Atomistry » Sodium » PDB 7bqj-7cdu » 7brs
Atomistry »
  Sodium »
    PDB 7bqj-7cdu »
      7brs »

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

Go back to Sodium Binding Sites List in 7brs
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

Go back to Sodium Binding Sites List in 7brs
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

Go back to Sodium Binding Sites List in 7brs
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

Go back to Sodium Binding Sites List in 7brs
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

Go back to Sodium Binding Sites List in 7brs
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

Go back to Sodium Binding Sites List in 7brs
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

Go back to Sodium Binding Sites List in 7brs
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

Last articles

Cl in 5F63
Cl in 5F4Q
Cl in 5F60
Cl in 5F5P
Cl in 5F53
Cl in 5F4U
Cl in 5F4S
Cl in 5F4R
Cl in 5F4P
Cl in 5F4L
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy