Sodium in PDB 8jfs: Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution
Enzymatic activity of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution
All present enzymatic activity of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution:
3.6.1.7;
Protein crystallography data
The structure of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution, PDB code: 8jfs
was solved by
Z.Khakerwala,
A.Kumar,
R.D.Makde,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.00 /
1.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
33.003,
28.472,
83.604,
90,
90.43,
90
|
R / Rfree (%)
|
19.3 /
20.5
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution
(pdb code 8jfs). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution, PDB code: 8jfs:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 8jfs
Go back to
Sodium Binding Sites List in 8jfs
Sodium binding site 1 out
of 3 in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na103
b:32.7
occ:1.00
|
NH1
|
A:ARG17
|
2.2
|
13.4
|
1.0
|
O
|
A:HOH246
|
2.3
|
17.6
|
1.0
|
O
|
A:TYR87
|
2.5
|
12.3
|
1.0
|
CB
|
A:ASN35
|
2.7
|
8.8
|
1.0
|
N
|
A:ASN35
|
2.8
|
6.8
|
1.0
|
OXT
|
A:TYR87
|
3.0
|
17.7
|
1.0
|
C
|
A:TYR87
|
3.1
|
12.3
|
1.0
|
CA
|
A:ASN35
|
3.2
|
7.1
|
1.0
|
CG
|
A:ASN35
|
3.3
|
7.7
|
1.0
|
CZ
|
A:ARG17
|
3.3
|
11.8
|
1.0
|
O
|
A:HOH285
|
3.5
|
28.8
|
1.0
|
ND2
|
A:ASN35
|
3.6
|
10.0
|
1.0
|
CD
|
A:ARG17
|
3.8
|
8.7
|
1.0
|
O
|
A:ASN35
|
3.8
|
9.9
|
1.0
|
O
|
A:HOH271
|
3.8
|
17.7
|
1.0
|
NE
|
A:ARG17
|
3.9
|
9.6
|
1.0
|
C
|
A:GLU34
|
3.9
|
6.8
|
1.0
|
OD1
|
A:ASN35
|
4.0
|
8.4
|
1.0
|
C
|
A:ASN35
|
4.0
|
7.6
|
1.0
|
NH2
|
A:ARG17
|
4.2
|
15.2
|
1.0
|
CA
|
A:GLU34
|
4.3
|
8.9
|
1.0
|
CA
|
A:TYR87
|
4.6
|
11.0
|
1.0
|
CG
|
A:GLU34
|
4.7
|
13.4
|
1.0
|
O
|
A:HOH289
|
4.8
|
20.1
|
1.0
|
|
Sodium binding site 2 out
of 3 in 8jfs
Go back to
Sodium Binding Sites List in 8jfs
Sodium binding site 2 out
of 3 in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na104
b:14.7
occ:1.00
|
O2
|
A:PO4101
|
2.7
|
7.8
|
1.0
|
O
|
A:HOH301
|
2.8
|
14.8
|
0.6
|
O
|
A:HOH301
|
2.9
|
19.4
|
0.4
|
N
|
A:LEU18
|
3.0
|
7.3
|
1.0
|
CA
|
A:GLY15
|
3.3
|
9.3
|
1.0
|
C
|
A:GLY15
|
3.3
|
7.8
|
1.0
|
N
|
A:ARG17
|
3.3
|
6.6
|
1.0
|
CG
|
A:LEU18
|
3.5
|
12.0
|
1.0
|
O
|
A:GLY15
|
3.6
|
9.1
|
1.0
|
CB
|
A:ARG17
|
3.6
|
6.9
|
1.0
|
CB
|
A:LEU18
|
3.6
|
9.7
|
1.0
|
N
|
A:TYR16
|
3.7
|
7.1
|
1.0
|
CA
|
A:ARG17
|
3.7
|
6.6
|
1.0
|
CD1
|
A:LEU18
|
3.8
|
14.8
|
1.0
|
C
|
A:ARG17
|
3.8
|
6.6
|
1.0
|
CA
|
A:LEU18
|
3.9
|
8.6
|
1.0
|
O
|
A:HOH253
|
4.0
|
15.5
|
1.0
|
NE
|
A:ARG17
|
4.1
|
9.6
|
1.0
|
N
|
A:GLY15
|
4.1
|
8.7
|
1.0
|
C
|
A:TYR16
|
4.2
|
6.7
|
1.0
|
P
|
A:PO4101
|
4.2
|
7.3
|
1.0
|
CG
|
A:ARG17
|
4.5
|
8.6
|
1.0
|
CA
|
A:TYR16
|
4.6
|
6.4
|
1.0
|
NH2
|
A:ARG17
|
4.6
|
15.2
|
1.0
|
O3
|
A:PO4101
|
4.6
|
7.1
|
1.0
|
CD1
|
A:ILE86
|
4.8
|
14.4
|
0.7
|
CZ
|
A:ARG17
|
4.8
|
11.8
|
1.0
|
CD2
|
A:LEU18
|
4.8
|
14.1
|
1.0
|
O1
|
A:PO4101
|
4.9
|
7.7
|
1.0
|
CD
|
A:ARG17
|
4.9
|
8.7
|
1.0
|
O
|
A:ARG17
|
5.0
|
7.0
|
1.0
|
|
Sodium binding site 3 out
of 3 in 8jfs
Go back to
Sodium Binding Sites List in 8jfs
Sodium binding site 3 out
of 3 in the Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Phosphate Bound Acylphosphatase From Deinococcus Radiodurans at 1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na103
b:14.7
occ:1.00
|
O4
|
B:PO4101
|
2.8
|
7.3
|
0.9
|
O
|
B:HOH282
|
2.8
|
15.8
|
0.4
|
N
|
B:LEU18
|
2.9
|
7.4
|
1.0
|
C
|
B:GLY15
|
3.3
|
7.3
|
1.0
|
CA
|
B:GLY15
|
3.3
|
8.6
|
1.0
|
N
|
B:ARG17
|
3.3
|
6.9
|
0.5
|
N
|
B:ARG17
|
3.3
|
6.8
|
0.5
|
CG
|
B:LEU18
|
3.4
|
11.6
|
1.0
|
CB
|
B:LEU18
|
3.6
|
8.5
|
1.0
|
CB
|
B:ARG17
|
3.6
|
7.8
|
0.5
|
O
|
B:GLY15
|
3.6
|
7.9
|
1.0
|
CB
|
B:ARG17
|
3.7
|
7.8
|
0.5
|
N
|
B:TYR16
|
3.7
|
6.9
|
1.0
|
CA
|
B:ARG17
|
3.7
|
7.4
|
0.5
|
CD1
|
B:LEU18
|
3.7
|
12.8
|
1.0
|
CA
|
B:ARG17
|
3.7
|
7.4
|
0.5
|
C
|
B:ARG17
|
3.7
|
7.4
|
0.5
|
C
|
B:ARG17
|
3.8
|
7.4
|
0.5
|
CA
|
B:LEU18
|
3.8
|
8.0
|
1.0
|
NE
|
B:ARG17
|
4.0
|
9.8
|
0.5
|
N
|
B:GLY15
|
4.1
|
8.2
|
1.0
|
C
|
B:TYR16
|
4.1
|
6.3
|
1.0
|
O
|
B:HOH201
|
4.2
|
22.4
|
1.0
|
NH2
|
B:ARG17
|
4.2
|
12.3
|
0.5
|
P
|
B:PO4101
|
4.2
|
6.5
|
0.9
|
NE
|
B:ARG17
|
4.2
|
10.3
|
0.5
|
CG
|
B:ARG17
|
4.5
|
7.7
|
0.5
|
CZ
|
B:ARG17
|
4.5
|
12.5
|
0.5
|
CA
|
B:TYR16
|
4.5
|
7.1
|
1.0
|
CG
|
B:ARG17
|
4.6
|
7.7
|
0.5
|
O1
|
B:PO4101
|
4.7
|
7.4
|
0.9
|
NH2
|
B:ARG17
|
4.8
|
13.6
|
0.5
|
CD2
|
B:LEU18
|
4.8
|
12.3
|
1.0
|
CD1
|
B:ILE86
|
4.9
|
15.2
|
0.6
|
CD
|
B:ARG17
|
4.9
|
9.2
|
0.5
|
O
|
B:ARG17
|
4.9
|
7.8
|
0.5
|
O2
|
B:PO4101
|
4.9
|
8.4
|
0.9
|
O
|
B:ARG17
|
4.9
|
7.6
|
0.5
|
CZ
|
B:ARG17
|
5.0
|
12.2
|
0.5
|
O
|
B:TYR16
|
5.0
|
7.5
|
1.0
|
CD
|
B:ARG17
|
5.0
|
8.9
|
0.5
|
|
Reference:
Z.Khakerwala,
A.Kumar,
R.D.Makde.
Crystal Structure of Phosphate Bound Acyl Phosphatase Mini-Enzyme From Deinococcus Radiodurans at 1A Resolution. Biochem.Biophys.Res.Commun. 2023.
ISSN: ESSN 1090-2104
DOI: 10.1016/J.BBRC.2023.06.003
Page generated: Fri Jul 28 03:36:32 2023
|