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Magnesium 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:

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 KSA02 (pdb code 7brs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02, PDB code: 7brs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7brs

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Magnesium binding site 1 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:27.5
occ:1.00
 OE2 A:GLU461 2.0 66.7 1.0
O A:HOH1233 2.0 32.7 1.0
OE1 A:GLU416 2.0 56.3 1.0
O A:HOH1220 2.1 41.9 1.0
ND1 A:HIS418 2.1 49.8 1.0
O A:HOH1249 2.4 38.9 1.0
CE1 A:HIS418 3.0 46.6 1.0
CD A:GLU461 3.1 62.4 1.0
CG A:HIS418 3.2 42.0 1.0
CD A:GLU416 3.2 52.9 1.0
CB A:HIS418 3.5 41.4 1.0
OE1 A:GLU461 3.7 65.9 1.0
OD1 A:ASN102 3.8 59.5 1.0
OE2 A:GLU416 3.9 53.6 1.0
O A:ASP199 4.1 41.6 1.0
N A:ASP201 4.1 49.7 1.0
CB A:ASP201 4.2 51.0 1.0
NE2 A:HIS418 4.2 50.2 1.0
CB A:GLU461 4.2 40.2 1.0
CG A:GLU461 4.2 56.6 1.0
CD2 A:HIS418 4.3 42.4 1.0
O A:HOH1274 4.3 29.9 1.0
CG A:GLU416 4.3 49.3 1.0
O12 A:F4X1101 4.5 45.4 1.0
ND2 A:ASN460 4.5 40.7 1.0
CA A:ASP201 4.7 50.2 1.0
CG2 A:VAL103 4.8 45.2 1.0
C A:GLN200 4.8 50.3 1.0
C07 A:F4X1101 4.9 50.1 1.0
O A:ASN102 4.9 44.9 1.0
CA A:GLN200 4.9 46.5 1.0
CG A:ASN102 5.0 48.3 1.0

Magnesium binding site 2 out of 8 in 7brs

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Magnesium binding site 2 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:40.0
occ:1.00
 O A:ASP15 1.9 54.9 1.0
OD2 A:ASP193 2.2 50.2 1.0
O A:VAL21 2.3 40.7 1.0
OE1 A:GLN163 2.4 42.9 1.0
O A:ASN18 2.4 36.7 1.0
CG A:ASP193 3.1 47.7 1.0
C A:ASP15 3.1 47.1 1.0
C A:ASN18 3.3 41.0 1.0
OD1 A:ASP193 3.3 50.2 1.0
CD A:GLN163 3.4 43.6 1.0
C A:VAL21 3.5 37.4 1.0
N A:ASN18 3.6 37.8 1.0
CA A:TRP16 3.8 38.4 1.0
OH A:TYR161 3.8 50.5 1.0
NE2 A:GLN163 3.9 50.9 1.0
N A:TRP16 3.9 41.8 1.0
CA A:ASN18 3.9 37.5 1.0
C A:TRP16 4.1 38.6 1.0
CB A:ASN18 4.2 37.5 1.0
CE2 A:TYR161 4.2 43.3 1.0
CA A:ASP15 4.2 42.1 1.0
N A:PRO19 4.2 36.9 1.0
CA A:VAL21 4.3 38.9 1.0
CB A:VAL21 4.3 36.6 1.0
N A:GLU17 4.3 38.6 1.0
N A:VAL21 4.4 36.1 1.0
CZ A:TYR161 4.4 46.0 1.0
N A:THR22 4.5 36.0 1.0
CA A:PRO19 4.5 46.3 1.0
CB A:ASP193 4.5 42.6 1.0
O A:TRP16 4.6 38.7 1.0
CG A:GLN163 4.6 37.4 1.0
CA A:THR22 4.7 36.2 1.0
CB A:ASP15 4.7 40.7 1.0
C A:GLU17 4.8 38.4 1.0
CG1 A:VAL21 4.8 36.7 1.0

