Sodium in PDB 6jd0: Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
Enzymatic activity of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
All present enzymatic activity of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding:
3.4.22.15;
Protein crystallography data
The structure of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding, PDB code: 6jd0
was solved by
D.Choudhury,
S.Biswas,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.41 /
1.81
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.835,
64.172,
92.857,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.1 /
21.5
|
Other elements in 6jd0:
The structure of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
(pdb code 6jd0). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Structure of Mutant Human Cathepsin L, Engineered For Gag Binding, PDB code: 6jd0:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6jd0
Go back to
Sodium Binding Sites List in 6jd0
Sodium binding site 1 out
of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na418
b:28.9
occ:1.00
|
CL
|
A:CL415
|
2.6
|
46.3
|
1.0
|
HE1
|
A:PHE135
|
2.7
|
28.7
|
1.0
|
O
|
A:GLY107
|
2.8
|
22.5
|
1.0
|
HA3
|
A:GLY107
|
2.8
|
25.1
|
1.0
|
HB2
|
A:LEU141
|
2.9
|
31.1
|
1.0
|
HD22
|
A:LEU141
|
3.1
|
30.6
|
1.0
|
CE1
|
A:PHE135
|
3.1
|
23.9
|
1.0
|
HA2
|
A:GLY107
|
3.3
|
25.1
|
1.0
|
CA
|
A:GLY107
|
3.4
|
20.9
|
1.0
|
C
|
A:GLY107
|
3.5
|
19.5
|
1.0
|
HZ
|
A:PHE135
|
3.5
|
23.2
|
1.0
|
CZ
|
A:PHE135
|
3.5
|
19.3
|
1.0
|
HB3
|
A:LEU141
|
3.6
|
31.1
|
1.0
|
CB
|
A:LEU141
|
3.7
|
25.9
|
1.0
|
CD2
|
A:LEU141
|
3.8
|
25.5
|
1.0
|
HD23
|
A:LEU141
|
3.8
|
30.6
|
1.0
|
CD1
|
A:PHE135
|
3.8
|
20.9
|
1.0
|
HO
|
A:POL438
|
4.0
|
59.4
|
1.0
|
HD1
|
A:PHE135
|
4.0
|
25.1
|
1.0
|
CG
|
A:LEU141
|
4.3
|
22.8
|
1.0
|
HD13
|
A:LEU141
|
4.4
|
27.8
|
1.0
|
H12
|
A:POL438
|
4.4
|
49.3
|
1.0
|
H
|
A:LEU141
|
4.5
|
31.8
|
1.0
|
CE2
|
A:PHE135
|
4.6
|
21.2
|
1.0
|
O
|
A:POL438
|
4.6
|
49.5
|
1.0
|
HD21
|
A:LEU141
|
4.6
|
30.6
|
1.0
|
N
|
A:GLY107
|
4.7
|
21.1
|
1.0
|
CG
|
A:PHE135
|
4.8
|
20.6
|
1.0
|
N
|
A:TYR108
|
4.8
|
21.1
|
1.0
|
CA
|
A:LEU141
|
4.9
|
24.4
|
1.0
|
N
|
A:LEU141
|
4.9
|
26.5
|
1.0
|
CD1
|
A:LEU141
|
4.9
|
23.2
|
1.0
|
C1
|
A:POL438
|
4.9
|
41.1
|
1.0
|
O
|
A:LYS106
|
5.0
|
22.0
|
1.0
|
|
Sodium binding site 2 out
of 5 in 6jd0
Go back to
Sodium Binding Sites List in 6jd0
Sodium binding site 2 out
of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na419
b:35.3
occ:1.00
|
O
|
A:POL435
|
2.6
|
46.9
|
1.0
|
O1
|
A:PO4428
|
2.6
|
