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Magnesium 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:

Sodium (Na) 7 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 7 in 7btk

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1102

b:30.0
occ:1.00
 O A:HOH1260 1.9 7.9 1.0
OE1 A:GLU416 2.0 30.5 1.0
OE2 A:GLU461 2.1 21.0 1.0
O A:HOH1384 2.2 11.9 1.0
ND1 A:HIS418 3.0 14.1 1.0
CD A:GLU416 3.0 24.8 1.0
O06 A:F6L1101 3.0 47.5 1.0
OE2 A:GLU416 3.3 25.7 1.0
CD A:GLU461 3.4 23.2 1.0
C12 A:F6L1101 3.4 49.2 1.0
O02 A:F6L1101 3.5 64.3 1.0
N A:ASP201 3.6 24.7 1.0
CB A:ASP201 3.8 22.3 1.0
CE1 A:HIS418 3.8 11.8 1.0
C11 A:F6L1101 3.9 53.7 1.0
CG A:HIS418 4.0 14.7 1.0
O A:ASP199 4.0 17.9 1.0
ND2 A:ASN460 4.1 9.0 1.0
OD1 A:ASN102 4.1 24.1 1.0
CB A:HIS418 4.2 16.1 1.0
OE1 A:GLU461 4.2 28.1 1.0
CA A:ASP201 4.3 21.1 1.0
CG A:GLU416 4.3 22.6 1.0
CG A:GLU461 4.3 18.9 1.0
CB A:GLU461 4.5 15.6 1.0
C A:GLN200 4.5 24.3 1.0
CA A:GLN200 4.5 22.8 1.0
C10 A:F6L1101 4.7 68.3 1.0
O A:ASN102 4.9 21.3 1.0
O01 A:F6L1101 5.0 71.1 1.0
O03 A:F6L1101 5.0 74.3 1.0

Magnesium binding site 2 out of 7 in 7btk

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1103

b:19.7
occ:1.00
 O A:ASP15 1.9 23.4 1.0
O A:VAL21 2.2 24.8 1.0
NE2 A:GLN163 2.4 18.7 1.0
OD2 A:ASP193 2.5 23.2 1.0
O A:ASN18 2.6 16.1 1.0
C A:ASP15 3.1 22.1 1.0
CG A:ASP193 3.3 24.0 1.0
CD A:GLN163 3.4 19.1 1.0
C A:VAL21 3.4 24.9 1.0
OH A:TYR161 3.4 17.0 1.0
OD1 A:ASP193 3.5 29.0 1.0
C A:ASN18 3.5 18.5 1.0
OE1 A:GLN163 3.8 20.8 1.0
CA A:TRP16 3.9 16.6 1.0
N A:ASN18 3.9 19.2 1.0
N A:TRP16 3.9 16.6 1.0
CE2 A:TYR161 4.0 14.6 1.0
CA A:ASN18 4.1 16.4 1.0
CZ A:TYR161 4.2 15.6 1.0
CA A:ASP15 4.2 23.0 1.0
CB A:VAL21 4.2 22.9 1.0
CA A:VAL21 4.2 23.0 1.0
C A:TRP16 4.2 19.4 1.0
CB A:ASN18 4.4 9.5 1.0
N A:VAL21 4.4 22.8 1.0
N A:THR22 4.4 24.6 1.0
N A:GLU17 4.5 20.0 1.0
N A:PRO19 4.5 21.1 1.0
CG1 A:VAL21 4.5 21.6 1.0
CB A:ASP15 4.6 20.4 1.0
CA A:THR22 4.6 27.6 1.0
CG A:GLN163 4.6 16.1 1.0
CA A:PRO19 4.7 20.7 1.0
CB A:ASP193 4.8 16.9 1.0
O A:TRP16 4.8 15.9 1.0

