Sodium in PDB 7q89: Olep Mutant G92W in Complex with 6DEB
Protein crystallography data
The structure of Olep Mutant G92W in Complex with 6DEB, PDB code: 7q89
was solved by
C.Savino,
L.C.Montemiglio,
B.Vallone,
C.Exertier,
I.Freda,
E.Gugole,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.03 /
2.08
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
247.758,
110.489,
159.818,
90,
129.66,
90
|
R / Rfree (%)
|
17 /
22.8
|
Other elements in 7q89:
The structure of Olep Mutant G92W in Complex with 6DEB also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Olep Mutant G92W in Complex with 6DEB
(pdb code 7q89). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Olep Mutant G92W in Complex with 6DEB, PDB code: 7q89:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 1 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na540
b:56.5
occ:1.00
|
OH
|
A:TYR31
|
2.5
|
43.0
|
1.0
|
O
|
A:SER292
|
2.8
|
37.8
|
1.0
|
O2
|
A:FMT510
|
2.8
|
46.9
|
1.0
|
O
|
A:HOH751
|
3.3
|
45.6
|
1.0
|
O
|
A:HOH605
|
3.3
|
57.8
|
1.0
|
CE2
|
A:TYR31
|
3.3
|
44.7
|
1.0
|
CZ
|
A:TYR31
|
3.3
|
37.4
|
1.0
|
NE2
|
A:HIS320
|
3.3
|
33.7
|
1.0
|
CE1
|
A:HIS320
|
3.5
|
36.0
|
1.0
|
C
|
A:FMT510
|
3.6
|
67.8
|
1.0
|
O1
|
A:FMT510
|
3.7
|
70.8
|
1.0
|
NH2
|
A:ARG398
|
3.7
|
44.8
|
1.0
|
CB
|
A:ALA293
|
3.8
|
38.5
|
1.0
|
C
|
A:SER292
|
3.9
|
38.3
|
1.0
|
CA
|
A:ALA293
|
3.9
|
35.3
|
1.0
|
CD2
|
A:HIS320
|
4.1
|
36.7
|
1.0
|
OH
|
A:TYR17
|
4.3
|
40.8
|
1.0
|
ND1
|
A:HIS320
|
4.3
|
34.6
|
1.0
|
N
|
A:ALA293
|
4.4
|
37.0
|
1.0
|
O
|
A:HOH700
|
4.5
|
48.3
|
1.0
|
CD2
|
A:TYR31
|
4.6
|
36.4
|
1.0
|
CE1
|
A:TYR31
|
4.6
|
42.6
|
1.0
|
CG
|
A:HIS320
|
4.6
|
36.1
|
1.0
|
CZ
|
A:ARG398
|
5.0
|
42.4
|
1.0
|
|
Sodium binding site 2 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 2 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na541
b:47.8
occ:1.00
|
O
|
A:HOH693
|
2.7
|
33.6
|
1.0
|
NE
|
A:ARG298
|
3.0
|
32.5
|
1.0
|
O
|
A:HOH660
|
3.1
|
36.9
|
1.0
|
O
|
A:HOH781
|
3.1
|
37.9
|
1.0
|
NH2
|
A:ARG298
|
3.5
|
35.3
|
1.0
|
O
|
A:LEU65
|
3.6
|
