Sodium in PDB 7zb0: Macrocyclase Ophp with 15MER
Protein crystallography data
The structure of Macrocyclase Ophp with 15MER, PDB code: 7zb0
was solved by
H.Song,
J.H.Naismith,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
64.35 /
2.47
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.22,
106.18,
114.79,
113.04,
101.67,
93.24
|
|
R / Rfree (%)
|
22.9 /
26.6
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Macrocyclase Ophp with 15MER
(pdb code 7zb0). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Macrocyclase Ophp with 15MER, PDB code: 7zb0:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 7zb0
Go back to
Sodium Binding Sites List in 7zb0
Sodium binding site 1 out
of 6 in the Macrocyclase Ophp with 15MER
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Macrocyclase Ophp with 15MER within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na803
b:60.7
occ:1.00
|
O
|
C:ASP311
|
2.6
|
66.0
|
1.0
|
|
O
|
C:GLN288
|
3.1
|
57.0
|
1.0
|
|
N
|
C:ALA315
|
3.2
|
63.6
|
1.0
|
|
N
|
C:GLU314
|
3.3
|
64.2
|
1.0
|
|
O
|
C:ALA315
|
3.4
|
63.1
|
1.0
|
|
N
|
C:TRP313
|
3.6
|
61.6
|
1.0
|
|
C
|
C:ASP311
|
3.8
|
66.5
|
1.0
|
|
CE1
|
C:PHE317
|
3.8
|
60.6
|
1.0
|
|
C
|
C:PRO312
|
3.9
|
62.6
|
1.0
|
|
ND1
|
C:HIS310
|
3.9
|
63.5
|
1.0
|
|
CA
|
C:GLU314
|
3.9
|
65.8
|
1.0
|
|
C
|
C:GLU314
|
4.0
|
64.8
|
1.0
|
|
CB
|
C:GLU314
|
4.0
|
68.2
|
1.0
|
|
CA
|
C:ALA315
|
4.0
|
62.6
|
1.0
|
|
CA
|
C:PRO312
|
4.1
|
64.4
|
1.0
|
|
C
|
C:ALA315
|
4.1
|
62.1
|
1.0
|
|
C
|
C:TRP313
|
4.2
|
62.1
|
1.0
|
|
CB
|
C:ALA315
|
4.2
|
63.1
|
1.0
|
|
C
|
C:GLN288
|
4.3
|
57.5
|
1.0
|
|
CA
|
C:TRP313
|
4.4
|
61.3
|
1.0
|
|
N
|
C:PRO312
|
4.4
|
65.7
|
1.0
|
|
O
|
C:PRO312
|
4.4
|
62.1
|
1.0
|
|
O
|
C:HIS310
|
4.5
|
66.5
|
1.0
|
|
N
|
C:GLN288
|
4.5
|
56.4
|
1.0
|
|
CB
|
C:HIS310
|
4.6
|
64.2
|
1.0
|
|
CZ
|
C:PHE317
|
4.6
|
60.8
|
1.0
|
|
CG
|
C:HIS310
|
4.6
|
63.6
|
1.0
|
|
C
|
C:HIS310
|
4.6
|
66.3
|
1.0
|
|
CG1
|
C:VAL290
|
4.7
|
60.8
|
1.0
|
|
CD1
|
C:PHE317
|
4.7
|
60.1
|
1.0
|
|
CE1
|
C:HIS310
|
4.8
|
63.5
|
1.0
|
|
N
|
C:ASP311
|
4.8
|
67.5
|
1.0
|
|
CA
|
C:GLN288
|
4.9
|
57.1
|
1.0
|
|
CA
|
C:ASP311
|
4.9
|
68.0
|
1.0
|
|
Sodium binding site 2 out
of 6 in 7zb0
Go back to
Sodium Binding Sites List in 7zb0
Sodium binding site 2 out
of 6 in the Macrocyclase Ophp with 15MER
