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Magnesium in PDB 1dp0: E. Coli Beta-Galactosidase at 1.7 Angstrom

Enzymatic activity of E. Coli Beta-Galactosidase at 1.7 Angstrom

All present enzymatic activity of E. Coli Beta-Galactosidase at 1.7 Angstrom:
3.2.1.23;

Protein crystallography data

The structure of E. Coli Beta-Galactosidase at 1.7 Angstrom, PDB code: 1dp0 was solved by D.H.Juers, R.H.Jacobson, D.Wigley, X.J.Zhang, R.E.Huber, D.E.Tronrud, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.600, 168.380, 200.690, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 21.1

Other elements in 1dp0:

The structure of E. Coli Beta-Galactosidase at 1.7 Angstrom also contains other interesting chemical elements:

Sodium (Na) 20 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the E. Coli Beta-Galactosidase at 1.7 Angstrom (pdb code 1dp0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the E. Coli Beta-Galactosidase at 1.7 Angstrom, PDB code: 1dp0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 1dp0

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Magnesium binding site 1 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:16.1
occ:1.00
 OE2 A:GLU416 2.1 11.7 1.0
O A:HOH8756 2.1 10.8 1.0
O A:HOH8616 2.1 10.9 1.0
O A:HOH8680 2.2 11.5 1.0
ND1 A:HIS418 2.2 11.4 1.0
OE1 A:GLU461 2.2 13.9 1.0
CE1 A:HIS418 3.1 12.3 1.0
CD A:GLU416 3.2 15.4 1.0
CD A:GLU461 3.3 19.5 1.0
CG A:HIS418 3.3 15.0 1.0
OE1 A:GLU416 3.6 11.8 1.0
CB A:HIS418 3.7 13.0 1.0
CB A:GLU461 4.0 10.0 1.0
OE2 A:GLU461 4.1 13.7 1.0
O A:HOH9160 4.1 43.6 1.0
CB A:ASP201 4.1 12.1 1.0
O A:HOH8603 4.1 16.4 1.0
OD1 A:ASN102 4.2 16.2 1.0
CG A:GLU461 4.2 9.5 1.0
N A:ASP201 4.2 10.8 1.0
NE2 A:HIS418 4.3 11.3 1.0
O A:ASP199 4.3 15.8 1.0
ND2 A:ASN460 4.3 13.9 1.0
CD2 A:HIS418 4.4 12.0 1.0
CG A:GLU416 4.4 8.0 1.0
O A:ASN102 4.6 13.8 1.0
O A:HOH8895 4.7 22.8 1.0
CA A:ASP201 4.8 11.0 1.0
CA A:GLN200 4.8 7.8 1.0
C A:GLN200 4.9 12.7 1.0
CG2 A:VAL103 4.9 14.1 1.0

Magnesium binding site 2 out of 16 in 1dp0

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Magnesium binding site 2 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:15.3
occ:1.00
 O A:ASP15 2.2 14.8 1.0
OE1 A:GLN163 2.3 13.8 1.0
OD2 A:ASP193 2.3 14.7 1.0
O A:ASN18 2.4 15.7 1.0
O A:VAL21 2.4 15.5 1.0
OD1 A:ASP193 3.0 15.4 1.0
CG A:ASP193 3.0 19.2 1.0
CD A:GLN163 3.2 15.2 1.0
C A:ASN18 3.2 18.4 1.0
C A:ASP15 3.4 15.9 1.0
NE2 A:GLN163 3.4 13.3 1.0
C A:VAL21 3.6 13.9 1.0
N A:ASN18 3.6 18.5 1.0
CA A:ASN18 3.9 18.4 1.0
CA A:TRP16 3.9 11.8 1.0
OH A:TYR161 4.0 13.2 1.0
N A:PRO19 4.1 19.0 1.0
N A:TRP16 4.1 11.4 1.0
CB A:ASN18 4.2 14.5 1.0
C A:TRP16 4.2 14.6 1.0
N A:VAL21 4.3 13.2 1.0
CA A:VAL21 4.3 11.2 1.0
CE2 A:TYR161 4.4 11.6 1.0
CA A:PRO19 4.4 14.3 1.0
CB A:VAL21 4.4 11.7 1.0
N A:GLU17 4.4 13.8 1.0
CB A:ASP193 4.4 13.9 1.0
CG A:GLN163 4.5 16.7 1.0
N A:THR22 4.5 11.3 1.0
CA A:ASP15 4.6 15.4 1.0
CA A:THR22 4.6 12.3 1.0
CZ A:TYR161 4.7 14.2 1.0
O A:TRP16 4.8 15.0 1.0
C A:GLU17 4.8 22.4 1.0
CG1 A:VAL21 4.9 18.3 1.0
C A:PRO19 4.9 15.5 1.0
CB A:ASP15 5.0 16.5 1.0