37.1
|
1.0
|
CD2
|
A:HIS354
|
3.7
|
36.8
|
1.0
|
CZ
|
A:ARG298
|
3.7
|
35.1
|
1.0
|
CG
|
A:ARG298
|
3.7
|
31.3
|
1.0
|
CD
|
A:ARG298
|
3.9
|
34.2
|
1.0
|
O
|
A:HOH690
|
3.9
|
38.8
|
1.0
|
CG2
|
A:THR72
|
3.9
|
35.1
|
1.0
|
O
|
A:HOH716
|
4.1
|
47.1
|
1.0
|
O
|
A:VAL64
|
4.2
|
35.6
|
1.0
|
C
|
A:LEU65
|
4.2
|
38.4
|
1.0
|
O
|
A:PHE70
|
4.2
|
50.2
|
1.0
|
NE2
|
A:HIS354
|
4.3
|
30.4
|
1.0
|
O
|
A:HOH827
|
4.4
|
57.5
|
1.0
|
CA
|
A:LEU65
|
4.4
|
34.9
|
1.0
|
CG
|
A:HIS354
|
4.8
|
32.3
|
1.0
|
OG1
|
A:THR72
|
5.0
|
38.6
|
1.0
|
|
Sodium binding site 3 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 3 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na540
b:52.3
occ:1.00
|
O
|
B:THR80
|
2.8
|
45.0
|
1.0
|
O
|
B:HOH715
|
3.0
|
39.1
|
1.0
|
O
|
B:ALA75
|
3.0
|
43.1
|
1.0
|
NH1
|
B:ARG82
|
3.1
|
53.5
|
1.0
|
O
|
B:ASP77
|
3.2
|
46.3
|
1.0
|
CD
|
B:PRO88
|
3.5
|
47.4
|
1.0
|
C
|
B:THR80
|
3.6
|
41.7
|
1.0
|
CD
|
B:ARG82
|
3.6
|
47.5
|
1.0
|
CB
|
B:THR80
|
3.6
|
39.0
|
1.0
|
CA
|
B:THR80
|
3.9
|
40.9
|
1.0
|
CB
|
B:ARG82
|
3.9
|
42.7
|
1.0
|
CG
|
B:ARG82
|
3.9
|
41.5
|
1.0
|
N
|
B:THR80
|
3.9
|
42.5
|
1.0
|
O
|
B:PRO81
|
4.1
|
44.9
|
1.0
|
CZ
|
B:ARG82
|
4.1
|
52.7
|
1.0
|
C
|
B:ALA75
|
4.2
|
45.8
|
1.0
|
C
|
B:ASP77
|
4.3
|
44.3
|
1.0
|
NE
|
B:ARG82
|
4.3
|
44.8
|
1.0
|
O
|
B:PRO78
|
4.3
|
43.3
|
1.0
|
CA
|
B:PRO78
|
4.3
|
44.9
|
1.0
|
CG
|
B:PRO88
|
4.3
|
46.6
|
1.0
|
C
|
B:PRO78
|
4.4
|
46.4
|
1.0
|
OG1
|
B:THR80
|
4.4
|
44.0
|
1.0
|
C
|
B:PRO81
|
4.4
|
43.1
|
1.0
|
CA
|
B:PRO87
|
4.5
|
49.4
|
1.0
|
CG2
|
B:THR80
|
4.6
|
43.0
|
1.0
|
N
|
B:PRO88
|
4.7
|
42.8
|
1.0
|
N
|
B:PRO81
|
4.7
|
37.6
|
1.0
|
N
|
B:PRO78
|
4.8
|
50.0
|
1.0
|
N
|
B:ARG82
|
4.9
|
43.8
|
1.0
|
CB
|
B:PRO87
|
4.9
|
46.2
|
1.0
|
CA
|
B:ALA75
|
4.9
|
47.0
|
1.0
|
C
|
B:ALA79
|
4.9
|
51.1
|
1.0
|
CA
|
B:ARG82
|
5.0
|
39.0
|
1.0
|
|
Sodium binding site 4 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 4 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na541
b:50.0
occ:1.00
|
O
|
B:HOH746
|
2.7
|
34.2
|
1.0
|
O
|
B:HOH715
|
2.8
|
39.1
|
1.0
|
N
|
B:VAL297
|
3.0
|
39.5
|
1.0
|
CD2
|
B:PHE296
|
3.6
|
35.5
|
1.0
|
CB
|
B:VAL297
|
3.6
|
36.8
|
1.0
|
CA
|
B:PHE296
|
3.7
|
30.4
|
1.0
|
CG
|
B:PHE296
|
3.7
|
34.6
|
1.0
|
CZ
|
B:PHE84
|
3.7
|
38.4
|
1.0
|
CE2
|
B:PHE296
|
3.8
|
33.8
|
1.0
|
CG2
|
B:VAL297
|
3.8
|
36.7
|
1.0
|
C
|
B:PHE296
|
3.8
|
35.5
|
1.0
|
CD1
|
B:PHE296
|
3.8
|
31.1
|
1.0
|
CE2
|
B:PHE84
|
3.9
|
36.4
|
1.0
|
CA
|
B:VAL297
|
3.9
|
38.4
|
1.0
|
CB
|
B:ARG82
|
3.9
|
42.7
|
1.0
|
CE1
|
B:PHE296
|
3.9
|
31.4
|
1.0
|
CZ
|
B:PHE296
|
3.9
|
32.6
|
1.0
|
CB
|
B:PHE296
|
4.3
|
35.6
|
1.0
|
CA
|
B:ARG82
|
4.3
|
39.0
|
1.0
|
CG
|
B:PRO88
|
4.3
|
46.6
|
1.0
|
O
|
B:PRO81
|
4.4
|
44.9
|
1.0
|
CB
|
B:ALA75
|
4.5
|
47.4
|
1.0
|
O
|
B:SER295
|
4.6
|
37.5
|
1.0
|
O
|
B:VAL297
|
4.6
|
39.5
|
1.0
|
CE1
|
B:PHE84
|
4.8
|
37.9
|
1.0
|
C
|
B:VAL297
|
4.8
|
34.9
|
1.0
|
N
|
B:PHE296
|
4.8
|
29.1
|
1.0
|
CG1
|
B:VAL297
|
4.9
|
44.8
|
1.0
|
CD2
|
B:PHE84
|
5.0
|
39.0
|
1.0
|
|
Sodium binding site 5 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 5 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na530
b:47.6
occ:1.00
|
O
|
C:HOH779
|
2.8
|
35.2
|
1.0
|
O
|
C:HOH785
|
2.9
|
38.7
|
1.0
|
N
|
C:VAL297
|
2.9
|
38.8
|
1.0
|
CD2
|
C:PHE296
|
3.5
|
35.6
|
1.0
|
CG
|
C:PHE296
|
3.6
|
34.4
|
1.0
|
CB
|
C:VAL297
|
3.6
|
39.3
|
1.0
|
CE2
|
C:PHE296
|
3.7
|
33.2
|
1.0
|
CZ
|
C:PHE84
|
3.7
|
41.5
|
1.0
|
CE2
|
C:PHE84
|
3.7
|
40.8
|
1.0
|
CD1
|
C:PHE296
|
3.7
|
33.6
|
1.0
|
CA
|
C:PHE296
|
3.7
|
33.6
|
1.0
|
CG2
|
C:VAL297
|
3.7
|
43.1
|
1.0
|
C
|
C:PHE296
|
3.8
|
35.8
|
1.0
|
CZ
|
C:PHE296
|
3.8
|
35.3
|
1.0
|
CE1
|
C:PHE296
|
3.8
|
33.3
|
1.0
|
CA
|
C:VAL297
|
3.9
|
35.4
|
1.0
|
CB
|
C:ARG82
|
4.1
|
37.8
|
1.0
|
CB
|
C:PHE296
|
4.3
|
35.8
|
1.0
|
CA
|
C:ARG82
|
4.5
|
36.9
|
1.0
|
CG
|
C:PRO88
|
4.5
|
52.9
|
1.0
|
O
|
C:SER295
|
4.5
|
40.8
|
1.0
|
O
|
C:PRO81
|
4.6
|
39.4
|
1.0
|
O
|
C:VAL297
|
4.7
|
33.4
|
1.0
|
CB
|
C:ALA75
|
4.7
|
46.6
|
1.0
|
CE1
|
C:PHE84
|
4.8
|
39.8
|
1.0
|
C
|
C:VAL297
|
4.8
|
38.5
|
1.0
|
CD2
|
C:PHE84
|
4.9
|
42.3
|
1.0
|
N
|
