Sodium in PDB 6j05: Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression
Protein crystallography data
The structure of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression, PDB code: 6j05
was solved by
C.Prabaharan,
P.Kandavelu,
C.Packianathan,
P.B.Rosen,
S.Thiyagarajan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.53 /
1.86
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.922,
42.727,
49.132,
90.00,
117.62,
90.00
|
R / Rfree (%)
|
16.5 /
23.1
|
Other elements in 6j05:
The structure of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression
(pdb code 6j05). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression, PDB code: 6j05:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 6j05
Go back to
Sodium Binding Sites List in 6j05
Sodium binding site 1 out
of 3 in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:25.0
occ:1.00
|
OE1
|
A:GLU33
|
2.6
|
15.0
|
1.0
|
O
|
A:LEU29
|
2.7
|
15.5
|
1.0
|
N
|
A:ALA79
|
3.1
|
15.3
|
1.0
|
CA
|
A:ARG78
|
3.4
|
17.1
|
1.0
|
CA
|
A:GLY36
|
3.5
|
17.3
|
1.0
|
CD
|
A:GLU33
|
3.5
|
17.0
|
1.0
|
C
|
A:LEU29
|
3.6
|
15.3
|
1.0
|
CG
|
A:GLU33
|
3.7
|
18.1
|
1.0
|
C
|
A:ARG78
|
3.8
|
16.4
|
1.0
|
N
|
A:GLU33
|
3.8
|
18.7
|
1.0
|
CB
|
A:ARG78
|
3.8
|
18.7
|
1.0
|
N
|
A:GLY36
|
3.8
|
18.5
|
1.0
|
C
|
A:GLN32
|
3.9
|
17.7
|
1.0
|
O
|
A:GLN32
|
3.9
|
17.4
|
1.0
|
CA
|
A:GLU33
|
3.9
|
18.2
|
1.0
|
CA
|
A:LEU29
|
3.9
|
14.7
|
1.0
|
CB
|
A:LEU29
|
4.0
|
14.7
|
1.0
|
CG
|
A:ARG78
|
4.0
|
20.3
|
1.0
|
CB
|
A:ALA79
|
4.2
|
16.8
|
1.0
|
CD2
|
A:LEU29
|
4.2
|
15.5
|
1.0
|
CA
|
A:ALA79
|
4.2
|
16.3
|
1.0
|
O
|
A:TYR77
|
4.3
|
14.2
|
1.0
|
CB
|
A:GLU33
|
4.5
|
18.1
|
1.0
|
OE2
|
A:GLU33
|
4.6
|
17.1
|
1.0
|
N
|
A:ARG78
|
4.6
|
15.7
|
1.0
|
CB
|
A:GLN32
|
4.6
|
16.0
|
1.0
|
O
|
A:ALA79
|
4.7
|
16.3
|
1.0
|
N
|
A:VAL30
|
4.7
|
15.4
|
1.0
|
CA
|
A:GLN32
|
4.7
|
17.2
|
1.0
|
CG
|
A:LEU29
|
4.7
|
15.3
|
1.0
|
C
|
A:GLY36
|
4.8
|
16.0
|
1.0
|
NE
|
A:ARG78
|
4.8
|
20.8
|
1.0
|
C
|
A:TYR77
|
4.9
|
16.7
|
1.0
|
C
|
A:ALA79
|
4.9
|
15.8
|
1.0
|
O
|
A:ARG78
|
4.9
|
15.8
|
1.0
|
N
|
A:GLN32
|
5.0
|
16.4
|
1.0
|
C
|
A:THR35
|
5.0
|
19.2
|
1.0
|
|
Sodium binding site 2 out
of 3 in 6j05
Go back to
Sodium Binding Sites List in 6j05
Sodium binding site 2 out
of 3 in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na201
b:28.2
occ:1.00
|
O
|
B:LEU29
|
2.7
|
17.2
|
1.0
|
OE2
|
B:GLU33
|
2.8
|
20.0
|
1.0
|
N
|
B:ALA79
|
3.2
|
18.6
|
1.0
|
CA
|
B:GLY36
|
3.4
|
24.0
|
1.0
|
CA
|
B:ARG78
|
3.4
|
20.2
|
1.0
|
C
|
B:LEU29
|
3.5
|
16.5
|
1.0
|
N
|
B:GLU33
|
3.6
|
18.5
|
1.0
|
CG
|
B:GLU33
|
3.6
|
19.5
|
1.0
|
C
|
B:GLN32
|
3.6
|
19.5
|
1.0
|
CD
|
B:GLU33
|
3.7
|
20.1
|
1.0
|
N
|
B:GLY36
|
3.7
|
24.4
|
1.0
|
O
|
B:GLN32
