Sodium in PDB 6x1q: 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Enzymatic activity of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
All present enzymatic activity of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope:
3.2.1.23;
Other elements in 6x1q:
The structure of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
(pdb code 6x1q). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope, PDB code: 6x1q:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 1 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1103
b:7.9
occ:1.00
|
O
|
A:PHE601
|
2.3
|
7.4
|
1.0
|
OD1
|
A:ASN604
|
2.3
|
4.8
|
1.0
|
O
|
A:HOH1659
|
2.4
|
7.0
|
1.0
|
OD2
|
A:ASP201
|
2.4
|
6.1
|
1.0
|
O
|
A:HOH1389
|
2.5
|
5.7
|
1.0
|
HH
|
A:TYR100
|
2.9
|
8.0
|
0.0
|
O
|
A:HOH1209
|
3.0
|
11.2
|
1.0
|
CG
|
A:ASP201
|
3.3
|
6.1
|
1.0
|
HE1
|
A:TRP568
|
3.3
|
2.5
|
1.0
|
OH
|
A:TYR100
|
3.3
|
8.0
|
1.0
|
CG
|
A:ASN604
|
3.3
|
4.8
|
1.0
|
HD21
|
A:ASN604
|
3.4
|
4.8
|
1.0
|
C
|
A:PHE601
|
3.4
|
7.4
|
1.0
|
HB3
|
A:PHE601
|
3.4
|
7.4
|
1.0
|
HA
|
A:CYS602
|
3.6
|
7.3
|
1.0
|
OD1
|
A:ASP201
|
3.7
|
6.1
|
1.0
|
ND2
|
A:ASN604
|
3.7
|
4.8
|
1.0
|
HE2
|
A:HIS540
|
3.9
|
3.7
|
1.0
|
O
|
A:HOH1535
|
4.0
|
9.5
|
1.0
|
NE1
|
A:TRP568
|
4.1
|
2.5
|
1.0
|
O
|
A:HOH1423
|
4.1
|
4.8
|
1.0
|
HD1
|
A:PHE601
|
4.2
|
7.4
|
1.0
|
N
|
A:CYS602
|
4.2
|
7.3
|
1.0
|
HB3
|
A:ASP201
|
4.3
|
6.1
|
1.0
|
CB
|
A:PHE601
|
4.3
|
7.4
|
1.0
|
CA
|
A:CYS602
|
4.3
|
7.3
|
1.0
|
HZ2
|
A:TRP568
|
4.3
|
2.5
|
1.0
|
CA
|
A:PHE601
|
4.4
|
7.4
|
1.0
|
CB
|
A:ASP201
|
4.4
|
6.1
|
1.0
|
HA
|
A:PHE601
|
4.5
|
7.4
|
1.0
|
CZ
|
A:TYR100
|
4.5
|
8.0
|
1.0
|
HD22
|
A:ASN604
|
4.6
|
4.8
|
1.0
|
NE2
|
A:HIS540
|
4.6
|
3.7
|
1.0
|
O
|
A:ASP201
|
4.6
|
6.1
|
1.0
|
CB
|
A:ASN604
|
4.7
|
4.8
|
1.0
|
HB2
|
A:ASN604
|
4.7
|
4.8
|
1.0
|
HE1
|
A:HIS540
|
4.7
|
3.7
|
1.0
|
C
|
A:CYS602
|
4.7
|
7.3
|
1.0
|
HE1
|
A:TYR100
|
4.8
|
8.0
|
1.0
|
HB2
|
A:PHE601
|
4.8
|
7.4
|
1.0
|
CE2
|
A:TRP568
|
4.9
|
2.5
|
1.0
|
CZ2
|
A:TRP568
|
4.9
|
2.5
|
1.0
|
HB2
|
A:ASP201
|
5.0
|
6.1
|
1.0
|
|
Sodium binding site 2 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 2 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1104
b:2.8
occ:1.00
|
O
|
A:TYR559
|
2.2
|
2.0
|
1.0
|
O
|
A:PHE556
|
2.3
|
1.4
|
1.0
|
O
|
A:LEU562
|
2.3
|
1.6
|
1.0
|
O
|
A:HOH1942
|
2.3
|
3.0
|
1.0
|
O
|
A:HOH1762
|
2.4
|
3.7
|
1.0
|
HA
|
A:PRO560
|
3.1
|
2.0
|
1.0
|
O
|
A:PRO560
|
3.2
|
2.0
|
1.0
|
C
|
A:TYR559
|
3.3
|
2.0
|
1.0
|
C
|
A:LEU562
|
3.3
|
1.6
|
1.0
|
C
|
A:PHE556
|
3.5
|
1.4
|
1.0
|
HA
|
A:GLN563
|
3.5
|
1.6
|
1.0
|
C
|
A:PRO560
|
3.5
|
2.0
|
1.0
|
CA
|
A:PRO560
|
3.6
|
2.0
|
1.0
|
H
|
A:LEU562
|
3.7
|
1.6
|
1.0
|
HB2
|
A:LEU562
|
3.7
|
1.6
|
1.0
|
HD13
|
A:LEU350
|
3.8
|
1.8
|
1.0
|
HA
|
A:PHE556
|
3.8
|
1.4
|
1.0
|
N
|
A:PRO560
|
3.9
|
2.0
|
1.0
|
O
|
A:HOH1274
|
4.0
|
3.0
|
1.0
|
N
|
A:LEU562
|
4.0
|
1.6
|
1.0
|
HG2
|
A:GLN563
|
4.1
|
1.6
|
1.0
|
CA
|
A:LEU562
|
4.1
|
1.6
|
1.0
|
HA
|
A:ARG557
|
4.2
|
2.2
|
1.0
|
CA
|
A:PHE556
|
4.2
|
1.4
|
1.0
|
N
|
A:GLN563
|
4.2
|
1.6
|
1.0
|
H
|
A:TYR559
|
4.2
|
2.0
|
1.0
|
CA
|
A:GLN563
|
4.3
|
1.6
|
1.0
|
HB3
|
A:PHE556
|
4.3
|
1.4
|
1.0
|
CB
|
A:LEU562
|
4.4
|
1.6
|
1.0
|
N
|
A:ARG561
|
4.4
|
1.9
|
1.0
|
CA
|
A:TYR559
|
4.4
|
2.0
|
1.0
|
N
|
A:TYR559
|
4.5
|
2.0
|
1.0
|
N
|
A:ARG557
|
4.5
|
2.2
|
1.0
|
HB2
|
A:TYR559
|
4.7
|
2.0
|
1.0
|
CA
|
A:ARG557
|
4.7
|
2.2
|
1.0
|
HG3
|
A:GLN563
|
4.7
|
1.6
|
1.0
|
CD1
|
A:LEU350
|
4.7
|
1.8
|
1.0
|
HB3
|
A:LEU562
|
4.7
|
1.6
|
1.0
|
CG
|
A:GLN563
|
4.8
|
1.6
|
1.0
|
C
|
A:ARG557
|
4.8
|
2.2
|
1.0
|
CB
|
A:PHE556
|
4.8
|
1.4
|
1.0
|
H
|
A:ARG561
|
4.9
|
1.9
|
1.0
|
C
|
A:ARG561
|
4.9
|
1.9
|
1.0
|
HD21
|
A:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
A:ARG557
|
4.9
|
2.2
|
1.0
|
HD12
|
A:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
A:ALA555
|
4.9
|
1.8
|
1.0
|
H
|
A:GLN563
|
5.0
|
1.6
|
1.0
|
|
Sodium binding site 3 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 3 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1103
b:7.9
occ:1.00
|
O
|
B:PHE601
|
2.3
|
7.4
|
1.0
|
OD1
|
B:ASN604
|
2.3
|
4.8
|
1.0
|
O
|
B:HOH1643
|
2.4
|
6.8
|
1.0
|
OD2
|
B:ASP201
|
2.4
|
6.1
|
1.0
|
O
|
B:HOH1407
|
2.5
|
5.6
|
1.0
|
HH
|
B:TYR100
|
2.9
|
8.0
|
0.0
|
O
|
B:HOH1206
|
2.9
|
10.8
|
1.0