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Macrocyclase Ophp with 15MER within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na804
b:61.3
occ:1.00
|
O
|
C:TYR499
|
2.5
|
59.0
|
1.0
|
|
O
|
C:ASN581
|
2.9
|
58.2
|
1.0
|
|
O
|
C:GLY500
|
2.9
|
57.3
|
1.0
|
|
NZ
|
C:LYS549
|
3.1
|
53.3
|
1.0
|
|
ND2
|
C:ASN581
|
3.1
|
57.1
|
1.0
|
|
OD1
|
C:ASN581
|
3.4
|
55.9
|
1.0
|
|
CG
|
C:ASN581
|
3.5
|
56.8
|
1.0
|
|
CB
|
C:LEU585
|
3.7
|
57.9
|
1.0
|
|
CE
|
C:LYS549
|
3.7
|
53.2
|
1.0
|
|
C
|
C:TYR499
|
3.7
|
58.6
|
1.0
|
|
CG1
|
C:VAL552
|
3.7
|
53.0
|
1.0
|
|
C
|
C:GLY500
|
3.8
|
56.4
|
1.0
|
|
C
|
C:ASN581
|
3.8
|
58.2
|
1.0
|
|
N
|
C:LEU585
|
4.0
|
57.4
|
1.0
|
|
CA
|
C:GLY500
|
4.0
|
57.0
|
1.0
|
|
CA
|
C:LEU585
|
4.2
|
57.8
|
1.0
|
|
N
|
C:GLY500
|
4.3
|
57.6
|
1.0
|
|
N
|
C:GLY582
|
4.4
|
58.5
|
1.0
|
|
CE1
|
C:PHE553
|
4.4
|
53.4
|
1.0
|
|
CA
|
C:GLY582
|
4.4
|
59.2
|
1.0
|
|
CB
|
C:VAL584
|
4.5
|
55.1
|
1.0
|
|
CG
|
C:LEU585
|
4.7
|
59.1
|
1.0
|
|
CB
|
C:ASN581
|
4.7
|
57.1
|
1.0
|
|
CD1
|
C:LEU585
|
4.8
|
58.9
|
1.0
|
|
CA
|
C:ASN581
|
4.8
|
57.7
|
1.0
|
|
CB
|
C:VAL552
|
4.8
|
52.7
|
1.0
|
|
C
|
C:VAL584
|
4.9
|
57.0
|
1.0
|
|
CA
|
C:TYR499
|
4.9
|
59.6
|
1.0
|
|
N
|
C:GLY501
|
4.9
|
55.5
|
1.0
|
|
CD
|
C:LYS549
|
4.9
|
52.9
|
1.0
|
|
Sodium binding site 3 out
of 6 in 7zb0
Go back to
Sodium Binding Sites List in 7zb0
Sodium binding site 3 out
of 6 in the Macrocyclase Ophp with 15MER
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Macrocyclase Ophp with 15MER within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na805
b:63.8
occ:1.00
|
O
|
C:LEU546
|
2.5
|
53.8
|
1.0
|
|
OH
|
C:TYR640
|
2.5
|
52.3
|
1.0
|
|
O
|
C:TYR625
|
2.6
|
54.1
|
1.0
|
|
CE2
|
C:TYR640
|
3.3
|
53.3
|
1.0
|
|
C
|
C:TYR625
|
3.3
|
53.3
|
1.0
|
|
CZ
|
C:TYR640
|
3.3
|
52.9
|
1.0
|
|
CA
|
C:TYR625
|
3.3
|
52.5
|
1.0
|
|
C
|
C:LEU546
|
3.3
|
54.5
|
1.0
|
|
CB
|
C:LYS549
|
3.5
|
52.5
|
1.0
|
|
CA
|
C:LEU546
|
3.6
|
53.9
|
1.0
|
|
N
|
C:LEU546
|
3.8
|
53.1
|
1.0
|
|
CE1
|
C:PHE636
|
3.9
|
54.2
|
1.0
|
|
CG
|
C:LYS549
|
3.9
|
52.8
|
1.0
|
|
CB
|
C:TYR625
|
4.0
|
52.5
|
1.0
|
|
CG1
|
C:ILE637
|
4.0
|
56.0
|
1.0
|
|
CD1
|
C:PHE636
|
4.1
|
54.8
|
1.0
|
|
O
|
C:GLU624
|
4.3
|
53.4
|
1.0
|
|
N
|
C:GLY626
|
4.5
|
53.8
|
1.0
|
|
N
|
C:TYR625
|
4.6
|
52.1
|
1.0
|
|
N
|
C:ASP547
|
4.6
|
55.4
|
1.0
|
|
CD1
|
C:TYR625
|
4.6
|
51.7
|
1.0
