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Magnesium in PDB 6kuz: E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01

Enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01

All present enzymatic activity of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01:
3.2.1.23;

Protein crystallography data

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01, PDB code: 6kuz was solved by X.Chen, Y.L.Hu, X.K.Li, Y.Guo, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.50 / 2.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 248.174, 85.506, 243.052, 90.00, 94.09, 90.00
R / Rfree (%) 18.2 / 22.4

Other elements in 6kuz:

The structure of E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 also contains other interesting chemical elements:

Sodium (Na) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01 (pdb code 6kuz). 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 KSL01, PDB code: 6kuz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6kuz

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Magnesium binding site 1 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1118

b:36.7
occ:1.00
 O A:HOH1232 1.8 22.7 1.0
OE1 A:GLU416 2.0 29.1 1.0
OE2 A:GLU461 2.0 33.6 1.0
O A:HOH1203 2.0 28.1 1.0
ND1 A:HIS418 2.3 33.8 1.0
O A:HOH1240 2.4 31.2 1.0
CD A:GLU461 3.1 36.0 1.0
CD A:GLU416 3.1 29.6 1.0
CE1 A:HIS418 3.2 31.8 1.0
CG A:HIS418 3.3 32.9 1.0
CB A:HIS418 3.6 34.6 1.0
O30 A:DVL1101 3.7 78.7 1.0
OE2 A:GLU416 3.7 29.9 1.0
O36 A:DVL1101 3.8 56.2 1.0
OE1 A:GLU461 3.8 38.4 1.0
CB A:GLU461 4.1 31.1 1.0
CG A:GLU461 4.1 33.5 1.0
O A:ASP199 4.2 30.0 1.0
C32 A:DVL1101 4.2 61.4 1.0
N A:ASP201 4.2 33.5 1.0
OD1 A:ASN102 4.2 35.7 1.0
ND2 A:ASN460 4.2 22.6 1.0
CG A:GLU416 4.3 28.2 1.0
NE2 A:HIS418 4.3 31.8 1.0
CB A:ASP201 4.4 35.4 1.0
CD2 A:HIS418 4.4 30.8 1.0
C31 A:DVL1101 4.5 68.5 1.0
O16 A:DVL1101 4.7 91.0 1.0
C29 A:DVL1101 4.7 89.5 1.0
CA A:ASP201 4.8 33.5 1.0
C24 A:DVL1101 4.8 77.2 1.0
O A:ASN102 4.9 32.8 1.0
CG2 A:VAL103 4.9 27.0 1.0
C A:GLN200 4.9 31.9 1.0
CA A:GLN200 4.9 33.0 1.0

Magnesium binding site 2 out of 8 in 6kuz

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Magnesium binding site 2 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1119

b:32.0
occ:1.00
 O A:ASP15 2.0 33.5 1.0
OD2 A:ASP193 2.3 28.8 1.0
O A:VAL21 2.3 43.7 1.0
NE2 A:GLN163 2.5 32.0 1.0
O A:ASN18 2.6 34.4 1.0
CG A:ASP193 3.1 31.5 1.0
C A:ASP15 3.2 31.7 1.0
OD1 A:ASP193 3.3 35.6 1.0
CD A:GLN163 3.4 34.2 1.0
C A:ASN18 3.4 34.3 1.0
C A:VAL21 3.5 39.9 1.0
OE1 A:GLN163 3.7 44.0 1.0
N A:ASN18 3.8 34.1 1.0
OH A:TYR161 3.8 30.5 1.0
CA A:TRP16 3.8 27.3 1.0
N A:TRP16 3.9 28.4 1.0
CA A:ASN18 4.0 32.7 1.0
C A:TRP16 4.1 27.4 1.0
CE2 A:TYR161 4.1 29.3 1.0
CA A:ASP15 4.3 33.1 1.0
CA A:VAL21 4.3 39.2 1.0
CB A:ASN18 4.3 32.0 1.0
CB A:VAL21 4.3 35.9 1.0
N A:PRO19 4.4 36.1 1.0
N A:GLU17 4.4 31.9 1.0
CZ A:TYR161 4.4 29.1 1.0
N A:VAL21 4.5 39.5 1.0
N A:THR22 4.5 37.5 1.0
CB A:ASP193 4.5 30.0 1.0
CA A:PRO19 4.6 37.6 1.0
CG A:GLN163 4.6 33.6 1.0
O A:TRP16 4.6 23.5 1.0
CA A:THR22 4.7 36.1 1.0
CG1 A:VAL21 4.7 32.9 1.0
CB A:ASP15 4.8 31.4 1.0
C A:GLU17 4.9 34.4 1.0