|
CG
|
B:ASP201
|
3.3
|
6.1
|
1.0
|
HE1
|
B:TRP568
|
3.3
|
2.5
|
1.0
|
OH
|
B:TYR100
|
3.3
|
8.0
|
1.0
|
CG
|
B:ASN604
|
3.3
|
4.8
|
1.0
|
HD21
|
B:ASN604
|
3.4
|
4.8
|
1.0
|
C
|
B:PHE601
|
3.4
|
7.4
|
1.0
|
HB3
|
B:PHE601
|
3.4
|
7.4
|
1.0
|
HA
|
B:CYS602
|
3.6
|
7.3
|
1.0
|
OD1
|
B:ASP201
|
3.7
|
6.1
|
1.0
|
ND2
|
B:ASN604
|
3.7
|
4.8
|
1.0
|
O
|
B:HOH1356
|
3.8
|
8.2
|
1.0
|
HE2
|
B:HIS540
|
3.9
|
3.7
|
1.0
|
NE1
|
B:TRP568
|
4.1
|
2.5
|
1.0
|
O
|
B:HOH1419
|
4.1
|
4.7
|
1.0
|
HD1
|
B:PHE601
|
4.2
|
7.4
|
1.0
|
N
|
B:CYS602
|
4.2
|
7.3
|
1.0
|
HB3
|
B:ASP201
|
4.3
|
6.1
|
1.0
|
CB
|
B:PHE601
|
4.3
|
7.4
|
1.0
|
CA
|
B:CYS602
|
4.3
|
7.3
|
1.0
|
HZ2
|
B:TRP568
|
4.3
|
2.5
|
1.0
|
CA
|
B:PHE601
|
4.4
|
7.4
|
1.0
|
CB
|
B:ASP201
|
4.4
|
6.1
|
1.0
|
HA
|
B:PHE601
|
4.5
|
7.4
|
1.0
|
CZ
|
B:TYR100
|
4.5
|
8.0
|
1.0
|
HD22
|
B:ASN604
|
4.6
|
4.8
|
1.0
|
O
|
B:HOH1854
|
4.6
|
5.9
|
1.0
|
NE2
|
B:HIS540
|
4.6
|
3.7
|
1.0
|
O
|
B:ASP201
|
4.6
|
6.1
|
1.0
|
CB
|
B:ASN604
|
4.7
|
4.8
|
1.0
|
HB2
|
B:ASN604
|
4.7
|
4.8
|
1.0
|
HE1
|
B:HIS540
|
4.7
|
3.7
|
1.0
|
C
|
B:CYS602
|
4.7
|
7.3
|
1.0
|
HE1
|
B:TYR100
|
4.8
|
8.0
|
1.0
|
HB2
|
B:PHE601
|
4.8
|
7.4
|
1.0
|
CE2
|
B:TRP568
|
4.9
|
2.5
|
1.0
|
CZ2
|
B:TRP568
|
4.9
|
2.5
|
1.0
|
HB2
|
B:ASP201
|
5.0
|
6.1
|
1.0
|
|
Sodium binding site 4 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 4 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1104
b:2.8
occ:1.00
|
O
|
B:TYR559
|
2.2
|
2.0
|
1.0
|
O
|
B:PHE556
|
2.3
|
1.4
|
1.0
|
O
|
B:LEU562
|
2.3
|
1.6
|
1.0
|
O
|
B:HOH1941
|
2.3
|
3.0
|
1.0
|
O
|
B:HOH1762
|
2.4
|
3.9
|
1.0
|
HA
|
B:PRO560
|
3.1
|
2.0
|
1.0
|
O
|
B:PRO560
|
3.2
|
2.0
|
1.0
|
C
|
B:TYR559
|
3.3
|
2.0
|
1.0
|
C
|
B:LEU562
|
3.3
|
1.6
|
1.0
|
C
|
B:PHE556
|
3.5
|
1.4
|
1.0
|
HA
|
B:GLN563
|
3.5
|
1.6
|
1.0
|
C
|
B:PRO560
|
3.5
|
2.0
|
1.0
|
CA
|
B:PRO560
|
3.6
|
2.0
|
1.0
|
H
|
B:LEU562
|
3.7
|
1.6
|
1.0
|
HB2
|
B:LEU562
|
3.7
|
1.6
|
1.0
|
HD13
|
B:LEU350
|
3.8
|
1.8
|
1.0
|
HA
|
B:PHE556
|
3.8
|
1.4
|
1.0
|
N
|
B:PRO560
|
3.9
|
2.0
|
1.0
|
O
|
B:HOH1273
|
4.0
|
3.0
|
1.0
|
N
|
B:LEU562
|
4.0
|
1.6
|
1.0
|
HG2
|
B:GLN563
|
4.1
|
1.6
|
1.0
|
CA
|
B:LEU562
|
4.1
|
1.6
|
1.0
|
HA
|
B:ARG557
|
4.2
|
2.2
|
1.0
|
CA
|
B:PHE556
|
4.2
|
1.4
|
1.0
|
N
|
B:GLN563
|
4.2
|
1.6
|
1.0
|
H
|
B:TYR559
|
4.2
|
2.0
|
1.0
|
CA
|
B:GLN563
|
4.3
|
1.6
|
1.0
|
HB3
|
B:PHE556
|
4.3
|
1.4
|
1.0
|
CB
|
B:LEU562
|
4.4
|
1.6
|
1.0
|
N
|
B:ARG561
|
4.4
|
1.9
|
1.0
|
CA
|
B:TYR559
|
4.4
|
2.0
|
1.0
|
N
|
B:TYR559
|
4.5
|
2.0
|
1.0
|
N
|
B:ARG557
|
4.5
|
2.2
|
1.0
|
HB2
|
B:TYR559
|
4.7
|
2.0
|
1.0
|
CA
|
B:ARG557
|
4.7
|
2.2
|
1.0
|
HG3
|
B:GLN563
|
4.7
|
1.6
|
1.0
|
CD1
|
B:LEU350
|
4.7
|
1.8
|
1.0
|
HB3
|
B:LEU562
|
4.7
|
1.6
|
1.0
|
CG
|
B:GLN563
|
4.8
|
1.6
|
1.0
|
C
|
B:ARG557
|
4.8
|
2.2
|
1.0
|
CB
|
B:PHE556
|
4.8
|
1.4
|
1.0
|
H
|
B:ARG561
|
4.9
|
1.9
|
1.0
|
C
|
B:ARG561
|
4.9
|
1.9
|
1.0
|
HD21
|
B:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
B:ARG557
|
4.9
|
2.2
|
1.0
|
HD12
|
B:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
B:ALA555
|
4.9
|
1.8
|
1.0
|
H
|
B:GLN563
|
5.0
|
1.6
|
1.0
|
|
Sodium binding site 5 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 5 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na1103
b:7.9
occ:1.00
|
O
|
C:PHE601
|
2.3
|
7.4
|
1.0
|
OD1
|
C:ASN604
|
2.3
|
4.8
|
1.0
|
O
|
C:HOH1652
|
2.4
|
6.7
|
1.0
|
OD2
|
C:ASP201
|
2.4
|
6.1
|
1.0
|
O
|
C:HOH1405
|
2.5
|
5.7
|
1.0
|
HH
|
C:TYR100
|
2.9
|
8.0
|
0.0
|
O
|
C:HOH1206
|
2.9
|
11.0
|
1.0
|
CG
|
C:ASP201
|
3.3
|
6.1
|
1.0
|
HE1
|
C:TRP568
|
3.3
|
2.5
|
1.0
|
OH
|
C:TYR100
|
3.3
|
8.0
|
1.0
|
CG
|
C:ASN604
|
3.3
|
4.8
|
1.0
|
HD21
|
C:ASN604
|
3.4
|
4.8
|
1.0
|
C
|
C:PHE601
|
3.4
|
7.4
|
1.0
|
HB3
|
C:PHE601
|
3.4
|
7.4
|
1.0
|
HA
|
C:CYS602
|
3.6
|
7.3
|
1.0
|
OD1
|
C:ASP201
|
3.7
|
6.1
|
1.0
|
ND2
|
C:ASN604
|
3.7
|
4.8
|
1.0
|
O
|
C:HOH1357
|
3.8
|
8.1
|
1.0
|
HE2
|
C:HIS540
|
3.9
|
3.7
|
1.0
|
NE1
|
C:TRP568
|
4.1
|
2.5
|
1.0
|
O
|
C:HOH1422
|
4.1
|
4.7
|
1.0
|
HD1
|
C:PHE601
|
4.2
|
7.4
|
1.0
|
N
|
C:CYS602
|
4.2
|
7.3
|
1.0
|
HB3
|
C:ASP201
|
4.3
|
6.1
|
1.0
|
CB
|
C:PHE601
|
4.3
|
7.4
|
1.0
|
CA
|
C:CYS602
|
4.3
|
7.3
|
1.0
|
HZ2
|
C:TRP568
|
4.3
|
2.5
|
1.0
|
CA
|
C:PHE601
|
4.4
|
7.4
|
1.0
|
CB
|
C:ASP201
|
4.4
|
6.1
|
1.0
|
HA
|