C:PHE296
|
4.9
|
39.7
|
1.0
|
CG1
|
C:VAL297
|
5.0
|
40.6
|
1.0
|
O
|
C:PHE296
|
5.0
|
38.6
|
1.0
|
|
Sodium binding site 6 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 6 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na519
b:56.2
occ:1.00
|
O
|
D:HOH712
|
2.4
|
39.8
|
1.0
|
N
|
D:VAL297
|
2.9
|
50.7
|
1.0
|
CG2
|
D:VAL297
|
3.2
|
51.9
|
1.0
|
O
|
D:HOH697
|
3.3
|
54.3
|
1.0
|
CB
|
D:VAL297
|
3.5
|
53.9
|
1.0
|
CA
|
D:PHE296
|
3.5
|
44.6
|
1.0
|
CG
|
D:PHE296
|
3.6
|
36.2
|
1.0
|
CD2
|
D:PHE296
|
3.6
|
44.2
|
1.0
|
C
|
D:PHE296
|
3.6
|
53.0
|
1.0
|
CA
|
D:VAL297
|
3.8
|
49.9
|
1.0
|
CB
|
D:ARG82
|
3.8
|
64.6
|
1.0
|
CZ
|
D:PHE84
|
3.8
|
48.9
|
1.0
|
CD1
|
D:PHE296
|
3.8
|
37.1
|
1.0
|
CE2
|
D:PHE84
|
3.9
|
45.8
|
1.0
|
CE2
|
D:PHE296
|
3.9
|
36.2
|
1.0
|
CB
|
D:PHE296
|
4.1
|
36.2
|
1.0
|
CE1
|
D:PHE296
|
4.1
|
36.1
|
1.0
|
CA
|
D:ARG82
|
4.2
|
56.1
|
1.0
|
CZ
|
D:PHE296
|
4.2
|
35.4
|
1.0
|
O
|
D:SER295
|
4.4
|
45.0
|
1.0
|
CG
|
D:PRO88
|
4.5
|
72.4
|
1.0
|
O
|
D:PRO81
|
4.5
|
59.7
|
1.0
|
O
|
D:VAL297
|
4.7
|
46.2
|
1.0
|
N
|
D:PHE296
|
4.7
|
40.3
|
1.0
|
C
|
D:VAL297
|
4.8
|
45.4
|
1.0
|
O
|
D:PHE296
|
4.8
|
42.9
|
1.0
|
CB
|
D:ALA75
|
4.9
|
59.4
|
1.0
|
CG1
|
D:VAL297
|
4.9
|
61.2
|
1.0
|
N
|
D:MET83
|
4.9
|
48.7
|
1.0
|
CE1
|
D:PHE84
|
4.9
|
49.8
|
1.0
|
CD2
|
D:PHE84
|
5.0
|
51.6
|
1.0
|
C
|
D:SER295
|
5.0
|
44.6
|
1.0
|
|
Sodium binding site 7 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 7 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na514
b:63.4
occ:1.00
|
O
|
E:HOH652
|
2.9
|
56.7
|
1.0
|
O
|
E:HOH671
|
2.9
|
50.5
|
1.0
|
N
|
E:VAL297
|
3.0
|
47.5
|
1.0
|
CB
|
E:VAL297
|
3.5
|
54.8
|
1.0
|
CD2
|
E:PHE296
|
3.5
|
44.0
|
1.0
|
CG
|
E:PHE296
|
3.6
|
45.4
|
1.0
|
CZ
|
E:PHE84
|
3.7
|
49.6
|
1.0
|
CA
|
E:PHE296
|
3.7
|
44.7
|
1.0
|
CE2
|
E:PHE296
|
3.7
|
48.4
|
1.0
|
CD1
|
E:PHE296
|
3.7
|
50.8
|
1.0
|
CE1
|
E:PHE296
|
3.8
|
52.0
|
1.0
|
C
|
E:PHE296
|
3.8
|
51.8
|
1.0
|
CA
|
E:VAL297
|
3.8
|
49.3
|
1.0
|
CB
|
E:ARG82
|
3.9
|
56.4
|
1.0
|
CZ
|
E:PHE296
|
3.9
|
50.1
|
1.0
|
CG2