Magnesium binding site 3 out of 8 in 6kuz

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Magnesium binding site 3 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1113

b:37.6
occ:1.00
 OE1 B:GLU416 1.9 33.8 1.0
O B:HOH1235 2.0 25.2 1.0
OE2 B:GLU461 2.1 42.8 1.0
O B:HOH1209 2.1 41.3 1.0
ND1 B:HIS418 2.6 37.2 1.0
O36 B:DVL1101 2.9 71.0 1.0
CD B:GLU416 3.0 36.0 1.0
CD B:GLU461 3.3 37.8 1.0
CE1 B:HIS418 3.5 34.4 1.0
OE2 B:GLU416 3.5 36.2 1.0
CG B:HIS418 3.6 37.9 1.0
N B:ASP201 3.8 40.5 1.0
O30 B:DVL1101 3.8 82.9 1.0
CB B:HIS418 3.8 37.3 1.0
CB B:ASP201 3.9 40.5 1.0
O B:ASP199 4.0 33.3 1.0
C32 B:DVL1101 4.0 82.0 1.0
ND2 B:ASN460 4.1 33.1 1.0
OE1 B:GLU461 4.1 40.1 1.0
CG B:GLU416 4.2 36.4 1.0
CB B:GLU461 4.3 33.3 1.0
OD1 B:ASN102 4.3 37.2 1.0
CG B:GLU461 4.3 35.9 1.0
O33 B:DVL1101 4.4 76.7 1.0
CA B:ASP201 4.4 40.9 1.0
C31 B:DVL1101 4.5 77.8 1.0
O B:ASN102 4.6 36.8 1.0
NE2 B:HIS418 4.6 35.8 1.0
C B:GLN200 4.6 34.5 1.0
CA B:GLN200 4.7 33.3 1.0
CD2 B:HIS418 4.7 37.1 1.0

Magnesium binding site 4 out of 8 in 6kuz

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Magnesium binding site 4 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1114

b:40.9
occ:1.00
 O B:ASP15 1.9 33.0 1.0
O B:VAL21 2.2 31.1 1.0
O B:ASN18 2.3 33.9 1.0
OD2 B:ASP193 2.4 36.2 1.0
OE1 B:GLN163 2.6 31.6 1.0
C B:ASP15 3.2 35.7 1.0
C B:ASN18 3.3 32.9 1.0
C B:VAL21 3.3 29.7 1.0
CG B:ASP193 3.3 39.0 1.0
OD1 B:ASP193 3.6 45.1 1.0
N B:ASN18 3.7 35.6 1.0
CD B:GLN163 3.7 31.1 1.0
OH B:TYR161 3.8 31.2 1.0
CA B:ASN18 3.9 34.4 1.0
CA B:TRP16 3.9 30.6 1.0
N B:TRP16 4.0 33.5 1.0
CA B:VAL21 4.0 30.4 1.0
CB B:VAL21 4.1 30.1 1.0
CB B:ASN18 4.1 35.0 1.0
C B:TRP16 4.2 31.8 1.0
N B:VAL21 4.2 31.3 1.0
CA B:ASP15 4.2 36.5 1.0
NE2 B:GLN163 4.2 31.9 1.0
CE2 B:TYR161 4.2 29.8 1.0
N B:PRO19 4.3 30.4 1.0
N B:THR22 4.3 31.9 1.0
N B:GLU17 4.4 31.7 1.0
CZ B:TYR161 4.4 30.4 1.0
CG1 B:VAL21 4.5 28.5 1.0
CA B:THR22 4.5 34.6 1.0
CA B:PRO19 4.5 29.7 1.0
CB B:ASP15 4.6 37.8 1.0
CB B:ASP193 4.7 35.8 1.0
O B:TRP16 4.7 32.9 1.0
CG B:ASN18 4.8 34.5 1.0
C B:GLU17 4.8 35.9 1.0
CG B:GLN163 4.9 31.3 1.0