|
3.7
|
19.3
|
1.0
|
C
|
B:ARG78
|
3.7
|
19.5
|
1.0
|
CA
|
B:GLU33
|
3.8
|
19.8
|
1.0
|
CB
|
B:ARG78
|
3.8
|
21.1
|
1.0
|
CA
|
B:LEU29
|
3.9
|
16.0
|
1.0
|
CG
|
B:ARG78
|
3.9
|
22.0
|
1.0
|
CB
|
B:LEU29
|
3.9
|
16.2
|
1.0
|
O
|
B:TYR77
|
4.2
|
18.2
|
1.0
|
CD2
|
B:LEU29
|
4.2
|
17.9
|
1.0
|
CB
|
B:GLU33
|
4.3
|
19.1
|
1.0
|
CA
|
B:ALA79
|
4.4
|
18.2
|
1.0
|
CB
|
B:GLN32
|
4.4
|
19.3
|
1.0
|
CA
|
B:GLN32
|
4.4
|
19.1
|
1.0
|
CB
|
B:ALA79
|
4.5
|
17.1
|
1.0
|
N
|
B:ARG78
|
4.6
|
19.9
|
1.0
|
N
|
B:VAL30
|
4.6
|
16.6
|
1.0
|
C
|
B:GLY36
|
4.6
|
23.3
|
1.0
|
CG
|
B:LEU29
|
4.7
|
17.2
|
1.0
|
C
|
B:THR35
|
4.7
|
26.6
|
1.0
|
NE
|
B:ARG78
|
4.8
|
23.7
|
1.0
|
C
|
B:TYR77
|
4.8
|
20.4
|
1.0
|
N
|
B:GLN32
|
4.8
|
17.6
|
1.0
|
OE1
|
B:GLU33
|
4.8
|
20.6
|
1.0
|
O
|
B:ALA79
|
4.9
|
19.7
|
1.0
|
CD
|
B:ARG78
|
4.9
|
22.6
|
1.0
|
N
|
B:THR35
|
5.0
|
24.0
|
1.0
|
|
Sodium binding site 3 out
of 3 in 6j05
Go back to
Sodium Binding Sites List in 6j05
Sodium binding site 3 out
of 3 in the Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structures of Two Arsr As(III)-Responsive Repressors: Implications For the Mechanism of Derepression within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na202
b:34.8
occ:1.00
|
O
|
A:HOH361
|
2.5
|
32.1
|
1.0
|
OE1
|
B:GLU24
|
2.7
|
17.4
|
1.0
|
NE
|
B:ARG27
|
3.0
|
16.9
|
0.9
|
CD
|
B:GLU24
|
3.1
|
18.9
|
1.0
|
NH1
|
B:ARG27
|
3.2
|
18.4
|
0.1
|
NH1
|
B:ARG27
|
3.5
|
19.0
|
0.9
|
CZ
|
B:ARG27
|
3.7
|
17.8
|
0.9
|
OE2
|
B:GLU24
|
3.7
|
18.3
|
1.0
|
CD
|
B:ARG27
|
3.8
|
17.6
|
0.1
|
CA
|
B:GLU24
|
3.8
|
18.8
|
1.0
|
CG
|
B:GLU24
|
3.9
|
17.8
|
1.0
|
O
|
B:HOH318
|
4.0
|
17.4
|
1.0
|
N
|
B:GLU24
|
4.0
|
17.8
|
1.0
|
O
|
B:LEU23
|
4.0
|
16.7
|
1.0
|
CD
|
B:ARG27
|
4.0
|
17.1
|
0.9
|
CG
|
B:ARG27
|
4.0
|
17.0
|
0.9
|
O
|
B:HOH330
|
4.0
|
35.2
|
1.0
|
CG
|
B:LEU23
|
4.1
|
21.9
|
1.0
|
CZ
|
B:ARG27
|
4.1
|
18.2
|
0.1
|
CB
|
B:ARG27
|
4.1
|
16.8
|
0.1
|
CB
|
B:ARG27
|
4.1
|
16.6
|
0.9
|
C
|
B:LEU23
|
4.1
|
18.2
|
1.0
|
CG
|
B:ARG27
|
4.2
|
17.1
|
0.1
|
OH
|
A:TYR90
|
4.3
|
22.9
|
1.0
|
NE
|
B:ARG27
|
4.3
|
17.8
|
0.1
|
O
|
B:HOH328
|
4.3
|
24.1
|
1.0
|
CB
|
B:GLU24
|
4.3
|
18.4
|
1.0
|
CD2
|
B:LEU23
|
4.5
|
21.7
|
1.0
|
CE2
|
A:TYR90
|
4.5
|
19.6
|
1.0
|
CB
|
B:LEU23
|
4.7
|
20.6
|
1.0
|
CZ
|
A:TYR90
|
4.8
|
20.8
|
1.0
|
C
|
B:GLU24
|
4.9
|
17.8
|
1.0
|
NH2
|
B:ARG27
|
5.0
|
16.2
|
0.9
|
|
Reference:
C.Prabaharan,
P.Kandavelu,
C.Packianathan,
B.P.Rosen,
S.Thiyagarajan.
Structures of Two Arsr As(III)-Responsive Transcriptional Repressors: Implications For the Mechanism of Derepression. J.Struct.Biol. V. 207 209 2019.
ISSN: ESSN 1095-8657
PubMed: 31136796
DOI: 10.1016/J.JSB.2019.05.009
Page generated: Tue Oct 8 09:40:46 2024
|