Sodium in PDB 7btk: E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01

Enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01

All present enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01:
3.2.1.23;

Protein crystallography data

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01, PDB code: 7btk was solved by X.Chen, Y.L.Hu, Q.M.Liu, Y.Gao, R.Yuan, Y.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 249.832, 85.454, 243.307, 90, 94.15, 90
R / Rfree (%) 21.8 / 23.3

Other elements in 7btk:

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01 also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01 (pdb code 7btk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01, PDB code: 7btk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7btk

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Sodium binding site 1 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01


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 KSA01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1104

b:21.1
occ:1.00
 O05 A:F6L1101 2.3 61.3 1.0
OD2 A:ASP201 2.3 24.6 1.0
O A:PHE601 2.4 34.1 1.0
O A:HOH1421 2.4 9.9 1.0
OD1 A:ASN604 2.5 24.4 1.0
CG A:ASP201 3.3 24.2 1.0
C09 A:F6L1101 3.4 71.5 1.0
C A:PHE601 3.5 30.8 1.0
CG A:ASN604 3.5 26.7 1.0
OH A:TYR100 3.6 19.5 1.0
OD1 A:ASP201 3.7 24.7 1.0
ND2 A:ASN604 3.8 20.1 1.0
C10 A:F6L1101 3.8 68.3 1.0
C08 A:F6L1101 4.1 66.4 1.0
CB A:PHE601 4.3 25.3 1.0
NE1 A:TRP568 4.3 20.9 1.0
CA A:PHE601 4.4 30.6 1.0
N A:CYS602 4.4 27.3 1.0
CB A:ASP201 4.5 22.3 1.0
CA A:CYS602 4.5 27.9 1.0
NE2 A:HIS540 4.5 37.9 1.0
O A:HOH1339 4.5 19.9 1.0
O01 A:F6L1101 4.6 71.1 1.0
ND2 A:ASN102 4.7 25.5 1.0
C11 A:F6L1101 4.7 53.7 1.0
O02 A:F6L1101 4.8 64.3 1.0
CZ A:TYR100 4.8 18.9 1.0
C A:CYS602 4.9 23.9 1.0
O A:ASP201 4.9 21.9 1.0
CB A:ASN604 4.9 25.6 1.0
C07 A:F6L1101 5.0 61.3 1.0
CD1 A:PHE601 5.0 26.5 1.0

Sodium binding site 2 out of 7 in 7btk

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Sodium binding site 2 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01


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 KSA01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1105

b:20.0
occ:1.00
 O A:PHE556 2.3 25.7 1.0
O A:LEU562 2.3 25.4 1.0
O A:HOH1458 2.4 18.4 1.0
O A:TYR559 2.6 27.6 1.0
O A:HOH1452 2.6 22.3 1.0
C A:LEU562 3.4 19.9 1.0
C A:PHE556 3.4 25.1 1.0
O A:PRO560 3.5 23.8 1.0
C A:TYR559 3.7 19.4 1.0
C A:PRO560 3.9 23.1 1.0
CA A:PRO560 4.0 21.3 1.0
CA A:PHE556 4.2 25.1 1.0
O A:HOH1231 4.2 26.1 1.0
CA A:GLN563 4.3 21.7 1.0
N A:GLN563 4.3 19.7 1.0
N A:LEU562 4.3 18.0 1.0
N A:PRO560 4.3 20.9 1.0
CA A:LEU562 4.3 16.9 1.0
N A:ARG557 4.5 24.9 1.0
O A:HOH1365 4.5 25.0 1.0
CB A:LEU562 4.6 13.8 1.0
CD1 A:LEU350 4.6 18.2 1.0
CA A:ARG557 4.6 21.1 1.0
N A:TYR559 4.7 16.5 1.0
CG A:GLN563 4.7 20.9 1.0
CB A:PHE556 4.7 28.3 1.0
N A:ARG561 4.8 23.4 1.0
CA A:TYR559 4.8 17.7 1.0
C A:ARG557 4.8 18.4 1.0
O A:ARG557 5.0 20.2 1.0

Sodium binding site 3 out of 7 in 7btk

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Sodium binding site 3 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01


