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Sodium in PDB 6kuz: E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01

Enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01

All present enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01:
3.2.1.23;

Protein crystallography data

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01, PDB code: 6kuz was solved by X.Chen, Y.L.Hu, X.K.Li, Y.Guo, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.50 / 2.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 248.174, 85.506, 243.052, 90.00, 94.09, 90.00
R / Rfree (%) 18.2 / 22.4

Other elements in 6kuz:

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 (pdb code 6kuz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01, PDB code: 6kuz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 6kuz

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Sodium binding site 1 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1102

b:44.7
occ:1.00
 OD2 A:ASP201 2.3 39.8 1.0
O A:PHE601 2.4 31.6 1.0
ND2 A:ASN604 2.5 28.2 1.0
O35 A:DVL1101 2.5 0.6 1.0
O A:HOH1213 2.6 16.5 1.0
CG A:ASN604 3.3 30.0 1.0
CG A:ASP201 3.4 37.9 1.0
OD1 A:ASN604 3.5 31.2 1.0
C A:PHE601 3.6 31.5 1.0
C28 A:DVL1101 3.7 94.0 1.0
OH A:TYR100 3.8 36.1 1.0
C29 A:DVL1101 3.8 89.5 1.0
OD1 A:ASP201 3.9 42.4 1.0
NE2 A:HIS540 4.1 32.3 1.0
ND2 A:ASN102 4.1 41.2 1.0
CB A:PHE601 4.2 34.1 1.0
CD1 A:PHE601 4.3 35.0 1.0
CA A:PHE601 4.3 33.1 1.0
NE1 A:TRP568 4.4 31.7 1.0
O16 A:DVL1101 4.5 91.0 1.0
N A:CYS602 4.6 30.8 1.0
CE1 A:HIS540 4.6 31.7 1.0
C31 A:DVL1101 4.6 68.5 1.0
CB A:ASP201 4.6 35.4 1.0
C27 A:DVL1101 4.7 84.0 1.0
CB A:ASN604 4.7 30.4 1.0
CG A:PHE601 4.7 35.5 1.0
O30 A:DVL1101 4.8 78.7 1.0
CA A:CYS602 4.8 32.9 1.0
CG A:ASN102 4.9 37.7 1.0
O A:HOH1217 5.0 40.6 1.0

Sodium binding site 2 out of 12 in 6kuz

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Sodium binding site 2 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1103

b:35.4
occ:1.00
 O A:PHE556 2.1 31.3 1.0
O A:HOH1318 2.3 19.2 1.0
O A:HOH1309 2.4 7.3 1.0
O A:TYR559 2.6 33.8 1.0
O A:LEU562 2.8 29.4 1.0
C A:PHE556 3.4 32.7 1.0
C A:TYR559 3.4 30.2 1.0
O A:PRO560 3.6 27.4 1.0
CA A:PRO560 3.7 30.1 1.0
C A:PRO560 3.9 29.3 1.0
N A:PRO560 3.9 29.4 1.0
C A:LEU562 4.0 28.9 1.0
O A:ARG557 4.1 28.6 1.0
CA A:ARG557 4.1 29.1 1.0
N A:ARG557 4.2 31.0 1.0
C A:ARG557 4.2 30.0 1.0
N A:TYR559 4.4 28.4 1.0
CA A:PHE556 4.4 31.8 1.0
CA A:TYR559 4.5 28.4 1.0
N A:LEU562 4.8 29.5 1.0
CA A:LEU562 4.8 27.7 1.0
N A:GLN558 4.8 30.8 1.0
CD1 A:LEU350 4.9 24.4 1.0
CB A:LEU562 4.9 27.4 1.0
N A:ARG561 4.9 31.6 1.0
N A:GLN563 5.0 28.0 1.0
CA A:GLN563 5.0 29.2 1.0