Magnesium binding site 3 out of 16 in 1dp0

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Magnesium binding site 3 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:45.2
occ:1.00
 O A:HOH8865 2.1 21.6 1.0
O A:HOH9044 2.2 39.0 1.0
OE1 A:GLN718 2.4 28.7 1.0
O A:HOH9307 2.4 31.5 1.0
O A:HOH8980 2.5 35.1 1.0
O A:HOH9237 2.6 31.1 1.0
CD A:GLN718 3.4 28.6 1.0
NE2 A:GLN718 3.7 23.2 1.0
C1 A:DMS8427 3.9 42.4 1.0
O A:HOH9495 3.9 25.9 1.0
O A:THR911 4.0 13.6 1.0
NE2 A:HIS622 4.1 15.1 1.0
O A:HOH8881 4.2 33.2 1.0
O A:HOH9027 4.3 33.8 1.0
O A:GLN719 4.5 13.8 1.0
O A:HOH8855 4.6 20.4 1.0
O A:HOH8682 4.6 16.1 1.0
N A:GLN719 4.7 10.3 1.0
CE1 A:HIS622 4.7 13.6 1.0
CG A:GLN718 4.8 14.2 1.0
C2 A:DMS8427 5.0 92.9 1.0
C A:THR911 5.0 12.5 1.0
O A:HOH8841 5.0 40.3 1.0

Magnesium binding site 4 out of 16 in 1dp0

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Magnesium binding site 4 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:30.2
occ:1.00
 O A:HOH9482 1.8 23.7 1.0
O A:HOH9483 2.0 35.0 1.0
O A:HOH9582 2.1 26.2 1.0
O A:HOH9262 2.1 23.9 1.0
C2 A:DMS8406 3.3 43.0 1.0
O A:HOH9473 3.8 39.9 1.0
O A:DMS8406 3.9 76.8 1.0
OE1 A:GLU314 4.1 14.5 1.0
OE2 A:GLU314 4.2 17.0 1.0
S A:DMS8406 4.2 66.8 1.0
O A:HOH9321 4.3 21.8 1.0
O A:HOH9635 4.3 19.1 1.0
CD A:GLU314 4.6 19.1 1.0

Magnesium binding site 5 out of 16 in 1dp0

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Magnesium binding site 5 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:12.1
occ:1.00
 O B:HOH8698 2.0 10.9 1.0
OE2 B:GLU416 2.0 11.8 1.0
OE1 B:GLU461 2.1 11.8 1.0
O B:HOH8774 2.1 9.9 1.0
O B:HOH8634 2.1 10.3 1.0
ND1 B:HIS418 2.2 11.8 1.0
CD B:GLU461 3.0 16.9 1.0
CE1 B:HIS418 3.1 10.7 1.0
CD B:GLU416 3.2 13.4 1.0
CG B:HIS418 3.3 12.3 1.0
OE1 B:GLU416 3.6 12.3 1.0
CB B:HIS418 3.7 10.9 1.0
OE2 B:GLU461 3.9 14.8 1.0
CB B:GLU461 4.0 11.6 1.0
O B:HOH8621 4.1 15.2 1.0
CG B:GLU461 4.1 12.5 1.0
CB B:ASP201 4.2 11.4 1.0
O B:HOH9176 4.2 33.6 1.0
N B:ASP201 4.2 10.0 1.0
OD1 B:ASN102 4.2 14.2 1.0
NE2 B:HIS418 4.3 10.1 1.0
ND2 B:ASN460 4.4 12.1 1.0
O B:ASP199 4.4 11.4 1.0
CG B:GLU416 4.4 8.1 1.0
CD2 B:HIS418 4.5 9.7 1.0
O B:ASN102 4.6 14.7 1.0
O B:HOH8914 4.6 24.4 1.0
CA B:ASP201 4.8 11.6 1.0
CA B:GLN200 4.9 8.6 1.0
CG2 B:VAL103 4.9 14.5 1.0
C B:GLN200 4.9 14.5 1.0

