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Sodium in PDB 7brs: E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02

Enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02

All present enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02:
3.2.1.23;

Protein crystallography data

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02, PDB code: 7brs was solved by X.Chen, Y.L.Hu, 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) 30.04 / 2.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 246.653, 84.423, 240.65, 90, 94.43, 90
R / Rfree (%) 20 / 24.4

Other elements in 7brs:

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02 (pdb code 7brs). 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 KSA02, PDB code: 7brs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7brs

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Sodium binding site 1 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1104

b:38.9
occ:1.00
 OD2 A:ASP201 2.1 56.8 1.0
O A:HOH1272 2.4 35.9 1.0
ND2 A:ASN604 2.5 49.6 1.0
O09 A:F4X1101 2.5 58.5 1.0
O A:PHE601 2.6 59.2 1.0
CG A:ASP201 3.0 57.8 1.0
C08 A:F4X1101 3.0 56.3 1.0
OD1 A:ASP201 3.4 68.1 1.0
CG A:ASN604 3.5 57.1 1.0
OH A:TYR100 3.5 49.3 1.0
C A:PHE601 3.7 58.1 1.0
OD1 A:ASN604 3.8 61.2 1.0
O12 A:F4X1101 3.9 45.4 1.0
NE1 A:TRP568 3.9 47.6 1.0
C05 A:F4X1101 4.1 49.1 1.0
C04 A:F4X1101 4.2 56.1 1.0
CB A:ASP201 4.2 51.0 1.0
CA A:CYS602 4.4 54.2 1.0
O A:ASP201 4.4 49.9 1.0
N A:CYS602 4.4 54.8 1.0
CZ2 A:TRP568 4.4 47.5 1.0
CE2 A:TRP568 4.6 46.5 1.0
CB A:PHE601 4.6 51.6 1.0
NE2 A:HIS540 4.6 58.2 1.0
CA A:PHE601 4.7 57.3 1.0
CZ A:TYR100 4.7 57.0 1.0
CB A:ASN604 4.8 51.2 1.0
C A:CYS602 4.8 52.2 1.0

Sodium binding site 2 out of 7 in 7brs

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Sodium binding site 2 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1104

b:43.9
occ:1.00
 OD2 B:ASP201 2.2 63.9 1.0
O B:HOH1250 2.4 35.2 1.0
ND2 B:ASN604 2.4 48.9 1.0
O B:PHE601 2.6 51.0 1.0
O09 B:F4X1101 2.7 71.4 1.0
CG B:ASP201 3.1 63.4 1.0
C08 B:F4X1101 3.3 65.4 1.0
OD1 B:ASP201 3.5 69.0 1.0
CG B:ASN604 3.5 54.5 1.0
OH B:TYR100 3.6 52.9 1.0
C B:PHE601 3.8 52.4 1.0
NE1 B:TRP568 3.9 48.6 1.0
OD1 B:ASN604 3.9 51.2 1.0
O12 B:F4X1101 3.9 55.1 1.0
C05 B:F4X1101 4.2 58.6 1.0
O B:ASP201 4.2 48.3 1.0
CB B:ASP201 4.2 55.8 1.0
CZ2 B:TRP568 4.3 44.6 1.0
CA B:CYS602 4.3 50.5 1.0
C04 B:F4X1101 4.4 61.5 1.0
CE2 B:TRP568 4.4 47.7 1.0
N B:CYS602 4.5 51.2 1.0
O B:HOH1215 4.6 47.2 1.0
CZ B:TYR100 4.7 54.1 1.0
C B:CYS602 4.7 51.3 1.0
CB B:ASN604 4.8 51.6 1.0
CA B:PHE601 4.8 54.7 1.0
NE2 B:GLN573 4.8 48.9 1.0
CB B:PHE601 4.8 52.1 1.0
NE2 B:HIS540 4.9 55.6 1.0
C B:ASP201 4.9 46.7 1.0
CE1 B:TYR100 4.9 56.1 1.0