Sodium binding site 3 out of 12 in 6kuz

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Sodium binding site 3 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1104

b:60.5
occ:1.00
 O A:DMS1105 2.4 62.5 1.0
O A:LEU670 2.5 46.4 1.0
O A:SER647 2.6 47.6 1.0
O A:GLU650 3.0 42.7 1.0
S A:DMS1105 3.3 73.3 1.0
C A:LEU670 3.6 45.7 1.0
C1 A:DMS1105 3.7 74.4 1.0
C A:SER647 3.8 40.1 1.0
N A:GLU650 3.9 40.3 1.0
N A:LEU670 3.9 53.1 1.0
C A:GLU650 4.1 39.7 1.0
CA A:ASP648 4.1 46.6 1.0
N A:ASN649 4.2 39.7 1.0
CA A:LEU670 4.3 47.9 1.0
C A:ASP648 4.3 43.6 1.0
N A:ASP648 4.4 41.5 1.0
CA A:GLU650 4.5 40.5 1.0
OG A:SER647 4.5 40.9 1.0
CB A:LEU670 4.6 50.1 1.0
N A:ASP671 4.7 42.7 1.0
CB A:GLU650 4.8 43.2 1.0
CB A:SER647 4.8 40.9 1.0
C A:ASN649 4.9 38.8 1.0
C A:PRO669 4.9 55.2 1.0
C2 A:DMS1105 4.9 68.3 1.0
CA A:SER647 5.0 39.5 1.0
CA A:ASN649 5.0 38.2 1.0

Sodium binding site 4 out of 12 in 6kuz

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Sodium binding site 4 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1102

b:44.5
occ:1.00
 OD2 B:ASP201 2.2 41.2 1.0
ND2 B:ASN604 2.3 39.3 1.0
O B:HOH1201 2.3 39.3 1.0
O B:PHE601 2.4 33.8 1.0
O B:HOH1274 2.5 28.3 1.0
CG B:ASP201 3.3 43.2 1.0
CG B:ASN604 3.4 37.4 1.0
C B:PHE601 3.6 36.7 1.0
OH B:TYR100 3.6 42.2 1.0
O35 B:DVL1101 3.7 0.4 1.0
OD1 B:ASN604 3.7 39.5 1.0
OD1 B:ASP201 3.8 44.1 1.0
C29 B:DVL1101 3.8 96.5 1.0
NE1 B:TRP568 4.2 31.3 1.0
C31 B:DVL1101 4.2 77.8 1.0
CA B:CYS602 4.3 37.4 1.0
O30 B:DVL1101 4.3 82.9 1.0
N B:CYS602 4.3 37.4 1.0
C28 B:DVL1101 4.4 94.6 1.0
O B:ASP201 4.5 42.2 1.0
CB B:ASP201 4.5 40.5 1.0
NE2 B:HIS540 4.6 32.1 1.0
CA B:PHE601 4.6 38.0 1.0
CB B:PHE601 4.7 37.5 1.0
CB B:ASN604 4.7 37.2 1.0
O16 B:DVL1101 4.7 95.3 1.0
C B:CYS602 4.7 36.9 1.0
CZ B:TYR100 4.8 37.2 1.0
ND2 B:ASN102 4.9 35.4 1.0
O B:HOH1212 4.9 32.9 1.0
CE2 B:TRP568 4.9 31.9 1.0
CZ2 B:TRP568 5.0 31.8 1.0

Sodium binding site 5 out of 12 in 6kuz

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Sodium binding site 5 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1103

b:30.0
occ:1.00
 O B:PHE556 2.4 30.6 1.0
O B:HOH1316 2.4 27.9 1.0
O B:LEU562 2.6 28.9 1.0
O B:TYR559 2.7 27.7 1.0
O B:HOH1299 3.1 14.5 1.0
C B:PHE556 3.5 28.0 1.0
C B:TYR559 3.5 30.1 1.0
O B:PRO560 3.7 25.0 1.0
CA B:PRO560 3.7 25.8 1.0
C B:LEU562 3.9 28.2 1.0
C B:PRO560 3.9 26.1 1.0
N B:PRO560 4.0 28.8 1.0
O B:ARG557 4.2 32.1 1.0
CA B:ARG557 4.3 29.2 1.0
N B:ARG557 4.3 28.5 1.0
C B:ARG557 4.4 29.3 1.0
N B:TYR559 4.4 29.0 1.0
CA B:PHE556 4.5 28.6 1.0
CA B:TYR559 4.6 28.2 1.0
N B:LEU562 4.7 27.3 1.0
CA B:LEU562 4.7 28.0 1.0
CD1 B:LEU350 4.7 23.2 1.0
N B:GLN563 4.8 26.6 1.0
CA B:GLN563 4.8 26.2 1.0
CB B:LEU562 4.8 29.3 1.0
N B:ARG561 4.9 27.6 1.0