Magnesium binding site 6 out of 16 in 1dp0

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Magnesium binding site 6 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:15.4
occ:1.00
 O B:ASN18 2.3 16.0 1.0
OD2 B:ASP193 2.3 11.8 1.0
OE1 B:GLN163 2.3 14.1 1.0
O B:ASP15 2.3 15.5 1.0
O B:VAL21 2.4 15.9 1.0
OD1 B:ASP193 3.0 16.6 1.0
CG B:ASP193 3.0 15.8 1.0
CD B:GLN163 3.2 16.0 1.0
C B:ASN18 3.2 14.0 1.0
NE2 B:GLN163 3.5 14.1 1.0
C B:VAL21 3.5 15.9 1.0
C B:ASP15 3.6 17.2 1.0
N B:ASN18 3.7 16.8 1.0
CA B:ASN18 4.0 13.0 1.0
OH B:TYR161 4.0 14.7 1.0
CA B:TRP16 4.1 11.3 1.0
N B:PRO19 4.1 15.5 1.0
CB B:ASN18 4.2 13.5 1.0
N B:TRP16 4.3 13.1 1.0
N B:VAL21 4.3 14.0 1.0
CA B:VAL21 4.3 14.6 1.0
C B:TRP16 4.3 15.2 1.0
CE2 B:TYR161 4.3 12.3 1.0
CB B:VAL21 4.4 13.3 1.0
CA B:PRO19 4.4 19.2 1.0
N B:GLU17 4.5 14.9 1.0
CB B:ASP193 4.5 8.9 1.0
N B:THR22 4.5 12.4 1.0
CG B:GLN163 4.5 12.7 1.0
CA B:THR22 4.6 10.6 1.0
CZ B:TYR161 4.6 15.6 1.0
CA B:ASP15 4.7 16.5 1.0
C B:PRO19 4.8 17.3 1.0
O B:TRP16 4.9 14.6 1.0
C B:GLU17 4.9 19.7 1.0
CG1 B:VAL21 5.0 19.7 1.0

Magnesium binding site 7 out of 16 in 1dp0

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Magnesium binding site 7 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:34.5
occ:1.00
 O B:HOH9060 2.1 33.4 1.0
OE1 B:GLN718 2.4 31.5 1.0
O B:HOH8998 2.4 27.4 1.0
O B:HOH8884 2.4 17.4 1.0
O B:HOH9251 2.4 23.8 1.0
O B:HOH9321 2.7 35.5 1.0
CD B:GLN718 3.4 22.2 1.0
NE2 B:GLN718 3.7 23.4 1.0
C1 B:DMS8427 4.0 34.2 1.0
O B:HOH8900 4.0 35.9 1.0
O B:HOH9043 4.1 24.4 1.0
O B:THR911 4.1 16.5 1.0
O B:DMS8427 4.4 63.6 1.0
NE2 B:HIS622 4.4 12.6 1.0
O B:GLN719 4.5 14.0 1.0
O B:HOH8874 4.5 17.3 1.0
O B:HOH8860 4.6 40.0 1.0
N B:GLN719 4.7 10.4 1.0
O B:HOH8700 4.7 13.3 1.0
CG B:GLN718 4.8 10.8 1.0
C2 B:DMS8427 4.8 34.9 1.0
S B:DMS8427 4.8 64.8 1.0
O B:HOH9511 4.8 51.6 1.0

Magnesium binding site 8 out of 16 in 1dp0

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Magnesium binding site 8 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