Magnesium binding site 5 out of 8 in 6kuz

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Magnesium binding site 5 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1110

b:40.9
occ:1.00
 OE1 C:GLU416 2.0 38.0 1.0
O C:HOH1237 2.0 39.1 1.0
O C:HOH1214 2.1 31.7 1.0
O36 C:DVL1101 2.3 76.2 1.0
OE2 C:GLU461 2.5 42.5 1.0
ND1 C:HIS418 2.9 34.4 1.0
CD C:GLU416 3.0 35.6 1.0
OE2 C:GLU416 3.4 32.6 1.0
C32 C:DVL1101 3.6 81.4 1.0
O30 C:DVL1101 3.6 82.1 1.0
N C:ASP201 3.6 37.7 1.0
CD C:GLU461 3.7 42.5 1.0
CE1 C:HIS418 3.7 32.7 1.0
CB C:ASP201 3.8 40.4 1.0
CG C:HIS418 3.9 36.4 1.0
O C:ASP199 3.9 30.4 1.0
CB C:HIS418 4.1 36.2 1.0
ND2 C:ASN460 4.1 35.1 1.0
C31 C:DVL1101 4.1 79.0 1.0
O33 C:DVL1101 4.2 87.4 1.0
OD1 C:ASN102 4.2 38.7 1.0
CG C:GLU416 4.2 35.7 1.0
CA C:ASP201 4.3 38.9 1.0
C C:GLN200 4.4 36.4 1.0
CA C:GLN200 4.4 34.0 1.0
OE1 C:GLU461 4.4 49.2 1.0
O C:ASN102 4.5 35.4 1.0
CB C:GLU461 4.6 37.5 1.0
CG C:GLU461 4.6 39.1 1.0
C26 C:DVL1101 4.9 79.4 1.0
C29 C:DVL1101 4.9 89.0 1.0
C C:ASP199 4.9 30.7 1.0
NE2 C:HIS418 4.9 34.6 1.0
CD2 C:HIS418 5.0 35.7 1.0

Magnesium binding site 6 out of 8 in 6kuz

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Magnesium binding site 6 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1111

b:42.4
occ:1.00
 O C:ASP15 2.0 40.8 1.0
OE1 C:GLN163 2.1 36.0 1.0
OD2 C:ASP193 2.2 32.7 1.0
O C:VAL21 2.3 31.2 1.0
O C:ASN18 2.7 40.7 1.0
C C:ASP15 3.2 40.4 1.0
CG C:ASP193 3.2 35.5 1.0
CD C:GLN163 3.3 34.1 1.0
OH C:TYR161 3.4 35.2 1.0
OD1 C:ASP193 3.5 36.2 1.0
C C:VAL21 3.6 30.7 1.0
C C:ASN18 3.6 36.6 1.0
CA C:TRP16 3.7 34.0 1.0
N C:TRP16 3.9 36.4 1.0
N C:ASN18 3.9 37.1 1.0
NE2 C:GLN163 3.9 35.0 1.0
CE2 C:TYR161 4.0 36.2 1.0
C C:TRP16 4.1 33.5 1.0
CZ C:TYR161 4.2 38.3 1.0
CA C:ASN18 4.2 35.3 1.0
CA C:ASP15 4.3 39.4 1.0
N C:GLU17 4.4 35.5 1.0
CA C:VAL21 4.4 31.5 1.0
CB C:VAL21 4.4 29.5 1.0
CG C:GLN163 4.5 33.4 1.0
N C:THR22 4.5 33.3 1.0
N C:PRO19 4.5 35.6 1.0
CB C:ASN18 4.5 33.1 1.0
CB C:ASP193 4.5 35.5 1.0
O C:TRP16 4.6 30.8 1.0
N C:VAL21 4.6 32.7 1.0
CA C:THR22 4.6 36.0 1.0
CB C:ASP15 4.7 38.7 1.0
CA C:PRO19 4.7 38.4 1.0
CG1 C:VAL21 4.8 27.4 1.0
C C:GLU17 5.0 37.6 1.0