C:PHE601
|
4.5
|
7.4
|
1.0
|
CZ
|
C:TYR100
|
4.5
|
8.0
|
1.0
|
HD22
|
C:ASN604
|
4.6
|
4.8
|
1.0
|
O
|
C:HOH1856
|
4.6
|
6.0
|
1.0
|
NE2
|
C:HIS540
|
4.6
|
3.7
|
1.0
|
O
|
C:ASP201
|
4.6
|
6.1
|
1.0
|
CB
|
C:ASN604
|
4.7
|
4.8
|
1.0
|
HB2
|
C:ASN604
|
4.7
|
4.8
|
1.0
|
HE1
|
C:HIS540
|
4.7
|
3.7
|
1.0
|
C
|
C:CYS602
|
4.7
|
7.3
|
1.0
|
HE1
|
C:TYR100
|
4.8
|
8.0
|
1.0
|
HB2
|
C:PHE601
|
4.8
|
7.4
|
1.0
|
CE2
|
C:TRP568
|
4.9
|
2.5
|
1.0
|
CZ2
|
C:TRP568
|
4.9
|
2.5
|
1.0
|
HB2
|
C:ASP201
|
5.0
|
6.1
|
1.0
|
|
Sodium binding site 6 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 6 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na1104
b:2.8
occ:1.00
|
O
|
C:TYR559
|
2.2
|
2.0
|
1.0
|
O
|
C:PHE556
|
2.3
|
1.4
|
1.0
|
O
|
C:LEU562
|
2.3
|
1.6
|
1.0
|
O
|
C:HOH1945
|
2.3
|
3.0
|
1.0
|
O
|
C:HOH1763
|
2.4
|
3.9
|
1.0
|
HA
|
C:PRO560
|
3.1
|
2.0
|
1.0
|
O
|
C:PRO560
|
3.2
|
2.0
|
1.0
|
C
|
C:TYR559
|
3.3
|
2.0
|
1.0
|
C
|
C:LEU562
|
3.3
|
1.6
|
1.0
|
C
|
C:PHE556
|
3.5
|
1.4
|
1.0
|
HA
|
C:GLN563
|
3.5
|
1.6
|
1.0
|
C
|
C:PRO560
|
3.5
|
2.0
|
1.0
|
CA
|
C:PRO560
|
3.6
|
2.0
|
1.0
|
H
|
C:LEU562
|
3.7
|
1.6
|
1.0
|
HB2
|
C:LEU562
|
3.7
|
1.6
|
1.0
|
HD13
|
C:LEU350
|
3.8
|
1.8
|
1.0
|
HA
|
C:PHE556
|
3.8
|
1.4
|
1.0
|
N
|
C:PRO560
|
3.9
|
2.0
|
1.0
|
O
|
C:HOH1272
|
4.0
|
3.0
|
1.0
|
N
|
C:LEU562
|
4.0
|
1.6
|
1.0
|
HG2
|
C:GLN563
|
4.1
|
1.6
|
1.0
|
CA
|
C:LEU562
|
4.1
|
1.6
|
1.0
|
HA
|
C:ARG557
|
4.2
|
2.2
|
1.0
|
CA
|
C:PHE556
|
4.2
|
1.4
|
1.0
|
N
|
C:GLN563
|
4.2
|
1.6
|
1.0
|
H
|
C:TYR559
|
4.2
|
2.0
|
1.0
|
CA
|
C:GLN563
|
4.3
|
1.6
|
1.0
|
HB3
|
C:PHE556
|
4.3
|
1.4
|
1.0
|
CB
|
C:LEU562
|
4.4
|
1.6
|
1.0
|
N
|
C:ARG561
|
4.4
|
1.9
|
1.0
|
CA
|
C:TYR559
|
4.4
|
2.0
|
1.0
|
N
|
C:TYR559
|
4.5
|
2.0
|
1.0
|
N
|
C:ARG557
|
4.5
|
2.2
|
1.0
|
HB2
|
C:TYR559
|
4.7
|
2.0
|
1.0
|
CA
|
C:ARG557
|
4.7
|
2.2
|
1.0
|
HG3
|
C:GLN563
|
4.7
|
1.6
|
1.0
|
CD1
|
C:LEU350
|
4.7
|
1.8
|
1.0
|
HB3
|
C:LEU562
|
4.7
|
1.6
|
1.0
|
CG
|
C:GLN563
|
4.8
|
1.6
|
1.0
|
C
|
C:ARG557
|
4.8
|
2.2
|
1.0
|
CB
|
C:PHE556
|
4.8
|
1.4
|
1.0
|
H
|
C:ARG561
|
4.9
|
1.9
|
1.0
|
C
|
C:ARG561
|
4.9
|
1.9
|
1.0
|
HD21
|
C:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
C:ARG557
|
4.9
|
2.2
|
1.0
|
HD12
|
C:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
C:ALA555
|
4.9
|
1.8
|
1.0
|
H
|
C:GLN563
|
5.0
|
1.6
|
1.0
|
|
Sodium binding site 7 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 7 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na1103
b:7.9
occ:1.00
|
O
|
D:PHE601
|
2.3
|
7.4
|
1.0
|
OD1
|
D:ASN604
|
2.3
|
4.8
|
1.0
|
O
|
D:HOH1650
|
2.4
|
7.0
|
1.0
|
OD2
|
D:ASP201
|
2.4
|
6.1
|
1.0
|
O
|
D:HOH1403
|
2.5
|
5.9
|
1.0
|
HH
|
D:TYR100
|
2.9
|
8.0
|
0.0
|
O
|
D:HOH1206
|
2.9
|
11.1
|
1.0
|
CG
|
D:ASP201
|
3.3
|
6.1
|
1.0
|
HE1
|
D:TRP568
|
3.3
|
2.5
|
1.0
|
OH
|
D:TYR100
|
3.3
|
8.0
|
1.0
|
CG
|
D:ASN604
|
3.3
|
4.8
|
1.0
|
HD21
|
D:ASN604
|
3.4
|
4.8
|
1.0
|
C
|
D:PHE601
|
3.4
|
7.4
|
1.0
|
HB3
|
D:PHE601
|
3.4
|
7.4
|
1.0
|
HA
|
D:CYS602
|
3.6
|
7.3
|
1.0
|
OD1
|
D:ASP201
|
3.7
|
6.1
|
1.0
|
ND2
|
D:ASN604
|
3.7
|
4.8
|
1.0
|
O
|
D:HOH1356
|
3.8
|
8.2
|
1.0
|
HE2
|
D:HIS540
|
3.9
|
3.7
|
1.0
|
NE1
|
D:TRP568
|
4.1
|
2.5
|
1.0
|
O
|
D:HOH1417
|
4.1
|
5.0
|
1.0
|
HD1
|
D:PHE601
|
4.2
|
7.4
|
1.0
|
N
|
D:CYS602
|
4.2
|
7.3
|
1.0
|
HB3
|
D:ASP201
|
4.3
|
6.1
|
1.0
|
CB
|
D:PHE601
|
4.3
|
7.4
|
1.0
|
CA
|
D:CYS602
|
4.3
|
7.3
|
1.0
|
HZ2
|
D:TRP568
|
4.3
|
2.5
|
1.0
|
CA
|
D:PHE601
|
4.3
|
7.4
|
1.0
|
CB
|
D:ASP201
|
4.4
|
6.1
|
1.0
|
HA
|
D:PHE601
|
4.5
|
7.4
|
1.0
|
CZ
|
D:TYR100
|
4.5
|
8.0
|
1.0
|
HD22
|
D:ASN604
|
4.6
|
4.8
|
1.0
|
O
|
D:HOH1854
|
4.6
|
6.1
|
1.0
|
NE2
|
D:HIS540
|
4.6
|
3.7
|
1.0
|
O
|
D:ASP201
|
4.6
|
6.1
|
1.0
|
CB
|
D:ASN604
|
4.7
|
4.8
|
1.0
|
HB2
|
D:ASN604
|
4.7
|
4.8
|
1.0
|
HE1
|
D:HIS540
|
4.7
|
3.7
|
1.0
|
C
|
D:CYS602
|
4.7
|
7.3
|
1.0
|
HE1
|
D:TYR100
|
4.8
|
8.0
|
1.0
|
HB2
|
D:PHE601
|
4.8
|
7.4
|
1.0
|
CE2
|
D:TRP568
|
4.9
|
2.5
|
1.0
|
CZ2
|
D:TRP568
|
4.9
|
2.5
|
1.0
|
HB2
|
D:ASP201
|
5.0
|
6.1
|
1.0
|
|
Sodium binding site 8 out
of 8 in 6x1q
Go back to
Sodium Binding Sites List in 6x1q
Sodium binding site 8 out
of 8 in the 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of 1.8 Angstrom Resolution Structure of B-Galactosidase with A 200 Kv Cryoarm Electron Microscope within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na1104