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 KSA01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1103

b:24.6
occ:1.00
 O05 B:F6L1101 2.3 64.6 1.0
O B:HOH1422 2.3 20.3 1.0
OD2 B:ASP201 2.3 24.0 1.0
ND2 B:ASN604 2.4 22.2 1.0
O B:PHE601 2.7 25.4 1.0
CG B:ASP201 3.3 23.6 1.0
C09 B:F6L1101 3.4 72.0 1.0
CG B:ASN604 3.5 26.9 1.0
OD1 B:ASN604 3.8 25.1 1.0
C B:PHE601 3.8 30.7 1.0
OH B:TYR100 3.8 22.4 1.0
OD1 B:ASP201 3.8 26.5 1.0
C10 B:F6L1101 3.8 69.7 1.0
C08 B:F6L1101 4.0 60.9 1.0
NE1 B:TRP568 4.1 22.8 1.0
CB B:ASP201 4.4 25.5 1.0
O B:HOH1276 4.4 20.6 1.0
NE2 B:HIS540 4.5 33.1 1.0
CB B:PHE601 4.6 27.0 1.0
N B:CYS602 4.6 29.2 1.0
CA B:CYS602 4.6 30.1 1.0
C11 B:F6L1101 4.6 54.4 1.0
O01 B:F6L1101 4.7 70.8 1.0
CA B:PHE601 4.7 30.5 1.0
O B:ASP201 4.7 27.1 1.0
O02 B:F6L1101 4.8 61.1 1.0
CB B:ASN604 4.8 28.1 1.0
C07 B:F6L1101 4.8 59.0 1.0
CE2 B:TRP568 4.8 17.9 1.0
C B:CYS602 4.9 29.7 1.0
CZ2 B:TRP568 4.9 16.4 1.0
CD1 B:TRP568 5.0 24.9 1.0
ND2 B:ASN102 5.0 27.0 1.0
CZ B:TYR100 5.0 22.9 1.0

Sodium binding site 4 out of 7 in 7btk

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Sodium binding site 4 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01


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 KSA01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1104

b:29.2
occ:1.00
 O C:HOH1352 2.3 23.2 1.0
O C:PHE601 2.3 33.5 1.0
OD2 C:ASP201 2.3 32.5 1.0
OD1 C:ASN604 2.6 38.4 1.0
O05 C:F6L1101 2.7 89.0 1.0
CG C:ASP201 3.3 31.3 1.0
C C:PHE601 3.4 32.3 1.0
OH C:TYR100 3.4 47.6 1.0
CG C:ASN604 3.6 34.3 1.0
OD1 C:ASP201 3.6 38.9 1.0
C09 C:F6L1101 3.8 89.3 1.0
ND2 C:ASN604 3.9 36.6 1.0
C10 C:F6L1101 4.1 87.3 1.0
N C:CYS602 4.2 26.7 1.0
CB C:PHE601 4.2 32.3 1.0
CA C:CYS602 4.2 25.4 1.0
CA C:PHE601 4.3 34.3 1.0
NE1 C:TRP568 4.5 22.8 1.0
C08 C:F6L1101 4.5 74.8 1.0
CZ C:TYR100 4.6 45.1 1.0
CB C:ASP201 4.6 26.6 1.0
ND2 C:ASN102 4.6 31.4 1.0
NE2 C:HIS540 4.7 35.5 1.0
C C:CYS602 4.7 25.6 1.0
O01 C:F6L1101 4.7 94.7 1.0
O C:ASP201 4.8 21.4 1.0
CB C:ASN604 4.9 30.6 1.0
CD2 C:PHE601 4.9 36.8 1.0

Sodium binding site 5 out of 7 in 7btk

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Sodium binding site 5 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01


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 KSA01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1105

b:18.4
occ:1.00
 O C:HOH1458 2.3 24.1 1.0
O C:TYR559 2.3 19.2 1.0
O C:PHE556 2.4 26.8 1.0
O C:HOH1413 2.4 26.4 1.0
O C:LEU562 2.4 20.8 1.0
C C:TYR559 3.4 20.4 1.0
O C:PRO560 3.4 17.5 1.0
C C:LEU562 3.5 16.5 1.0
C C:PHE556 3.6 24.9 1.0
C C:PRO560 3.7 18.2 1.0
CA C:PRO560 3.7 17.1 1.0
N C:PRO560 4.0 19.0 1.0
N C:LEU562 4.2 14.8 1.0
CA C:LEU562 4.3 15.6 1.0
N C:GLN563 4.4 15.8 1.0
CA C:PHE556 4.4 23.2 1.0
CA C:GLN563 4.4 15.6 1.0
CA C:TYR559 4.6 18.7 1.0
CB C:LEU562 4.6 16.9 1.0
N C:TYR559 4.6 20.4 1.0
N C:ARG561 4.6 19.2 1.0
N C:ARG557 4.6 28.5 1.0
CA C:ARG557 4.7 27.5 1.0
C C:ARG557 4.8 20.0 1.0
CD1 C:LEU350 4.8 22.1 1.0
O C:ARG557 4.8 17.7 1.0
CG C:GLN563 4.8 14.0 1.0