|
E:VAL297
|
3.9
|
52.2
|
1.0
|
CE2
|
E:PHE84
|
3.9
|
47.5
|
1.0
|
CG
|
E:PRO88
|
4.1
|
54.5
|
1.0
|
CB
|
E:PHE296
|
4.2
|
47.6
|
1.0
|
CB
|
E:ALA75
|
4.4
|
56.1
|
1.0
|
CA
|
E:ARG82
|
4.4
|
55.9
|
1.0
|
O
|
E:PRO81
|
4.4
|
55.4
|
1.0
|
O
|
E:VAL297
|
4.6
|
54.5
|
1.0
|
CE1
|
E:PHE84
|
4.7
|
49.0
|
1.0
|
CG1
|
E:VAL297
|
4.7
|
63.1
|
1.0
|
O
|
E:SER295
|
4.7
|
47.2
|
1.0
|
C
|
E:VAL297
|
4.8
|
60.5
|
1.0
|
N
|
E:PHE296
|
4.9
|
47.4
|
1.0
|
|
Sodium binding site 8 out
of 8 in 7q89
Go back to
Sodium Binding Sites List in 7q89
Sodium binding site 8 out
of 8 in the Olep Mutant G92W in Complex with 6DEB
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na513
b:63.4
occ:1.00
|
O
|
F:HOH679
|
2.5
|
61.1
|
1.0
|
O
|
F:HOH671
|
3.1
|
60.2
|
1.0
|
N
|
F:VAL297
|
3.1
|
57.5
|
1.0
|
CB
|
F:VAL297
|
3.5
|
55.8
|
1.0
|
CZ
|
F:PHE84
|
3.7
|
58.9
|
1.0
|
CG2
|
F:VAL297
|
3.7
|
59.0
|
1.0
|
CE2
|
F:PHE84
|
3.7
|
54.8
|
1.0
|
CG
|
F:PHE296
|
3.8
|
52.7
|
1.0
|
CD2
|
F:PHE296
|
3.8
|
57.5
|
1.0
|
CD1
|
F:PHE296
|
3.8
|
45.0
|
1.0
|
CB
|
F:ARG82
|
3.9
|
58.1
|
1.0
|
CA
|
F:VAL297
|
3.9
|
57.5
|
1.0
|
CE2
|
F:PHE296
|
3.9
|
51.2
|
1.0
|
CA
|
F:PHE296
|
3.9
|
50.5
|
1.0
|
C
|
F:PHE296
|
3.9
|
51.2
|
1.0
|
CZ
|
F:PHE296
|
3.9
|
49.7
|
1.0
|
CE1
|
F:PHE296
|
4.0
|
49.6
|
1.0
|
CG
|
F:PRO88
|
4.2
|
77.8
|
1.0
|
CA
|
F:ARG82
|
4.3
|
52.1
|
1.0
|
O
|
F:PRO81
|
4.3
|
54.1
|
1.0
|
CB
|
F:ALA75
|
4.5
|
59.4
|
1.0
|
CB
|
F:PHE296
|
4.5
|
48.3
|
1.0
|
O
|
F:SER295
|
4.7
|
49.8
|
1.0
|
CE1
|
F:PHE84
|
4.8
|
65.3
|
1.0
|
O
|
F:VAL297
|
4.8
|
55.7
|
1.0
|
CG1
|
F:VAL297
|
4.8
|
64.7
|
1.0
|
C
|
F:VAL297
|
4.9
|
63.5
|
1.0
|
CD2
|
F:PHE84
|
4.9
|
59.8
|
1.0
|
O
|
F:ALA75
|
4.9
|
62.1
|
1.0
|
|
Reference:
L.C.Montemiglio,
E.Gugole,
I.Freda,
C.Exertier,
L.D'auria,
C.G.Chen,
A.N.Nardi,
G.Cerutti,
G.Parisi,
M.D'abramo,
C.Savino,
B.Vallone.
Point Mutations at A Key Site Alter the Cytochrome P450 Olep Structural Dynamics. Biomolecules V. 12 2021.
ISSN: ESSN 2218-273X
PubMed: 35053203
DOI: 10.3390/BIOM12010055
Page generated: Wed Oct 9 08:19:58 2024
|