Sodium binding site 6 out of 12 in 6kuz

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Sodium binding site 6 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1104

b:46.1
occ:1.00
 O B:PRO932 2.7 31.9 1.0
O B:THR970 2.8 31.0 1.0
O B:LEU967 2.9 38.5 1.0
CZ B:PHE931 3.1 39.6 1.0
CE1 B:PHE931 3.4 37.0 1.0
O B:MET968 3.7 46.5 1.0
CE2 B:PHE931 3.7 40.0 1.0
C B:THR970 3.8 33.6 1.0
C B:PRO932 3.9 31.6 1.0
C B:MET968 4.0 45.6 1.0
C B:LEU967 4.1 36.3 1.0
CD1 B:PHE931 4.1 36.6 1.0
CD B:PRO932 4.2 31.6 1.0
CA B:MET968 4.3 43.0 1.0
N B:THR970 4.3 38.7 1.0
N B:PRO932 4.3 30.7 1.0
CD2 B:PHE931 4.3 37.3 1.0
CA B:PRO932 4.5 32.4 1.0
CB B:PRO932 4.5 33.2 1.0
CG B:PHE931 4.5 35.3 1.0
N B:SER971 4.6 36.5 1.0
N B:MET968 4.6 39.3 1.0
CA B:SER971 4.6 35.4 1.0
CA B:THR970 4.7 35.9 1.0
N B:GLU969 4.7 43.5 1.0
CG B:PRO932 4.8 32.4 1.0
N B:SER933 5.0 29.9 1.0
C B:PHE931 5.0 32.4 1.0

Sodium binding site 7 out of 12 in 6kuz

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Sodium binding site 7 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1102

b:37.5
occ:1.00
 OD2 C:ASP201 2.1 36.6 1.0
OD1 C:ASN604 2.4 40.1 1.0
O C:HOH1249 2.5 17.1 1.0
O C:HOH1218 2.5 32.5 1.0
O C:PHE601 2.5 32.9 1.0
O35 C:DVL1101 3.0 81.3 1.0
CG C:ASP201 3.2 41.7 1.0
CG C:ASN604 3.4 39.5 1.0
OD1 C:ASP201 3.6 47.1 1.0
C29 C:DVL1101 3.7 89.0 1.0
C C:PHE601 3.7 37.7 1.0
OH C:TYR100 3.7 41.3 1.0
ND2 C:ASN604 3.8 42.7 1.0
C28 C:DVL1101 3.9 82.7 1.0
NE1 C:TRP568 4.2 34.4 1.0
O30 C:DVL1101 4.4 82.1 1.0
CA C:CYS602 4.4 37.0 1.0
CB C:ASP201 4.4 40.4 1.0
O16 C:DVL1101 4.4 92.7 1.0
C31 C:DVL1101 4.5 79.0 1.0
N C:CYS602 4.5 39.6 1.0
NE2 C:HIS540 4.5 33.0 1.0
ND2 C:ASN102 4.5 41.1 1.0
O C:ASP201 4.5 40.0 1.0
O C:HOH1242 4.6 33.5 1.0
CB C:PHE601 4.6 40.7 1.0
CA C:PHE601 4.7 41.0 1.0
CB C:ASN604 4.8 39.1 1.0
C C:CYS602 4.8 34.1 1.0
CZ C:TYR100 4.9 39.6 1.0
CE2 C:TRP568 5.0 33.1 1.0

Sodium binding site 8 out of 12 in 6kuz

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Sodium binding site 8 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1103

b:28.4
occ:1.00
 O C:PHE556 2.3 38.4 1.0
O C:LEU562 2.6 27.7 1.0
O C:TYR559 2.8 32.7 1.0
O C:HOH1277 2.9 28.1 1.0
C C:PHE556 3.4 33.8 1.0
O C:PRO560 3.7 31.4 1.0
C C:TYR559 3.7 33.1 1.0
C C:LEU562 3.8 30.0 1.0
CA C:PRO560 4.0 29.2 1.0
C C:PRO560 4.1 30.3 1.0
CA C:ARG557 4.2 35.0 1.0
N C:PRO560 4.3 30.8 1.0
N C:ARG557 4.3 33.3 1.0
O C:ARG557 4.3 35.6 1.0
CA C:PHE556 4.4 32.4 1.0
C C:ARG557 4.4 32.9 1.0
CD1 C:LEU350 4.6 25.4 1.0
N C:TYR559 4.7 32.2 1.0
CA C:GLN563 4.7 29.2 1.0
N C:GLN563 4.7 30.4 1.0
CA C:LEU562 4.7 29.0 1.0
N C:LEU562 4.8 28.8 1.0
CA C:TYR559 4.8 31.9 1.0
CB C:LEU562 4.9 29.6 1.0
CB C:PHE556 4.9 33.2 1.0