Magnesium binding site 3 out of 7 in 7btk

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1102

b:26.1
occ:1.00
 O B:HOH1271 2.0 8.1 1.0
OE1 B:GLU416 2.0 31.6 1.0
OE2 B:GLU461 2.1 22.1 1.0
O B:HOH1331 2.1 6.9 1.0
O06 B:F6L1101 2.6 49.6 1.0
ND1 B:HIS418 2.9 12.8 1.0
CD B:GLU416 3.0 27.0 1.0
OE2 B:GLU416 3.3 25.1 1.0
C12 B:F6L1101 3.4 51.3 1.0
CD B:GLU461 3.4 25.8 1.0
O02 B:F6L1101 3.5 61.1 1.0
N B:ASP201 3.7 30.1 1.0
CE1 B:HIS418 3.8 12.3 1.0
CB B:ASP201 3.8 25.5 1.0
C11 B:F6L1101 3.9 54.4 1.0
CG B:HIS418 3.9 13.8 1.0
O B:ASP199 4.0 18.8 1.0
OD1 B:ASN102 4.1 23.5 1.0
ND2 B:ASN460 4.1 11.1 1.0
CB B:HIS418 4.1 14.8 1.0
OE1 B:GLU461 4.2 26.9 1.0
CA B:ASP201 4.3 27.2 1.0
CG B:GLU461 4.3 21.4 1.0
CG B:GLU416 4.4 25.5 1.0
CB B:GLU461 4.4 15.1 1.0
C B:GLN200 4.5 28.3 1.0
CA B:GLN200 4.5 26.4 1.0
C10 B:F6L1101 4.7 69.7 1.0
O B:ASN102 4.9 25.4 1.0
NE2 B:HIS418 5.0 7.5 1.0

Magnesium binding site 4 out of 7 in 7btk

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1102

b:38.0
occ:1.00
 O C:ASP15 2.0 21.2 1.0
OD2 C:ASP193 2.3 15.3 1.0
O C:VAL21 2.3 26.2 1.0
O C:ASN18 2.4 21.5 1.0
OE1 C:GLN163 2.5 27.1 1.0
CG C:ASP193 3.2 16.5 1.0
C C:ASP15 3.2 23.7 1.0
C C:ASN18 3.3 19.8 1.0
OD1 C:ASP193 3.4 20.2 1.0
C C:VAL21 3.5 21.6 1.0
CD C:GLN163 3.5 24.0 1.0
OH C:TYR161 3.6 23.6 1.0
N C:ASN18 3.7 22.1 1.0
CA C:TRP16 3.9 24.1 1.0
CA C:ASN18 3.9 21.6 1.0
NE2 C:GLN163 3.9 23.7 1.0
N C:TRP16 4.0 23.2 1.0
C C:TRP16 4.2 26.1 1.0
CB C:VAL21 4.2 18.9 1.0
CE2 C:TYR161 4.2 24.6 1.0
CB C:ASN18 4.2 19.9 1.0
CA C:VAL21 4.2 19.6 1.0
N C:PRO19 4.3 21.3 1.0
CA C:ASP15 4.3 23.6 1.0
N C:GLU17 4.3 27.8 1.0
CZ C:TYR161 4.4 23.0 1.0
N C:VAL21 4.4 21.5 1.0
N C:THR22 4.5 26.1 1.0
CA C:PRO19 4.6 21.2 1.0
CB C:ASP193 4.6 14.6 1.0
CG1 C:VAL21 4.6 18.0 1.0
O C:TRP16 4.7 24.3 1.0
CA C:THR22 4.7 24.7 1.0
CG C:GLN163 4.8 27.1 1.0
CB C:ASP15 4.8 24.3 1.0
C C:GLU17 4.8 24.1 1.0

Magnesium binding site 5 out of 7 in 7btk

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1103

b:27.0
occ:1.00
 O C:HOH1206 1.9 8.9 1.0
O C:HOH1369 2.1 32.1 1.0
OE1 C:GLU416 2.1 30.6 1.0
OE2 C:GLU461 2.2 23.7 1.0
O06 C:F6L1101 2.4 56.2 1.0
CD C:GLU416 3.0 26.5 1.0
ND1 C:HIS418 3.0 25.4 1.0
C12 C:F6L1101 3.1 62.1 1.0
OE2 C:GLU416 3.2 20.4 1.0
O02 C:F6L1101 3.4 84.2 1.0
CD C:GLU461 3.5 22.4 1.0
N C:ASP201 3.6 25.0 1.0
CB C:ASP201 3.7 26.6 1.0
C11 C:F6L1101 3.7 74.3 1.0
CE1 C:HIS418 3.9 23.2 1.0
O C:ASP199 4.0 19.9 1.0
CG C:HIS418 4.0 26.1 1.0
ND2 C:ASN460 4.1 25.4 1.0
OD1 C:ASN102 4.1 30.8 1.0
CB C:HIS418 4.2 24.6 1.0
CA C:ASP201 4.2 26.5 1.0
OE1 C:GLU461 4.3 23.6 1.0
CG C:GLU416 4.3 26.1 1.0
C C:GLN200 4.4 25.4 1.0
CA C:GLN200 4.4 23.7 1.0
CG C:GLU461 4.5 18.1 1.0
C10 C:F6L1101 4.5 87.3 1.0
CB C:GLU461 4.6 15.7 1.0
O C:ASN102 4.8 28.9 1.0
O01 C:F6L1101 4.8 94.7 1.0
C C:ASP199 4.9 21.3 1.0
O03 C:F6L1101 5.0 79.0 1.0
C07 C:F6L1101 5.0 73.0 1.0