Magnesium binding site 3 out of 8 in 7brs

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Magnesium binding site 3 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:23.8
occ:1.00
 OE2 B:GLU461 1.9 63.0 1.0
O B:HOH1234 2.0 31.8 1.0
OE1 B:GLU416 2.0 56.0 1.0
ND1 B:HIS418 2.0 41.6 1.0
O B:HOH1233 2.2 36.2 1.0
O B:HOH1259 2.2 28.0 1.0
CE1 B:HIS418 2.9 46.4 1.0
CD B:GLU461 3.0 58.4 1.0
CG B:HIS418 3.1 46.0 1.0
CD B:GLU416 3.2 46.2 1.0
CB B:HIS418 3.5 40.9 1.0
OE1 B:GLU461 3.7 61.1 1.0
OE2 B:GLU416 3.9 39.0 1.0
OD1 B:ASN102 3.9 53.0 1.0
CG B:GLU461 4.0 46.8 1.0
NE2 B:HIS418 4.1 48.1 1.0
CB B:GLU461 4.1 39.2 1.0
O B:ASP199 4.1 39.9 1.0
CD2 B:HIS418 4.2 49.4 1.0
N B:ASP201 4.2 49.7 1.0
CB B:ASP201 4.2 55.8 1.0
CG B:GLU416 4.3 42.8 1.0
O B:HOH1245 4.4 39.4 1.0
ND2 B:ASN460 4.5 39.4 1.0
O12 B:F4X1101 4.7 55.1 1.0
CA B:ASP201 4.8 48.0 1.0
O B:ASN102 4.8 52.1 1.0
C07 B:F4X1101 4.9 53.9 1.0
CG2 B:VAL103 4.9 44.5 1.0
CA B:HIS418 4.9 39.7 1.0
C B:GLN200 5.0 47.4 1.0

Magnesium binding site 4 out of 8 in 7brs

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Magnesium binding site 4 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:33.9
occ:1.00
 O B:VAL21 2.1 57.9 1.0
O B:ASP15 2.1 56.9 1.0
OD2 B:ASP193 2.2 50.7 1.0
NE2 B:GLN163 2.4 34.7 1.0
O B:ASN18 2.5 36.3 1.0
CG B:ASP193 3.1 55.4 1.0
CD B:GLN163 3.2 48.3 1.0
OD1 B:ASP193 3.3 61.9 1.0
C B:VAL21 3.3 48.0 1.0
C B:ASP15 3.3 49.7 1.0
C B:ASN18 3.4 39.4 1.0
OE1 B:GLN163 3.5 55.2 1.0
OH B:TYR161 3.7 36.0 1.0
N B:ASN18 3.9 35.2 1.0
CA B:TRP16 4.0 35.4 1.0
N B:TRP16 4.1 39.7 1.0
CE2 B:TYR161 4.1 34.7 1.0
CA B:ASN18 4.1 35.0 1.0
CA B:VAL21 4.1 46.6 1.0
CB B:VAL21 4.2 44.6 1.0
C B:TRP16 4.2 35.9 1.0
N B:THR22 4.2 33.8 1.0
N B:PRO19 4.3 45.5 1.0
N B:VAL21 4.3 40.7 1.0
CZ B:TYR161 4.3 35.4 1.0
CA B:THR22 4.4 33.9 1.0
CA B:ASP15 4.4 41.6 1.0
CG B:GLN163 4.4 34.7 1.0
CB B:ASN18 4.5 35.0 1.0
CA B:PRO19 4.5 34.3 1.0
CB B:ASP193 4.5 35.2 1.0
CG1 B:VAL21 4.5 42.5 1.0
N B:GLU17 4.5 35.6 1.0
O B:TRP16 4.7 35.8 1.0
CB B:ASP15 4.8 45.2 1.0
C B:PRO19 5.0 40.5 1.0