Magnesium binding site 7 out of 8 in 6kuz

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Magnesium binding site 7 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1115

b:43.4
occ:1.00
 O D:HOH1221 1.7 19.7 1.0
OE2 D:GLU461 1.9 38.7 1.0
O D:HOH1202 1.9 29.7 1.0
OE1 D:GLU416 1.9 33.0 1.0
O D:HOH1259 2.0 26.1 1.0
ND1 D:HIS418 2.3 33.9 1.0
CD D:GLU461 3.0 38.7 1.0
CD D:GLU416 3.1 31.0 1.0
CE1 D:HIS418 3.2 31.7 1.0
CG D:HIS418 3.3 33.0 1.0
O36 D:DVL1101 3.6 90.7 1.0
CB D:HIS418 3.7 33.2 1.0
OE2 D:GLU416 3.7 33.8 1.0
O30 D:DVL1101 3.7 91.1 1.0
OE1 D:GLU461 3.8 42.4 1.0
CB D:GLU461 4.0 32.6 1.0
CG D:GLU461 4.0 35.4 1.0
C32 D:DVL1101 4.1 85.4 1.0
N D:ASP201 4.2 35.1 1.0
O D:ASP199 4.2 25.9 1.0
ND2 D:ASN460 4.3 26.9 1.0
CG D:GLU416 4.3 28.7 1.0
OD1 D:ASN102 4.3 35.0 1.0
NE2 D:HIS418 4.3 32.7 1.0
CB D:ASP201 4.4 36.5 1.0
CD2 D:HIS418 4.4 31.9 1.0
C31 D:DVL1101 4.5 85.6 1.0
O16 D:DVL1101 4.7 99.1 1.0
C29 D:DVL1101 4.8 98.3 1.0
C24 D:DVL1101 4.8 82.4 1.0
CA D:ASP201 4.9 35.0 1.0
O D:ASN102 4.9 31.4 1.0
C D:GLN200 4.9 34.9 1.0
CA D:GLN200 4.9 34.0 1.0
CG2 D:VAL103 4.9 30.3 1.0

Magnesium binding site 8 out of 8 in 6kuz

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Magnesium binding site 8 out of 8 in the E.Coli Beta-Galactosidase (E537Q) in Complex with Fluorescent Probe KSL01


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 KSL01 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1116

b:42.3
occ:1.00
 O D:ASP15 2.0 35.3 1.0
O D:VAL21 2.2 37.2 1.0
OE1 D:GLN163 2.3 33.2 1.0
OD2 D:ASP193 2.4 35.6 1.0
O D:ASN18 2.6 36.1 1.0
CG D:ASP193 3.2 35.8 1.0
C D:ASP15 3.2 33.9 1.0
OD1 D:ASP193 3.2 41.2 1.0
C D:VAL21 3.4 35.1 1.0
CD D:GLN163 3.4 35.4 1.0
C D:ASN18 3.4 34.7 1.0
N D:ASN18 3.8 33.4 1.0
OH D:TYR161 3.8 30.8 1.0
CA D:TRP16 3.9 30.6 1.0
NE2 D:GLN163 4.0 42.1 1.0
N D:TRP16 4.0 31.2 1.0
CA D:ASN18 4.1 33.5 1.0
CE2 D:TYR161 4.1 29.4 1.0
CB D:VAL21 4.2 33.2 1.0
CA D:VAL21 4.2 35.2 1.0
C D:TRP16 4.2 29.7 1.0
CA D:ASP15 4.3 34.6 1.0
N D:VAL21 4.4 37.2 1.0
CB D:ASN18 4.4 33.3 1.0
N D:PRO19 4.4 36.5 1.0
N D:THR22 4.4 32.7 1.0
CZ D:TYR161 4.4 28.7 1.0
CG1 D:VAL21 4.5 31.7 1.0
N D:GLU17 4.5 31.4 1.0
CA D:THR22 4.6 31.9 1.0
CG D:GLN163 4.6 32.7 1.0
CA D:PRO19 4.6 36.9 1.0
CB D:ASP193 4.6 32.5 1.0
O D:TRP16 4.6 29.6 1.0
CB D:ASP15 4.7 35.4 1.0
C D:GLU17 4.9 33.0 1.0

Reference:

X.K.Li, W.J.Qiu, J.W.Li, X.Chen, Y.L.Hu, Y.Gao, D.L.Shi, X.M.Li, H.T.Lin, Z.Hu, G.Q.Dong, C.Q.Sheng, B.Jiang, C.L.Xia, C.Y.Kim, Y.Guo, J.Li. First-Generation Species-Selective Chemical Probes For Fluorescence Imaging of Human Senescence-Associated Beta-Galactosidase Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC01234C
Page generated: Tue Oct 1 09:55:47 2024

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