Sodium binding site 3 out of 7 in 7brs

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Sodium binding site 3 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1105

b:55.7
occ:1.00
 O B:THR970 2.6 79.6 1.0
O B:HOH1276 2.6 41.2 1.0
O B:HOH1220 2.7 55.5 1.0
O B:LEU967 2.8 77.7 1.0
O B:MET968 3.0 88.8 1.0
CZ B:PHE931 3.3 71.0 1.0
O B:PRO932 3.3 72.0 1.0
C B:MET968 3.5 85.5 1.0
CE1 B:PHE931 3.6 68.1 1.0
CA B:MET968 3.7 83.7 1.0
C B:THR970 3.8 74.3 1.0
CE2 B:PHE931 3.9 69.2 1.0
C B:LEU967 3.9 81.4 1.0
N B:THR970 4.2 77.0 1.0
N B:MET968 4.3 81.7 1.0
N B:GLU969 4.4 79.5 1.0
C B:PRO932 4.5 73.2 1.0
CD1 B:PHE931 4.5 71.4 1.0
CA B:THR970 4.6 75.7 1.0
CD2 B:PHE931 4.7 66.9 1.0
N B:SER971 4.7 71.6 1.0
C B:GLU969 4.8 79.5 1.0
CA B:SER971 4.8 69.1 1.0
CD B:PRO932 4.9 71.3 1.0
O B:PRO788 4.9 82.8 1.0
CG B:PHE931 5.0 64.7 1.0

Sodium binding site 4 out of 7 in 7brs

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Sodium binding site 4 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1104

b:67.5
occ:1.00
 OD2 C:ASP201 2.4 60.8 1.0
OD1 C:ASN604 2.6 69.5 1.0
O C:PHE601 2.8 65.8 1.0
CG C:ASP201 3.1 54.6 1.0
O09 C:F4X1101 3.2 58.0 1.0
OH C:TYR100 3.5 61.9 1.0
OD1 C:ASP201 3.5 58.0 1.0
O C:ASP201 3.6 52.2 1.0
CG C:ASN604 3.7 63.5 1.0
C08 C:F4X1101 3.8 51.6 1.0
CA C:CYS602 3.9 52.4 1.0
C C:PHE601 3.9 65.1 1.0
O C:HOH1251 4.0 56.7 1.0
NE1 C:TRP568 4.1 59.9 1.0
CB C:ASP201 4.2 44.8 1.0
O12 C:F4X1101 4.2 56.9 1.0
CZ2 C:TRP568 4.2 47.9 1.0
NE2 C:GLN573 4.2 65.3 1.0
C C:CYS602 4.3 60.6 1.0
N C:CYS602 4.3 58.7 1.0
O C:CYS602 4.3 65.7 1.0
ND2 C:ASN604 4.4 65.9 1.0
C C:ASP201 4.5 49.8 1.0
CZ C:TYR100 4.5 56.2 1.0
CE2 C:TRP568 4.5 51.2 1.0
C05 C:F4X1101 4.6 51.9 1.0
CE1 C:TYR100 4.7 51.9 1.0
C04 C:F4X1101 4.8 50.2 1.0
CB C:ASN604 4.9 55.4 1.0
CB C:CYS602 5.0 55.5 1.0

Sodium binding site 5 out of 7 in 7brs

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Sodium binding site 5 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1105

b:57.3
occ:1.00
 O C:PHE556 2.4 46.4 1.0
O C:HOH1263 2.5 58.2 1.0
O C:LEU562 2.5 56.9 1.0
O C:TYR559 2.7 50.8 1.0
O C:PRO560 3.2 46.0 1.0
C C:LEU562 3.5 49.7 1.0
C C:PHE556 3.6 46.9 1.0
C C:TYR559 3.7 43.8 1.0
C C:PRO560 3.8 43.4 1.0
CA C:PRO560 3.9 42.6 1.0
CA C:GLN563 4.2 42.0 1.0
CD1 C:LEU350 4.2 45.9 1.0
N C:PRO560 4.3 43.2 1.0
N C:GLN563 4.3 42.3 1.0
CA C:PHE556 4.4 46.5 1.0
N C:LEU562 4.5 41.5 1.0
CA C:LEU562 4.5 45.8 1.0
N C:ARG557 4.6 51.4 1.0
CA C:ARG557 4.6 52.8 1.0
CG C:GLN563 4.8 40.7 1.0
CB C:LEU562 4.8 43.0 1.0
O C:ARG557 4.9 48.2 1.0
N C:TYR559 4.9 49.6 1.0
C C:ARG557 4.9 48.4 1.0
CA C:TYR559 4.9 44.5 1.0
N C:ARG561 4.9 41.0 1.0
CB C:PHE556 5.0 49.6 1.0