Sodium binding site 9 out of 12 in 6kuz

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Sodium binding site 9 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1104

b:41.2
occ:1.00
 O C:HOH1281 2.5 16.0 1.0
O C:LEU670 2.5 49.4 1.0
O C:GLU650 2.6 54.4 1.0
O C:SER647 2.6 55.3 1.0
N C:GLU650 3.6 38.6 1.0
C C:GLU650 3.7 43.1 1.0
C C:LEU670 3.7 52.5 1.0
C C:SER647 3.8 49.4 1.0
N C:LEU670 4.0 54.9 1.0
CA C:GLU650 4.1 41.2 1.0
N C:ASN649 4.1 42.1 1.0
CA C:LEU670 4.3 52.6 1.0
CB C:SER647 4.3 47.4 1.0
CB C:GLU650 4.4 41.7 1.0
C C:ASP648 4.4 44.2 1.0
CB C:LEU670 4.5 51.6 1.0
C C:ASN649 4.6 38.0 1.0
N C:ASP648 4.7 50.0 1.0
CA C:ASN649 4.7 38.3 1.0
CA C:SER647 4.7 47.8 1.0
CA C:ASP648 4.8 47.4 1.0
N C:LEU651 4.8 40.5 1.0
N C:ASP671 4.8 51.0 1.0
O C:ASP648 5.0 41.1 1.0

Sodium binding site 10 out of 12 in 6kuz

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Sodium binding site 10 out of 12 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1102

b:34.6
occ:1.00
 ND2 D:ASN604 2.2 30.1 1.0
OD2 D:ASP201 2.3 39.3 1.0
O D:PHE601 2.3 36.4 1.0
O35 D:DVL1101 2.5 0.1 1.0
O D:HOH1261 2.6 38.0 1.0
CG D:ASN604 3.2 35.0 1.0
CG D:ASP201 3.4 37.2 1.0
OD1 D:ASN604 3.4 35.9 1.0
C D:PHE601 3.6 35.3 1.0
C28 D:DVL1101 3.7 0.9 1.0
OH D:TYR100 3.8 28.9 1.0
OD1 D:ASP201 3.8 38.5 1.0
C29 D:DVL1101 3.9 98.3 1.0
NE1 D:TRP568 4.1 35.2 1.0
NE2 D:HIS540 4.4 32.4 1.0
CA D:CYS602 4.4 33.4 1.0
N D:CYS602 4.4 32.9 1.0
C27 D:DVL1101 4.4 94.3 1.0
CA D:PHE601 4.5 33.6 1.0
CB D:PHE601 4.5 32.4 1.0
ND2 D:ASN102 4.5 35.9 1.0
C31 D:DVL1101 4.5 85.6 1.0
CB D:ASN604 4.6 34.5 1.0
CB D:ASP201 4.6 36.5 1.0
O16 D:DVL1101 4.7 99.1 1.0
O30 D:DVL1101 4.8 91.1 1.0
C D:CYS602 4.8 33.0 1.0
O D:ASP201 4.9 34.5 1.0
CD1 D:PHE601 4.9 35.2 1.0
CE1 D:HIS540 4.9 32.3 1.0
O D:HOH1212 5.0 32.4 1.0
CE2 D:TRP568 5.0 34.1 1.0
CZ D:TYR100 5.0 33.6 1.0
CD1 D:TRP568 5.0 35.0 1.0

Reference:

X.K.Li, W.J.Qiu, J.W.Li, X.Chen, Y.L.Hu, Y.Gao, D.L.Shi, X.M.Li, H.T.Lin, Z.Hu, G.Q.Dong, C.Q.Sheng, B.Jiang, C.L.Xia, C.Y.Kim, Y.Guo, J.Li. First-Generation Species-Selective Chemical Probes For Fluorescence Imaging of Human Senescence-Associated Beta-Galactosidase Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC01234C
Page generated: Tue Oct 8 11:35:04 2024

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