Magnesium binding site 6 out of 7 in 7btk

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1102

b:35.6
occ:1.00
 O06 D:F6L1101 1.9 69.3 1.0
O D:HOH1288 2.1 22.4 1.0
O D:HOH1236 2.2 24.9 1.0
OE1 D:GLU416 2.4 24.5 1.0
OE2 D:GLU461 2.6 27.2 1.0
CD D:GLU416 3.0 25.8 1.0
OE2 D:GLU416 3.0 16.8 1.0
N D:ASP201 3.1 24.1 1.0
C12 D:F6L1101 3.2 68.9 1.0
CB D:ASP201 3.3 20.0 1.0
O02 D:F6L1101 3.6 92.1 1.0
ND1 D:HIS418 3.6 25.6 1.0
CA D:ASP201 3.8 21.6 1.0
CD D:GLU461 3.9 26.3 1.0
C11 D:F6L1101 3.9 80.0 1.0
O D:ASP199 3.9 21.7 1.0
ND2 D:ASN460 4.0 27.6 1.0
C D:GLN200 4.0 27.7 1.0
CA D:GLN200 4.1 25.9 1.0
OD1 D:ASN102 4.2 34.4 1.0
CG D:GLU416 4.4 25.4 1.0
CE1 D:HIS418 4.5 25.6 1.0
O03 D:F6L1101 4.5 99.3 1.0
O D:HOH1231 4.6 30.9 1.0
CG D:HIS418 4.6 26.1 1.0
OE1 D:GLU461 4.6 23.6 1.0
CG D:ASP201 4.6 22.5 1.0
CB D:HIS418 4.7 24.9 1.0
CG D:GLU461 4.8 21.7 1.0
C D:ASP199 4.9 20.9 1.0
O D:ASN102 4.9 29.7 1.0
NE2 D:HIS391 4.9 20.2 1.0
C07 D:F6L1101 4.9 85.6 1.0
C10 D:F6L1101 4.9 97.7 1.0
N D:GLN200 5.0 25.2 1.0
CB D:GLU461 5.0 18.7 1.0
OD2 D:ASP201 5.0 20.6 1.0

Magnesium binding site 7 out of 7 in 7btk

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1103

b:32.4
occ:1.00
 O D:ASP15 2.1 24.9 1.0
OD2 D:ASP193 2.1 23.7 1.0
OE1 D:GLN163 2.4 30.3 1.0
O D:ASN18 2.4 21.1 1.0
O D:VAL21 2.5 17.0 1.0
CG D:ASP193 3.0 24.9 1.0
OD1 D:ASP193 3.2 28.6 1.0
C D:ASN18 3.2 21.3 1.0
C D:ASP15 3.3 24.0 1.0
CD D:GLN163 3.4 29.9 1.0
N D:ASN18 3.6 22.9 1.0
OH D:TYR161 3.6 26.8 1.0
C D:VAL21 3.6 17.8 1.0
NE2 D:GLN163 3.8 31.6 1.0
CA D:ASN18 3.9 21.4 1.0
CA D:TRP16 3.9 20.9 1.0
N D:TRP16 4.1 19.3 1.0
C D:TRP16 4.1 23.0 1.0
N D:PRO19 4.2 20.8 1.0
CB D:ASN18 4.3 19.4 1.0
N D:GLU17 4.3 23.4 1.0
CE2 D:TYR161 4.3 24.3 1.0
CB D:ASP193 4.4 19.2 1.0
CZ D:TYR161 4.4 24.9 1.0
CA D:VAL21 4.5 15.5 1.0
CA D:PRO19 4.5 19.6 1.0
CA D:ASP15 4.5 26.0 1.0
N D:VAL21 4.5 15.7 1.0
CB D:VAL21 4.6 14.7 1.0
O D:TRP16 4.6 20.3 1.0
N D:THR22 4.6 24.8 1.0
CG D:GLN163 4.7 28.2 1.0
C D:GLU17 4.8 21.0 1.0
CA D:THR22 4.8 27.0 1.0
CB D:ASP15 4.9 29.9 1.0
CG1 D:VAL21 4.9 15.5 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: Wed Oct 2 13:34:29 2024

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