:47.1
occ:1.00
|
OD2
|
A:ASP417
|
2.1
|
64.3
|
0.7
|
H
|
A:ASP417
|
2.1
|
39.0
|
0.3
|
H
|
A:ASP417
|
2.1
|
38.6
|
0.7
|
HB3
|
A:ASP417
|
2.6
|
44.7
|
0.3
|
O
|
A:HOH849
|
2.7
|
45.7
|
1.0
|
N
|
A:ASP417
|
3.0
|
32.4
|
0.3
|
N
|
A:ASP417
|
3.0
|
32.0
|
0.7
|
CG
|
A:ASP417
|
3.0
|
49.1
|
0.7
|
HB2
|
A:ASP417
|
3.1
|
45.2
|
0.7
|
HB3
|
A:PRO415
|
3.1
|
41.3
|
1.0
|
OD1
|
A:ASP417
|
3.1
|
42.1
|
0.3
|
O
|
A:HOH710
|
3.2
|
56.1
|
1.0
|
CB
|
A:ASP417
|
3.3
|
37.1
|
0.3
|
H
|
A:PHE416
|
3.4
|
36.7
|
1.0
|
HB3
|
A:PHE416
|
3.4
|
39.8
|
1.0
|
CB
|
A:ASP417
|
3.4
|
37.5
|
0.7
|
CG
|
A:ASP417
|
3.5
|
38.2
|
0.3
|
N
|
A:PHE416
|
3.6
|
30.5
|
1.0
|
CA
|
A:ASP417
|
3.7
|
33.4
|
0.3
|
HA2
|
A:GLY100
|
3.7
|
52.1
|
1.0
|
CA
|
A:ASP417
|
3.8
|
33.1
|
0.7
|
CB
|
A:PRO415
|
3.8
|
34.3
|
1.0
|
HA3
|
A:GLY103
|
3.9
|
64.1
|
1.0
|
O
|
A:PHE99
|
3.9
|
35.5
|
1.0
|
HB2
|
A:PRO415
|
3.9
|
41.3
|
1.0
|
C
|
A:PRO415
|
3.9
|
32.6
|
1.0
|
C
|
A:PHE416
|
3.9
|
29.3
|
1.0
|
OD1
|
A:ASP417
|
4.0
|
44.0
|
0.7
|
CA
|
A:PHE416
|
4.1
|
29.4
|
1.0
|
HA
|
A:PRO415
|
4.1
|
39.8
|
1.0
|
HB2
|
A:ASP417
|
4.2
|
44.7
|
0.3
|
CB
|
A:PHE416
|
4.2
|
33.0
|
1.0
|
CA
|
A:PRO415
|
4.2
|
33.0
|
1.0
|
HB3
|
A:PHE99
|
4.2
|
42.2
|
1.0
|
H
|
A:LYS418
|
4.2
|
41.2
|
0.7
|
H
|
A:LYS418
|
4.3
|
41.2
|
0.3
|
O
|
A:HOH896
|
4.3
|
51.0
|
1.0
|
HB3
|
A:ASP417
|
4.4
|
45.2
|
0.7
|
HA
|
A:ASP417
|
4.4
|
40.2
|
0.3
|
OD1
|
A:ASN380
|
4.4
|
29.2
|
1.0
|
C
|
A:PHE99
|
4.4
|
35.7
|
1.0
|
H
|
A:GLY103
|
4.5
|
60.4
|
1.0
|
HA
|
A:ASP417
|
4.5
|
39.8
|
0.7
|
O
|
A:HOH868
|
4.5
|
34.4
|
1.0
|
OD2
|
A:ASP417
|
4.5
|
43.1
|
0.3
|
HD2
|
A:PHE416
|
4.5
|
42.7
|
1.0
|
O
|
A:PRO415
|
4.6
|
32.2
|
1.0
|
CA
|
A:GLY100
|
4.6
|
43.3
|
1.0
|
HB2
|
A:PHE416
|
4.7
|
39.8
|
1.0
|
CA
|
A:GLY103
|
4.7
|
53.3
|
1.0
|
N
|
A:GLY100
|
4.8
|
31.7
|
1.0
|
C
|
A:ASP417
|
4.8
|
34.3
|
0.3
|
N
|
A:LYS418
|
4.8
|
34.2
|
1.0
|
C
|
A:ASP417
|
4.8
|
34.1
|
0.7
|
HA2
|
A:GLY103
|
5.0
|
64.1
|
1.0
|
|
Sodium binding site 6 out
of 7 in 8qnf
Go back to
Sodium Binding Sites List in 8qnf
Sodium binding site 6 out
of 7 in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na619
b:43.4
occ:1.00
|
O
|
A:HOH861
|
2.5
|
44.7
|
1.0
|
OD2
|
A:ASP295
|
2.7
|
42.4
|
1.0
|
O
|
A:ASP295
|
2.8
|
31.0
|
1.0
|
O
|
A:THR352
|
2.8
|
35.8
|
1.0
|
CG
|
A:ASP295
|
3.2
|
44.0
|
1.0
|
O
|
A:HOH720
|
3.3
|
53.6
|
1.0
|
HA
|
A:THR352
|
3.4
|
34.6
|
1.0
|
HB3
|
A:ASP295
|
3.4
|
47.0
|
1.0
|
C
|
A:THR352
|
3.6
|
29.5
|
1.0
|
OD1
|
A:ASP295
|
3.8
|
39.1
|
1.0
|
CB
|
A:ASP295
|
3.9
|
39.0
|
1.0
|
C
|
A:ASP295
|
3.9
|
30.1
|
1.0
|
CA
|
A:THR352
|
4.0
|
28.7
|
1.0
|
HD3
|
A:PRO297
|
4.1
|
49.4
|
1.0
|
HB
|
A:THR352
|
4.3
|
33.0
|
1.0
|
O
|
A:HIS351
|
4.4
|
35.9
|
1.0
|
CA
|
A:ASP295
|
4.6
|
37.5
|
1.0
|
O2
|
A:GOL613
|
4.6
|
59.0
|
1.0
|
HB2
|
A:ASP295
|
4.7
|
47.0
|
1.0
|
HG3
|
A:PRO297
|
4.7
|
47.3
|
1.0
|
HA3
|
A:GLY353
|
4.7
|
42.9
|
1.0
|
CB
|
A:THR352
|
4.7
|
27.4
|
1.0
|
N
|
A:GLY353
|
4.8
|
34.4
|
1.0
|
HA
|
A:LEU296
|
4.8
|
37.0
|
1.0
|
CD
|
A:PRO297
|
4.9
|
41.0
|
1.0
|
N
|
A:PRO297
|
4.9
|
33.0
|
1.0
|
|
Sodium binding site 7 out
of 7 in 8qnf
Go back to
Sodium Binding Sites List in 8qnf
Sodium binding site 7 out
of 7 in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na620
b:29.0
occ:1.00
|
OE1
|
A:GLU494
|
2.7
|
36.3
|
1.0
|
O
|
A:HOH942
|
2.9
|
46.1
|
1.0
|
CD
|
A:GLU494
|
3.4
|
31.1
|
1.0
|
OE2
|
A:GLU494
|
3.6
|
39.4
|
1.0
|
O
|
A:HOH841
|
3.8
|
31.8
|
1.0
|
HD13
|
A:LEU313
|
4.4
|
55.6
|
1.0
|
HD12
|
A:LEU313
|
4.6
|
55.6
|
1.0
|
CG
|
A:GLU494
|
4.7
|
31.9
|
1.0
|
HG3
|
A:GLU494
|
4.8
|
38.4
|
1.0
|
CD1
|
A:LEU313
|
4.8
|
46.2
|
1.0
|
HD11
|
A:LEU313
|
4.9
|
55.6
|
1.0
|
|
Reference:
M.N.Karanth,
J.P.Kirkpatrick,
J.Krausze,
S.Schmelz,
A.Scrima,
T.Carlomagno.
The Specificity of Intermodular Recognition in A Prototypical Nonribosomal Peptide Synthetase Depends on An Adaptor Domain Sci Adv V. 10 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADM9404
Page generated: Wed Oct 9 13:11:27 2024
|