Sodium binding site 6 out of 7 in 7brs

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Sodium binding site 6 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1104

b:67.5
occ:1.00
 OD2 D:ASP201 2.6 55.6 1.0
O D:PHE601 2.9 67.3 1.0
OD1 D:ASN604 3.1 68.5 1.0
CG D:ASP201 3.2 48.5 1.0
O D:ASP201 3.4 52.9 1.0
O D:HOH1274 3.5 61.6 1.0
O09 D:F4X1101 3.6 45.5 1.0
CA D:CYS602 3.6 52.0 1.0
OD1 D:ASP201 3.6 43.5 1.0
OH D:TYR100 3.7 58.3 1.0
CG D:ASN604 3.9 64.4 1.0
C D:PHE601 3.9 60.1 1.0
NE2 D:GLN573 4.0 56.6 1.0
C D:CYS602 4.1 56.2 1.0
O D:CYS602 4.1 60.8 1.0
N D:CYS602 4.2 52.4 1.0
CB D:ASP201 4.3 40.7 1.0
C08 D:F4X1101 4.3 44.8 1.0
NE1 D:TRP568 4.3 48.3 1.0
C D:ASP201 4.3 41.8 1.0
CZ2 D:TRP568 4.4 45.4 1.0
ND2 D:ASN604 4.5 63.3 1.0
CZ D:TYR100 4.5 57.4 1.0
CE1 D:TYR100 4.5 58.3 1.0
O12 D:F4X1101 4.6 58.5 1.0
CB D:CYS602 4.7 51.4 1.0
CE2 D:TRP568 4.7 45.8 1.0
CB D:ASN604 4.8 57.2 1.0
CD D:GLN573 4.9 62.0 1.0
C05 D:F4X1101 5.0 49.1 1.0
N D:MET603 5.0 51.3 1.0
CA D:ASP201 5.0 42.0 1.0

Sodium binding site 7 out of 7 in 7brs

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Sodium binding site 7 out of 7 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1105

b:46.5
occ:1.00
 O D:PHE556 2.5 43.8 1.0
O D:LEU562 2.5 49.2 1.0
O D:TYR559 2.6 46.2 1.0
O D:HOH1280 2.6 108.4 1.0
O D:HOH1270 2.6 44.8 1.0
O D:PRO560 3.1 50.2 1.0
C D:LEU562 3.4 46.7 1.0
C D:TYR559 3.6 45.1 1.0
C D:PHE556 3.6 48.7 1.0
C D:PRO560 3.7 49.4 1.0
CA D:PRO560 3.8 48.7 1.0
CA D:GLN563 4.1 40.8 1.0
N D:PRO560 4.2 46.1 1.0
N D:GLN563 4.2 38.7 1.0
N D:LEU562 4.3 38.0 1.0
CA D:LEU562 4.3 38.6 1.0
CA D:PHE556 4.5 47.0 1.0
CD1 D:LEU350 4.5 44.3 1.0
N D:ARG557 4.6 46.4 1.0
CA D:ARG557 4.7 50.2 1.0
CB D:LEU562 4.7 39.7 1.0
N D:ARG561 4.7 37.5 1.0
CG D:GLN563 4.7 37.7 1.0
N D:TYR559 4.8 49.5 1.0
CA D:TYR559 4.8 41.5 1.0
O D:ARG557 4.8 47.7 1.0
C D:ARG557 4.8 46.6 1.0
CB D:GLN563 5.0 38.3 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: Tue Oct 8 16:16:43 2024

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