Sodium binding site 6 out of 7 in 7btk

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Sodium binding site 6 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01


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 KSA01 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1104

b:32.1
occ:1.00
 O D:HOH1206 2.3 24.8 1.0
OD2 D:ASP201 2.3 20.6 1.0
O D:HOH1394 2.3 17.5 1.0
O D:PHE601 2.4 38.5 1.0
OD1 D:ASN604 2.7 39.2 1.0
O05 D:F6L1101 3.1 116.1 1.0
CG D:ASP201 3.2 22.5 1.0
OH D:TYR100 3.3 39.5 1.0
C D:PHE601 3.5 36.3 1.0
OD1 D:ASP201 3.5 23.7 1.0
CG D:ASN604 3.7 29.1 1.0
C10 D:F6L1101 3.9 97.7 1.0
C09 D:F6L1101 4.1 99.3 1.0
ND2 D:ASN604 4.1 23.6 1.0
CA D:CYS602 4.2 32.8 1.0
N D:CYS602 4.3 32.0 1.0
CB D:PHE601 4.3 38.9 1.0
O D:HOH1315 4.4 15.2 1.0
CA D:PHE601 4.4 39.2 1.0
NE1 D:TRP568 4.5 24.0 1.0
CB D:ASP201 4.5 20.0 1.0
CZ D:TYR100 4.5 43.3 1.0
O02 D:F6L1101 4.6 92.1 1.0
O01 D:F6L1101 4.6 95.0 1.0
O D:ASP201 4.6 28.1 1.0
C D:CYS602 4.7 31.5 1.0
C11 D:F6L1101 4.8 80.0 1.0
ND2 D:ASN102 4.8 33.4 1.0
NE2 D:HIS540 4.8 40.6 1.0
CE1 D:TYR100 5.0 40.6 1.0

Sodium binding site 7 out of 7 in 7btk

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Sodium binding site 7 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA01


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 KSA01 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1105

b:19.9
occ:1.00
 O D:HOH1432 2.2 31.9 1.0
O D:LEU562 2.4 22.0 1.0
O D:PHE556 2.4 29.2 1.0
O D:HOH1423 2.5 33.6 1.0
O D:TYR559 2.5 16.6 1.0
O D:PRO560 3.4 21.8 1.0
C D:LEU562 3.5 15.6 1.0
C D:TYR559 3.6 18.5 1.0
C D:PHE556 3.6 25.6 1.0
C D:PRO560 3.7 19.7 1.0
CA D:PRO560 3.8 15.6 1.0
N D:PRO560 4.1 16.9 1.0
N D:LEU562 4.3 13.2 1.0
O D:HOH1237 4.3 32.6 1.0
N D:GLN563 4.3 15.5 1.0
CA D:LEU562 4.4 15.3 1.0
CA D:GLN563 4.4 16.4 1.0
CA D:PHE556 4.4 25.4 1.0
N D:ARG557 4.6 26.7 1.0
CB D:LEU562 4.6 14.0 1.0
N D:ARG561 4.6 17.8 1.0
N D:TYR559 4.7 15.7 1.0
CA D:ARG557 4.7 27.9 1.0
CA D:TYR559 4.7 16.7 1.0
CG D:GLN563 4.7 16.6 1.0
CD1 D:LEU350 4.7 16.2 1.0
C D:ARG557 4.8 24.4 1.0
O D:ARG557 4.9 20.6 1.0

Reference:

Y.Guo, Y.Gao, Y.L.Hu, Q.M.Liu, X.K.Li, X.M.Li, C.Y.Kim, T.D.James, J.Li, X.Chen. Two-Dimensional Design Strategy to Construct Smart Fluorescent Probes For the Precise Tracking of Senescence Angew.Chem.Int.Ed.Engl. 2021.
ISSN: ESSN 1521-3773
DOI: 10.1002/ANIE.202101278
Page generated: Sat Apr 3 17:52:59 2021

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