b:2.8
occ:1.00
|
O
|
D:TYR559
|
2.2
|
2.0
|
1.0
|
O
|
D:PHE556
|
2.3
|
1.4
|
1.0
|
O
|
D:LEU562
|
2.3
|
1.6
|
1.0
|
O
|
D:HOH1942
|
2.3
|
3.1
|
1.0
|
O
|
D:HOH1765
|
2.4
|
3.7
|
1.0
|
HA
|
D:PRO560
|
3.1
|
2.0
|
1.0
|
O
|
D:PRO560
|
3.2
|
2.0
|
1.0
|
C
|
D:TYR559
|
3.3
|
2.0
|
1.0
|
C
|
D:LEU562
|
3.3
|
1.6
|
1.0
|
C
|
D:PHE556
|
3.5
|
1.4
|
1.0
|
HA
|
D:GLN563
|
3.5
|
1.6
|
1.0
|
C
|
D:PRO560
|
3.5
|
2.0
|
1.0
|
CA
|
D:PRO560
|
3.6
|
2.0
|
1.0
|
H
|
D:LEU562
|
3.7
|
1.6
|
1.0
|
HB2
|
D:LEU562
|
3.7
|
1.6
|
1.0
|
HD13
|
D:LEU350
|
3.8
|
1.8
|
1.0
|
HA
|
D:PHE556
|
3.8
|
1.4
|
1.0
|
N
|
D:PRO560
|
3.9
|
2.0
|
1.0
|
O
|
D:HOH1271
|
4.0
|
3.1
|
1.0
|
N
|
D:LEU562
|
4.0
|
1.6
|
1.0
|
HG2
|
D:GLN563
|
4.1
|
1.6
|
1.0
|
CA
|
D:LEU562
|
4.1
|
1.6
|
1.0
|
HA
|
D:ARG557
|
4.2
|
2.2
|
1.0
|
CA
|
D:PHE556
|
4.2
|
1.4
|
1.0
|
N
|
D:GLN563
|
4.2
|
1.6
|
1.0
|
H
|
D:TYR559
|
4.2
|
2.0
|
1.0
|
CA
|
D:GLN563
|
4.3
|
1.6
|
1.0
|
HB3
|
D:PHE556
|
4.3
|
1.4
|
1.0
|
CB
|
D:LEU562
|
4.4
|
1.6
|
1.0
|
N
|
D:ARG561
|
4.4
|
1.9
|
1.0
|
CA
|
D:TYR559
|
4.4
|
2.0
|
1.0
|
N
|
D:TYR559
|
4.5
|
2.0
|
1.0
|
N
|
D:ARG557
|
4.5
|
2.2
|
1.0
|
HB2
|
D:TYR559
|
4.7
|
2.0
|
1.0
|
CA
|
D:ARG557
|
4.7
|
2.2
|
1.0
|
HG3
|
D:GLN563
|
4.7
|
1.6
|
1.0
|
CD1
|
D:LEU350
|
4.7
|
1.8
|
1.0
|
HB3
|
D:LEU562
|
4.7
|
1.6
|
1.0
|
CG
|
D:GLN563
|
4.8
|
1.6
|
1.0
|
C
|
D:ARG557
|
4.8
|
2.2
|
1.0
|
CB
|
D:PHE556
|
4.8
|
1.4
|
1.0
|
H
|
D:ARG561
|
4.9
|
1.9
|
1.0
|
C
|
D:ARG561
|
4.9
|
1.9
|
1.0
|
HD21
|
D:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
D:ARG557
|
4.9
|
2.2
|
1.0
|
HD12
|
D:LEU350
|
4.9
|
1.8
|
1.0
|
O
|
D:ALA555
|
4.9
|
1.8
|
1.0
|
H
|
D:GLN563
|
5.0
|
1.6
|
1.0
|
|
Reference:
A.Merk,
T.Fukumura,
X.Zhu,
J.E.Darling,
R.Grisshammer,
J.Ognjenovic,
S.Subramaniam.
1.8 Angstrom Resolution Structure of Beta-Galactosidase with A 200 Kv Cryo Arm Electron Microscope. Iucrj V. 7 639 2020.
ISSN: ESSN 2052-2525
PubMed: 32695410
DOI: 10.1107/S2052252520006855
Page generated: Tue Oct 8 14:46:11 2024
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