33.3
|
1.0
|
HA2
|
A:GLY286
|
2.7
|
28.2
|
1.0
|
O
|
A:VAL112
|
2.9
|
21.3
|
1.0
|
HO
|
A:POL435
|
2.9
|
56.3
|
1.0
|
HA
|
A:LYS113
|
2.9
|
24.9
|
1.0
|
HB2
|
A:ASN114
|
3.1
|
29.2
|
1.0
|
C
|
A:LYS113
|
3.4
|
21.7
|
1.0
|
CA
|
A:LYS113
|
3.5
|
20.8
|
1.0
|
H12
|
A:POL435
|
3.5
|
61.0
|
1.0
|
C1
|
A:POL435
|
3.6
|
50.9
|
1.0
|
H
|
A:GLU287
|
3.6
|
25.5
|
1.0
|
C
|
A:VAL112
|
3.6
|
26.3
|
1.0
|
O3
|
A:PO4428
|
3.6
|
33.6
|
1.0
|
HG12
|
A:VAL112
|
3.6
|
29.4
|
1.0
|
CA
|
A:GLY286
|
3.6
|
23.5
|
1.0
|
P
|
A:PO4428
|
3.7
|
49.5
|
1.0
|
N
|
A:ASN114
|
3.7
|
21.7
|
1.0
|
H21
|
A:POL435
|
3.7
|
30.0
|
1.0
|
O
|
A:LYS113
|
3.8
|
20.1
|
1.0
|
HA3
|
A:GLY286
|
3.8
|
28.2
|
1.0
|
N
|
A:LYS113
|
3.8
|
21.9
|
1.0
|
O
|
A:HOH511
|
3.9
|
31.2
|
1.0
|
CB
|
A:ASN114
|
3.9
|
24.3
|
1.0
|
H
|
A:ASN114
|
3.9
|
26.0
|
1.0
|
HG3
|
A:GLU287
|
4.0
|
38.4
|
1.0
|
HB3
|
A:ASN114
|
4.1
|
29.2
|
1.0
|
N
|
A:GLU287
|
4.2
|
21.2
|
1.0
|
C2
|
A:POL435
|
4.2
|
25.0
|
1.0
|
H
|
A:GLY286
|
4.3
|
25.8
|
1.0
|
H11
|
A:POL435
|
4.4
|
61.0
|
1.0
|
C
|
A:GLY286
|
4.4
|
20.4
|
1.0
|
CA
|
A:ASN114
|
4.4
|
19.1
|
1.0
|
N
|
A:GLY286
|
4.5
|
21.5
|
1.0
|
CG1
|
A:VAL112
|
4.5
|
24.5
|
1.0
|
HD22
|
A:ASN114
|
4.6
|
26.9
|
1.0
|
H22
|
A:POL435
|
4.6
|
30.0
|
1.0
|
H
|
A:LYS113
|
4.6
|
26.3
|
1.0
|
HB
|
A:VAL112
|
4.6
|
27.3
|
1.0
|
O4
|
A:PO4428
|
4.7
|
65.1
|
1.0
|
O2
|
A:PO4428
|
4.7
|
30.2
|
1.0
|
HA
|
A:ASN114
|
4.7
|
22.9
|
1.0
|
CA
|
A:VAL112
|
4.8
|
22.9
|
1.0
|
CB
|
A:LYS113
|
4.9
|
22.8
|
1.0
|
CB
|
A:VAL112
|
4.9
|
22.7
|
1.0
|
CG
|
A:GLU287
|
4.9
|
32.0
|
1.0
|
HG11
|
A:VAL112
|
5.0
|
29.4
|
1.0
|
|
Sodium binding site 3 out
of 5 in 6jd0
Go back to
Sodium Binding Sites List in 6jd0
Sodium binding site 3 out
of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na420
b:49.2
occ:1.00
|
O2
|
A:PO4424
|
3.0
|
63.8
|
1.0
|
OE2
|
A:GLU244
|
3.1
|
33.5
|
1.0
|
NA
|
A:NA422
|
3.1
|
50.5
|
1.0
|
O2
|
A:PO4425
|
3.8
|
89.0
|
1.0
|
CD
|
A:GLU244
|
4.1
|
40.9
|
1.0
|
P
|
A:PO4424
|
4.2
|
91.7
|
1.0
|
O3
|
A:PO4424
|
4.2
|
87.2
|
1.0
|
OE1
|
A:GLU244
|
4.4
|
42.0
|
1.0
|
HE3
|
A:LYS243
|
4.8
|
67.6
|
1.0
|
O1
|
A:PO4424
|
5.0
|
61.9
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6jd0
Go back to
Sodium Binding Sites List in 6jd0
Sodium binding site 4 out
of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na421
b:58.2
occ:1.00
|
O3
|
A:PO4423
|
2.2
|
63.1
|
1.0
|
HH22
|
A:ARG50
|
2.3
|
55.6
|
1.0
|
O
|
A:GLU43
|
2.9
|
30.0
|
1.0
|
HB2
|
A:GLN47
|
2.9
|
54.0
|
1.0
|
HB3
|
A:GLU43
|
3.0
|
35.9
|
1.0
|
NH2