|
|
CD2
|
C:TYR640
|
4.6
|
53.8
|
1.0
|
|
CE1
|
C:TYR640
|
4.7
|
53.4
|
1.0
|
|
C
|
C:MET545
|
4.7
|
52.9
|
1.0
|
|
CG
|
C:TYR625
|
4.8
|
52.1
|
1.0
|
|
CA
|
C:LYS549
|
4.8
|
52.9
|
1.0
|
|
C
|
C:GLU624
|
4.9
|
52.5
|
1.0
|
|
CD1
|
C:ILE637
|
4.9
|
56.5
|
1.0
|
|
CA
|
C:ILE637
|
4.9
|
56.6
|
1.0
|
|
CD
|
C:LYS549
|
4.9
|
52.9
|
1.0
|
|
Sodium binding site 4 out
of 6 in 7zb0
Go back to
Sodium Binding Sites List in 7zb0
Sodium binding site 4 out
of 6 in the Macrocyclase Ophp with 15MER
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Macrocyclase Ophp with 15MER within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na804
b:62.1
occ:1.00
|
CE
|
D:MET330
|
3.1
|
63.0
|
1.0
|
|
O
|
D:LEU364
|
3.4
|
55.6
|
1.0
|
|
O
|
D:VAL365
|
3.5
|
53.6
|
1.0
|
|
CE1
|
D:TYR338
|
3.9
|
50.1
|
1.0
|
|
CZ
|
D:TYR338
|
3.9
|
49.7
|
1.0
|
|
CE2
|
D:PHE363
|
4.0
|
55.7
|
1.0
|
|
CD1
|
D:TYR338
|
4.0
|
50.6
|
1.0
|
|
CE2
|
D:TYR338
|
4.0
|
49.7
|
1.0
|
|
C
|
D:VAL365
|
4.1
|
53.2
|
1.0
|
|
CA
|
D:VAL365
|
4.1
|
53.7
|
1.0
|
|
CD2
|
D:TYR338
|
4.2
|
50.4
|
1.0
|
|
CG
|
D:TYR338
|
4.2
|
51.2
|
1.0
|
|
CZ
|
D:PHE363
|
4.4
|
56.3
|
1.0
|
|
C
|
D:LEU364
|
4.4
|
55.9
|
1.0
|
|
OH
|
D:TYR338
|
4.5
|
49.3
|
1.0
|
|
NH1
|
D:ARG316
|
4.5
|
65.5
|
1.0
|
|
N
|
D:VAL365
|
4.8
|
54.8
|
1.0
|
|
SD
|
D:MET330
|
4.8
|
62.6
|
1.0
|
|
CD2
|
D:PHE363
|
4.8
|
55.5
|
1.0
|
|
Sodium binding site 5 out
of 6 in 7zb0
Go back to
Sodium Binding Sites List in 7zb0
Sodium binding site 5 out
of 6 in the Macrocyclase Ophp with 15MER
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Macrocyclase Ophp with 15MER within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na805
b:64.3
occ:1.00
|
O
|
D:VAL600
|
2.9
|
61.7
|
1.0
|
|
O
|
D:LEU658
|
3.0
|
64.6
|
1.0
|
|
OG1
|
D:THR602
|
3.0
|
62.1
|
1.0
|
|
N
|
D:THR602
|
3.3
|
62.5
|
1.0
|
|
CB
|
D:THR602
|
3.4
|
63.3
|
1.0
|
|
C
|
D:VAL600
|
3.4
|
62.2
|
1.0
|
|
CE1
|
D:PHE659
|
3.4
|
68.1
|
1.0
|
|
CZ
|
D:PHE659
|
3.5
|
68.0
|
1.0
|
|
CG1
|
D:VAL600
|
3.7
|
62.5
|
1.0
|
|
N
|
D:LEU658
|
3.7
|
66.0
|
1.0
|
|
CE
|
D:MET657
|
3.7
|
65.7
|
1.0
|
|
C
|
D:LEU658
|
3.8
|
65.9
|
1.0
|
|
CD1
|
D:PHE659
|
3.8
|
67.9
|
1.0
|
|
CE2
|
D:PHE659
|
3.8
|
67.2
|
1.0
|
|
C
|
D:ILE601
|
3.8
|
61.4
|
1.0
|
|
CB
|
D:MET657
|
3.8
|
67.0
|
1.0
|
|
N
|
D:ILE601
|
3.9
|
62.2
|
1.0
|
|
CA
|
D:THR602
|
3.9
|
63.0