Magnesium binding site 5 out of 8 in 7brs

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Magnesium binding site 5 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:40.6
occ:1.00
 OE2 C:GLU461 1.9 63.0 1.0
OE1 C:GLU416 1.9 64.5 1.0
O C:HOH1241 2.1 40.4 1.0
O C:HOH1225 2.1 44.3 1.0
O C:HOH1253 2.2 53.2 1.0
ND1 C:HIS418 2.5 50.8 1.0
CD C:GLU416 3.0 61.6 1.0
CD C:GLU461 3.1 57.0 1.0
CE1 C:HIS418 3.4 42.4 1.0
CG C:HIS418 3.5 43.6 1.0
OE2 C:GLU416 3.6 63.1 1.0
CB C:HIS418 3.8 42.6 1.0
OE1 C:GLU461 3.8 61.6 1.0
N C:ASP201 3.9 46.5 1.0
CB C:ASP201 3.9 44.8 1.0
OD1 C:ASN102 4.0 55.9 1.0
CG C:GLU461 4.1 51.3 1.0
O C:ASP199 4.1 40.9 1.0
CB C:GLU461 4.2 39.2 1.0
CG C:GLU416 4.3 53.2 1.0
ND2 C:ASN460 4.3 41.7 1.0
CA C:ASP201 4.5 46.0 1.0
O12 C:F4X1101 4.5 56.9 1.0
NE2 C:HIS418 4.6 44.5 1.0
CD2 C:HIS418 4.7 47.6 1.0
O C:ASN102 4.7 56.1 1.0
C C:GLN200 4.8 46.8 1.0
CA C:GLN200 4.8 43.8 1.0
C07 C:F4X1101 4.9 50.8 1.0

Magnesium binding site 6 out of 8 in 7brs

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Magnesium binding site 6 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:42.3
occ:1.00
 O C:ASP15 1.9 60.3 1.0
OD2 C:ASP193 2.2 51.5 1.0
O C:ASN18 2.2 41.8 1.0
O C:VAL21 2.4 35.5 1.0
OE1 C:GLN163 2.5 47.9 1.0
CG C:ASP193 3.1 50.9 1.0
C C:ASP15 3.1 51.9 1.0
C C:ASN18 3.2 42.9 1.0
OD1 C:ASP193 3.4 56.0 1.0
N C:ASN18 3.5 37.1 1.0
C C:VAL21 3.6 35.3 1.0
CD C:GLN163 3.6 39.3 1.0
CA C:TRP16 3.8 37.7 1.0
CA C:ASN18 3.8 36.7 1.0
OH C:TYR161 3.8 37.0 1.0
N C:TRP16 3.9 41.8 1.0
C C:TRP16 4.0 40.8 1.0
CB C:ASN18 4.1 36.8 1.0
NE2 C:GLN163 4.1 38.5 1.0
CA C:ASP15 4.2 46.0 1.0
N C:GLU17 4.2 42.9 1.0
N C:PRO19 4.3 53.4 1.0
CB C:VAL21 4.3 39.2 1.0
CA C:VAL21 4.3 39.0 1.0
CE2 C:TYR161 4.3 36.6 1.0
N C:VAL21 4.4 43.8 1.0
CB C:ASP193 4.5 40.3 1.0
CZ C:TYR161 4.5 37.0 1.0
CA C:PRO19 4.5 37.9 1.0
O C:TRP16 4.6 38.0 1.0
N C:THR22 4.6 35.0 1.0
C C:GLU17 4.7 45.2 1.0
CB C:ASP15 4.7 43.8 1.0
CG1 C:VAL21 4.8 36.7 1.0
CA C:THR22 4.8 35.0 1.0
CG C:GLN163 4.8 44.9 1.0
CG C:ASN18 4.9 44.5 1.0
CA C:GLU17 5.0 38.1 1.0

