Sodium in PDB 9b7e: S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422
Enzymatic activity of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422
All present enzymatic activity of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422:
3.2.1.17;
Protein crystallography data
The structure of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422, PDB code: 9b7e
was solved by
J.Jakoncic,
H.J.Bernstein,
A.S.Soares,
K.Horvat,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.73 /
1.65
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.893,
78.893,
36.952,
90,
90,
90
|
R / Rfree (%)
|
16.1 /
20
|
Other elements in 9b7e:
The structure of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422
(pdb code 9b7e). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422, PDB code: 9b7e:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 9b7e
Go back to
Sodium Binding Sites List in 9b7e
Sodium binding site 1 out
of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na213
b:7.7
occ:1.00
|
O
|
A:SER60
|
2.3
|
8.3
|
1.0
|
O
|
A:ARG73
|
2.3
|
7.8
|
1.0
|
O
|
A:CYS64
|
2.4
|
6.0
|
1.0
|
O
|
A:HOH378
|
2.4
|
7.6
|
1.0
|
OG
|
A:SER72
|
2.5
|
8.9
|
1.0
|
O
|
A:HOH362
|
2.6
|
2.8
|
1.0
|
CB
|
A:SER72
|
3.2
|
8.6
|
1.0
|
C
|
A:CYS64
|
3.4
|
5.2
|
1.0
|
C
|
A:ARG73
|
3.4
|
8.0
|
1.0
|
C
|
A:SER60
|
3.4
|
7.4
|
1.0
|
N
|
A:ARG73
|
3.9
|
8.3
|
1.0
|
CA
|
A:ASN65
|
3.9
|
5.2
|
1.0
|
CA
|
A:SER60
|
4.1
|
6.7
|
1.0
|
N
|
A:ASN65
|
4.1
|
5.1
|
1.0
|
C
|
A:SER72
|
4.1
|
9.3
|
1.0
|
CB
|
A:SER60
|
4.2
|
6.5
|
1.0
|
CA
|
A:ARG73
|
4.3
|
8.5
|
1.0
|
CA
|
A:SER72
|
4.3
|
9.0
|
1.0
|
N
|
A:ASN74
|
4.4
|
7.5
|
1.0
|
N
|
A:CYS64
|
4.4
|
5.2
|
1.0
|
O
|
A:ARG61
|
4.4
|
8.8
|
1.0
|
C
|
A:ARG61
|
4.5
|
9.6
|
1.0
|
N
|
A:ARG61
|
4.5
|
8.7
|
1.0
|
CA
|
A:ASN74
|
4.5
|
7.2
|
1.0
|
CA
|
A:CYS64
|
4.6
|
5.2
|
1.0
|
OD1
|
A:ASN65
|
4.7
|
5.9
|
1.0
|
N
|
A:ASP66
|
4.7
|
5.1
|
1.0
|
O
|
A:HOH398
|
4.7
|
25.1
|
1.0
|
CB
|
A:ASN74
|
4.7
|
7.1
|
1.0
|
O
|
A:SER72
|
4.7
|
9.5
|
1.0
|
CL
|
A:CL205
|
4.7
|
8.6
|
1.0
|
CA
|
A:ARG61
|
4.7
|
9.5
|
0.5
|
CB
|
A:THR69
|
4.8
|
7.5
|
1.0
|
CA
|
A:ARG61
|
4.8
|
9.7
|
0.5
|
CB
|
A:ASN65
|
4.8
|
5.2
|
1.0
|
C
|
A:ASN65
|
4.8
|
5.1
|
1.0
|
N
|
A:TRP62
|
4.9
|
8.8
|
1.0
|
N
|
A:TRP63
|
5.0
|
6.3
|
1.0
|
|
Sodium binding site 2 out
of 4 in 9b7e
Go back to
Sodium Binding Sites List in 9b7e
Sodium binding site 2 out
of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na214
b:13.0
occ:1.00
|
O
|
A:ALA82
|
2.6
|
8.2
|
1.0
|
O
|
A:ASP87
|
2.6
|
12.3
|
1.0
|
N
|
A:SER91
|
2.8
|
8.0
|
1.0
|
O
|
A:HOH321
|
3.1
|
6.9
|
1.0
|
O
|
A:HOH329
|
3.3
|
8.8
|
1.0
|
N
|
A:ALA90
|
3.4
|
7.7
|
1.0
|
CB
|
A:ALA90
|
3.5
|
7.6
|
1.0
|
C
|
A:ALA90
|
3.6
|
7.6
|
1.0
|
CA
|
A:ALA90
|
3.7
|
7.6
|
1.0
|
C
|
A:ILE88
|
3.7
|
8.6
|
1.0
|
CA
|
A:ILE88
|
3.7
|
8.7
|
1.0
|
C
|
A:ASP87
|
3.7
|
9.3
|
1.0
|
C
|
A:ALA82
|
3.8
|
6.3
|
1.0
|
O
|
A:ILE88
|
3.8
|
7.9
|
1.0
|
CB
|
A:SER91
|
3.8
|
7.6
|
1.0
|
CA
|
A:SER91
|
3.8
|
7.2
|
1.0
|
CA
|
A:LEU83
|
3.9
|
5.8
|
1.0
|
OG
|
A:SER91
|
3.9
|
8.5
|
1.0
|
N
|
A:THR89
|
4.1
|
8.6
|
1.0
|
C
|
A:LEU83
|
4.1
|
5.7
|
1.0
|
CB
|
A:SER85
|
4.2
|
7.4
|
1.0
|
N
|
A:ILE88
|
4.2
|
9.3
|
1.0
|
O
|
A:HOH386
|
4.2
|
17.0
|
1.0
|
N
|
A:LEU83
|
4.3
|
5.7
|
1.0
|
O
|
A:LEU83
|
4.3
|
5.5
|
1.0
|
C
|
A:THR89
|
4.4
|
8.4
|
1.0
|
O
|
A:HOH313
|
4.4
|
10.9
|
1.0
|
O
|
A:SER85
|
4.5
|
7.3
|
1.0
|
N
|
A:SER85
|
4.5
|
6.7
|
1.0
|
N
|
A:LEU84
|
4.8
|
6.0
|
1.0
|
CD2
|
A:LEU83
|
4.8
|
6.2
|
1.0
|
O
|
A:ALA90
|
4.8
|
7.4
|
1.0
|
CA
|
A:SER85
|
4.8
|
7.2
|
1.0
|
CA
|
A:THR89
|
4.9
|
8.6
|
1.0
|
CB
|
A:ILE88
|
5.0
|
8.2
|
1.0
|
|
Sodium binding site 3 out
of 4 in 9b7e
Go back to
Sodium Binding Sites List in 9b7e
Sodium binding site 3 out
of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na215
b:9.3
occ:1.00
|
O
|
A:TYR53
|
2.6
|
5.6
|
1.0
|
N
|
A:LEU56
|
2.7
|
6.4
|
1.0
|
OG
|
A:SER91
|
2.7
|
8.5
|
1.0
|
N
|
A:ILE55
|
3.2
|
5.3
|
1.0
|
C
|
A:GLY54
|
3.3
|
5.2
|
1.0
|
N
|
A:GLN57
|
3.4
|
4.2
|
1.0
|
CA
|
A:LEU56
|
3.4
|
5.3
|
1.0
|
CA
|
A:GLY54
|
3.5
|
4.7
|
1.0
|
C
|
A:LEU56
|
3.6
|
4.8
|
1.0
|
C
|
A:TYR53
|
3.6
|
4.6
|
1.0
|
CB
|
A:SER91
|
3.7
|
7.6
|
1.0
|
CB
|
A:LEU56
|
3.8
|
5.5
|
1.0
|
C
|
A:ILE55
|
3.8
|
6.4
|
1.0
|
CD1
|
A:ILE58
|
3.8
|
5.1
|
1.0
|
O
|
A:GLY54
|
3.8
|
4.9
|
1.0
|
O
|
A:HOH313
|
3.9
|
10.9
|
1.0
|
CG1
|
A:ILE58
|
3.9
|
4.7
|
1.0
|
N
|
A:ILE58
|
4.0
|
4.5
|
1.0
|
N
|
A:GLY54
|
4.0
|
4.6
|
1.0
|
CA
|
A:ILE55
|
4.1
|
6.5
|
1.0
|
CG1
|
A:ILE55
|
4.2
|
8.3
|
1.0
|
CB
|
A:ILE58
|
4.3
|
4.8
|
1.0
|
O
|
A:LEU83
|
4.4
|
5.5
|
1.0
|
CA
|
A:GLN57
|
4.4
|
4.2
|
1.0
|
CB
|
A:LEU83
|
4.5
|
5.7
|
1.0
|
O
|
A:LEU56
|
4.5
|
4.5
|
1.0
|
CD2
|
A:LEU83
|
4.6
|
6.2
|
1.0
|
CA
|
A:SER91
|
4.6
|
7.2
|
1.0
|
C
|
A:GLN57
|
4.7
|
4.3
|
1.0
|
CB
|
A:ILE55
|
4.7
|
7.6
|
1.0
|
CG
|
A:LEU56
|
4.8
|
5.6
|
1.0
|
CA
|
A:ILE58
|
4.8
|
4.8
|
1.0
|
O
|
A:ILE55
|
4.9
|
6.5
|
1.0
|
CG
|
A:LEU83
|
5.0
|
5.7
|
1.0
|
|
Sodium binding site 4 out
of 4 in 9b7e
Go back to
Sodium Binding Sites List in 9b7e
Sodium binding site 4 out
of 4 in the S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of S_SAD Structure of Hewl Using Lossy Compression Data with A Compression Ratio of 422 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na216
b:12.6
occ:1.00
|
NE
|
A:ARG114
|
2.5
|
7.3
|
1.0
|
O
|
A:HOH332
|
3.1
|
10.7
|
1.0
|
NH2
|
A:ARG114
|
3.3
|
6.1
|
1.0
|
CZ
|
A:ARG114
|
3.3
|
6.5
|
1.0
|
CB
|
A:ARG114
|
3.6
|
6.1
|
1.0
|
CD
|
A:ARG114
|
3.6
|
6.5
|
1.0
|
CG
|
A:ARG114
|
3.6
|
6.4
|
1.0
|
CZ
|
A:PHE34
|
3.9
|
6.0
|
1.0
|
CE1
|
A:PHE34
|
4.2
|
6.0
|
1.0
|
CE2
|
A:PHE34
|
4.2
|
5.9
|
1.0
|
CA
|
A:ARG114
|
4.3
|
6.0
|
1.0
|
O
|
A:ARG114
|
4.4
|
6.7
|
1.0
|
NH1
|
A:ARG114
|
4.6
|
6.4
|
1.0
|
CD1
|
A:PHE34
|
4.7
|
5.6
|
1.0
|
CD2
|
A:PHE34
|
4.7
|
5.7
|
1.0
|
C
|
A:ARG114
|
4.9
|
6.2
|
1.0
|
CG
|
A:PHE34
|
5.0
|
5.3
|
1.0
|
|
Reference:
J.Jakoncic,
H.J.Bernstein,
A.S.Soares,
K.Horvat.
Investigation of Fast and Efficient Lossless Compression Algorithms For Macromolecular Crystallography Experiments To Be Published.
Page generated: Wed Oct 9 14:28:10 2024
|