|
1.0
|
|
CB
|
D:VAL600
|
3.9
|
62.5
|
1.0
|
|
CG
|
D:PHE659
|
4.0
|
67.8
|
1.0
|
|
CA
|
D:ILE601
|
4.0
|
61.9
|
1.0
|
|
CD2
|
D:PHE659
|
4.0
|
67.1
|
1.0
|
|
CA
|
D:MET657
|
4.1
|
67.3
|
1.0
|
|
C
|
D:MET657
|
4.3
|
67.4
|
1.0
|
|
CA
|
D:VAL600
|
4.3
|
62.1
|
1.0
|
|
CG
|
D:MET657
|
4.4
|
67.0
|
1.0
|
|
CA
|
D:LEU658
|
4.4
|
66.6
|
1.0
|
|
N
|
D:PHE659
|
4.5
|
67.2
|
1.0
|
|
O
|
D:ILE601
|
4.7
|
61.2
|
1.0
|
|
CA
|
D:PHE659
|
4.7
|
67.2
|
1.0
|
|
CG2
|
D:THR602
|
4.8
|
64.1
|
1.0
|
|
SD
|
D:MET657
|
4.9
|
66.7
|
1.0
|
|
CB
|
D:PHE659
|
5.0
|
68.0
|
1.0
|
|
Sodium binding site 6 out
of 6 in 7zb0
Go back to
Sodium Binding Sites List in 7zb0
Sodium binding site 6 out
of 6 in the Macrocyclase Ophp with 15MER
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Macrocyclase Ophp with 15MER within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na806
b:58.5
occ:1.00
|
OG1
|
D:THR481
|
2.9
|
50.1
|
1.0
|
|
O
|
D:TYR525
|
2.9
|
51.4
|
1.0
|
|
N
|
D:THR481
|
3.2
|
52.9
|
1.0
|
|
CB
|
D:THR481
|
3.3
|
51.1
|
1.0
|
|
O
|
D:PHE479
|
3.6
|
54.8
|
1.0
|
|
CE2
|
D:PHE427
|
3.6
|
48.5
|
1.0
|
|
CD2
|
D:TYR525
|
3.6
|
51.8
|
1.0
|
|
C
|
D:PHE479
|
3.7
|
54.1
|
1.0
|
|
CZ
|
D:PHE427
|
3.7
|
48.2
|
1.0
|
|
CD2
|
D:PHE427
|
3.7
|
48.5
|
1.0
|
|
CB
|
D:PHE479
|
3.7
|
52.0
|
1.0
|
|
CA
|
D:THR481
|
3.8
|
52.6
|
1.0
|
|
C
|
D:ILE480
|
3.8
|
54.4
|
1.0
|
|
N
|
D:ILE480
|
3.9
|
54.4
|
1.0
|
|
C
|
D:TYR525
|
3.9
|
51.9
|
1.0
|
|
CE1
|
D:PHE427
|
3.9
|
47.7
|
1.0
|
|
CG
|
D:PHE427
|
3.9
|
48.9
|
1.0
|
|
CA
|
D:ILE480
|
3.9
|
55.1
|
1.0
|
|
CG1
|
D:ILE527
|
4.0
|
48.8
|
1.0
|
|
CD1
|
D:PHE427
|
4.0
|
48.2
|
1.0
|
|
N
|
D:ILE527
|
4.3
|
50.0
|
1.0
|
|
CE2
|
D:TYR525
|
4.3
|
51.8
|
1.0
|
|
CA
|
D:PHE479
|
4.4
|
53.3
|
1.0
|
|
CB
|
D:ILE527
|
4.4
|
49.0
|
1.0
|
|
CG
|
D:TYR525
|
4.4
|
52.4
|
1.0
|
|
CB
|
D:TYR525
|
4.5
|
52.8
|
1.0
|
|
CG2
|
D:THR481
|
4.6
|
51.2
|
1.0
|
|
N
|
D:ALA526
|
4.7
|
51.2
|
1.0
|
|
CA
|
D:ALA526
|
4.7
|
51.6
|
1.0
|
|
CG2
|
D:THR463
|
4.7
|
54.5
|
1.0
|
|
CB
|
D:PHE427
|
4.7
|
50.1
|
1.0
|
|
C
|
D:ALA526
|
4.8
|
50.4
|
1.0
|
|
O
|
D:ILE480
|
4.8
|
55.4
|
1.0
|
|
CA
|
D:TYR525
|
4.8
|
52.7
|
1.0
|
|
CG
|
D:PHE479
|
4.9
|
51.5
|
1.0
|
|
C
|
D:THR481
|
5.0
|
54.1
|
1.0
|
|
Reference:
H.Song,
J.H.Naismith.
Apo Macrocyclase Ophp To Be Published.
Page generated: Mon Aug 18 12:46:01 2025
|