Magnesium binding site 7 out of 8 in 7brs

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Magnesium binding site 7 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


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 KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1102

b:41.5
occ:1.00
 OE2 D:GLU461 1.8 71.1 1.0
O D:HOH1255 2.1 39.1 1.0
OE1 D:GLU416 2.1 51.5 1.0
O D:HOH1209 2.1 38.3 1.0
O D:HOH1221 2.2 40.3 1.0
ND1 D:HIS418 2.2 48.8 1.0
CD D:GLU461 3.0 68.6 1.0
CE1 D:HIS418 3.1 48.4 1.0
CD D:GLU416 3.2 49.1 1.0
CG D:HIS418 3.3 48.4 1.0
OE1 D:GLU461 3.6 69.5 1.0
CB D:HIS418 3.7 44.3 1.0
OE2 D:GLU416 3.8 52.7 1.0
OD1 D:ASN102 3.9 61.6 1.0
CG D:GLU461 4.0 51.5 1.0
CB D:GLU461 4.0 40.2 1.0
CB D:ASP201 4.1 40.7 1.0
N D:ASP201 4.2 51.7 1.0
O D:HOH1223 4.2 43.0 1.0
O D:ASP199 4.3 37.0 1.0
NE2 D:HIS418 4.3 48.2 1.0
CD2 D:HIS418 4.4 50.8 1.0
CG D:GLU416 4.4 43.2 1.0
ND2 D:ASN460 4.4 39.2 1.0
O12 D:F4X1101 4.5 58.5 1.0
CA D:ASP201 4.7 42.0 1.0
C07 D:F4X1101 4.7 44.2 1.0
O D:ASN102 4.9 56.0 1.0
CG2 D:VAL103 4.9 40.8 1.0

Magnesium binding site 8 out of 8 in 7brs

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Magnesium binding site 8 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSA02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1103

b:43.6
occ:1.00
 O D:ASP15 2.0 49.0 1.0
OD2 D:ASP193 2.1 47.2 1.0
OE1 D:GLN163 2.1 53.9 1.0
O D:VAL21 2.4 37.5 1.0
O D:ASN18 2.6 43.5 1.0
CG D:ASP193 3.1 45.3 1.0
C D:ASP15 3.2 48.7 1.0
CD D:GLN163 3.2 42.1 1.0
OD1 D:ASP193 3.3 53.8 1.0
C D:ASN18 3.5 50.4 1.0
OH D:TYR161 3.5 35.4 1.0
CA D:TRP16 3.6 35.7 1.0
C D:VAL21 3.7 33.5 1.0
N D:ASN18 3.7 34.6 1.0
NE2 D:GLN163 3.7 34.8 1.0
N D:TRP16 3.8 40.4 1.0
C D:TRP16 3.9 35.6 1.0
CA D:ASN18 4.1 34.3 1.0
CE2 D:TYR161 4.2 35.3 1.0
N D:GLU17 4.2 35.6 1.0
CZ D:TYR161 4.3 35.6 1.0
CA D:ASP15 4.3 45.4 1.0
N D:PRO19 4.4 48.0 1.0
CB D:ASP193 4.5 34.8 1.0
CG D:GLN163 4.5 40.6 1.0
CA D:VAL21 4.5 33.6 1.0
CB D:VAL21 4.5 34.3 1.0
O D:TRP16 4.5 39.6 1.0
CB D:ASN18 4.5 35.5 1.0
N D:THR22 4.6 34.6 1.0
CA D:PRO19 4.6 36.1 1.0
N D:VAL21 4.6 33.2 1.0
CA D:THR22 4.7 40.6 1.0
CB D:ASP15 4.8 44.3 1.0
C D:GLU17 4.8 42.7 1.0
CG1 D:VAL21 5.0 34.7 1.0
CB D:TRP16 5.0 38.2 1.0
CA D:GLU17 5.0 35.6 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: Wed Oct 2 13:34:36 2024

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