|
A:ARG50
|
3.1
|
46.3
|
1.0
|
HH21
|
A:ARG50
|
3.4
|
55.6
|
1.0
|
HA
|
A:GLU43
|
3.6
|
36.2
|
1.0
|
C
|
A:GLU43
|
3.6
|
28.7
|
1.0
|
H
|
A:GLN47
|
3.7
|
43.3
|
1.0
|
P
|
A:PO4423
|
3.7
|
82.7
|
1.0
|
CB
|
A:GLU43
|
3.8
|
29.9
|
1.0
|
HH12
|
A:ARG50
|
3.8
|
53.5
|
1.0
|
CA
|
A:GLU43
|
3.9
|
30.2
|
1.0
|
CB
|
A:GLN47
|
3.9
|
45.0
|
1.0
|
HG2
|
A:GLU43
|
4.1
|
43.0
|
1.0
|
OE1
|
A:GLN47
|
4.1
|
60.9
|
1.0
|
N
|
A:GLN47
|
4.2
|
36.1
|
1.0
|
CZ
|
A:ARG50
|
4.2
|
51.0
|
1.0
|
HB3
|
A:GLN47
|
4.3
|
54.0
|
1.0
|
HB2
|
A:ASN46
|
4.3
|
39.4
|
1.0
|
NH1
|
A:ARG50
|
4.4
|
44.6
|
1.0
|
HA
|
A:GLN47
|
4.4
|
46.0
|
1.0
|
O2
|
A:PO4423
|
4.4
|
61.6
|
1.0
|
O1
|
A:PO4423
|
4.4
|
48.6
|
1.0
|
CA
|
A:GLN47
|
4.4
|
38.4
|
1.0
|
HB2
|
A:GLU43
|
4.5
|
35.9
|
1.0
|
CG
|
A:GLU43
|
4.5
|
35.8
|
1.0
|
O4
|
A:PO4423
|
4.5
|
87.6
|
1.0
|
N
|
A:LEU44
|
4.7
|
27.5
|
1.0
|
HA
|
A:LEU44
|
4.7
|
36.1
|
1.0
|
HG3
|
A:GLN47
|
4.7
|
67.5
|
1.0
|
CG
|
A:GLN47
|
4.8
|
56.2
|
1.0
|
CD
|
A:GLN47
|
4.9
|
61.0
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6jd0
Go back to
Sodium Binding Sites List in 6jd0
Sodium binding site 5 out
of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na422
b:50.5
occ:1.00
|
HG1
|
A:THR57
|
2.1
|
32.4
|
1.0
|
OE2
|
A:GLU244
|
2.2
|
33.5
|
1.0
|
HB2
|
A:GLU244
|
2.4
|
34.3
|
1.0
|
OG1
|
A:THR57
|
2.9
|
27.0
|
1.0
|
NA
|
A:NA420
|
3.1
|
49.2
|
1.0
|
HG3
|
A:LYS243
|
3.3
|
27.9
|
1.0
|
CB
|
A:GLU244
|
3.3
|
28.6
|
1.0
|
CD
|
A:GLU244
|
3.3
|
40.9
|
1.0
|
HG21
|
A:THR57
|
3.4
|
32.6
|
1.0
|
HB3
|
A:GLU244
|
3.5
|
34.3
|
1.0
|
CG
|
A:GLU244
|
3.8
|
32.8
|
1.0
|
HG2
|
A:LYS243
|
3.9
|
27.9
|
1.0
|
O2
|
A:PO4425
|
3.9
|
89.0
|
1.0
|
CB
|
A:THR57
|
3.9
|
23.3
|
1.0
|
CG
|
A:LYS243
|
4.0
|
23.2
|
1.0
|
CG2
|
A:THR57
|
4.0
|
27.1
|
1.0
|
HE3
|
A:LYS243
|
4.1
|
67.6
|
1.0
|
HB
|
A:THR57
|
4.1
|
27.9
|
1.0
|
HG3
|
A:GLU244
|
4.1
|
39.4
|
1.0
|
HG23
|
A:THR57
|
4.1
|
32.6
|
1.0
|
H
|
A:GLU244
|
4.3
|
27.7
|
1.0
|
OE1
|
A:GLU244
|
4.4
|
42.0
|
1.0
|
CA
|
A:GLU244
|
4.4
|
21.3
|
1.0
|
N
|
A:GLU244
|
4.5
|
23.1
|
1.0
|
HB3
|
A:LYS243
|
4.5
|
26.9
|
1.0
|
HG2
|
A:GLU244
|
4.7
|
39.4
|
1.0
|
O3
|
A:PO4425
|
4.8
|
60.1
|
1.0
|
CB
|
A:LYS243
|
4.9
|
22.4
|
1.0
|
HG22
|
A:THR57
|
4.9
|
32.6
|
1.0
|
CE
|
A:LYS243
|
4.9
|
56.3
|
1.0
|
H
|
A:THR57
|
4.9
|
30.9
|
1.0
|
P
|
A:PO4425
|
5.0
|
0.8
|
1.0
|
C
|
A:GLU244
|
5.0
|
21.0
|
1.0
|
|
Reference:
D.Choudhury,
S.Biswas.
Structure of Mutant Human Cathepsin L, Engineered For Gag Binding To Be Published.
Page generated: Tue Oct 8 11:25:40 2024
|