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 at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:13.2
occ:1.00
 OE2 C:GLU416 2.0 13.4 1.0
O C:HOH8786 2.0 10.6 1.0
OE1 C:GLU461 2.1 11.8 1.0
O C:HOH8645 2.1 11.1 1.0
O C:HOH8709 2.2 11.5 1.0
ND1 C:HIS418 2.3 16.2 1.0
CD C:GLU461 3.1 15.9 1.0
CD C:GLU416 3.2 15.6 1.0
CE1 C:HIS418 3.2 15.3 1.0
CG C:HIS418 3.4 10.0 1.0
OE1 C:GLU416 3.6 10.9 1.0
CB C:HIS418 3.7 11.0 1.0
OE2 C:GLU461 4.0 14.2 1.0
CB C:GLU461 4.1 8.1 1.0
CG C:GLU461 4.1 10.7 1.0
O C:HOH9189 4.2 36.5 1.0
O C:HOH8632 4.2 14.9 1.0
N C:ASP201 4.2 11.7 1.0
CB C:ASP201 4.2 13.3 1.0
O C:ASP199 4.3 13.1 1.0
ND2 C:ASN460 4.3 12.4 1.0
OD1 C:ASN102 4.3 15.3 1.0
NE2 C:HIS418 4.4 10.7 1.0
CG C:GLU416 4.4 8.0 1.0
CD2 C:HIS418 4.5 11.9 1.0
O C:HOH8926 4.6 25.6 1.0
O C:ASN102 4.6 13.4 1.0
CA C:ASP201 4.8 11.6 1.0
CA C:GLN200 4.9 11.1 1.0
CG2 C:VAL103 4.9 16.3 1.0
C C:GLN200 4.9 18.0 1.0

Magnesium binding site 9 out of 16 in 1dp0

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Magnesium binding site 9 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:13.8
occ:1.00
 O C:VAL21 2.2 11.6 1.0
O C:ASP15 2.3 14.3 1.0
O C:ASN18 2.3 13.8 1.0
OE1 C:GLN163 2.4 12.1 1.0
OD2 C:ASP193 2.4 13.1 1.0
OD1 C:ASP193 3.1 15.5 1.0
CG C:ASP193 3.1 14.5 1.0
CD C:GLN163 3.2 11.8 1.0
C C:ASN18 3.3 16.7 1.0
C C:VAL21 3.4 12.4 1.0
C C:ASP15 3.5 14.4 1.0
NE2 C:GLN163 3.5 11.6 1.0
N C:ASN18 3.8 17.9 1.0
OH C:TYR161 4.0 15.9 1.0
CA C:ASN18 4.0 14.1 1.0
CA C:TRP16 4.1 11.9 1.0
N C:PRO19 4.2 18.6 1.0
N C:TRP16 4.2 12.8 1.0
CA C:VAL21 4.2 9.9 1.0
N C:VAL21 4.3 11.6 1.0
CB C:ASN18 4.3 14.6 1.0
CE2 C:TYR161 4.3 10.8 1.0
CB C:VAL21 4.3 13.1 1.0
C C:TRP16 4.3 15.3 1.0
N C:THR22 4.4 9.4 1.0
CA C:PRO19 4.4 17.3 1.0
CA C:THR22 4.5 12.0 1.0
CG C:GLN163 4.5 11.5 1.0
N C:GLU17 4.5 16.4 1.0
CB C:ASP193 4.6 10.5 1.0
CZ C:TYR161 4.6 15.0 1.0
CA C:ASP15 4.6 14.6 1.0
CG1 C:VAL21 4.8 15.1 1.0
O C:TRP16 4.9 15.9 1.0
C C:PRO19 4.9 15.2 1.0
C C:GLU17 5.0 22.1 1.0

Magnesium binding site 10 out of 16 in 1dp0

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Magnesium binding site 10 out of 16 in the E. Coli Beta-Galactosidase at 1.7 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E. Coli Beta-Galactosidase at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3003

b:22.6
occ:0.50
 O C:HOH8896 2.0 17.9 1.0
OE1 C:GLN718 2.1 30.0 1.0
O C:HOH9265 2.2 29.9 1.0
O C:HOH9010 2.3 35.9 1.0
O C:HOH9073 2.5 40.0 1.0
O C:HOH9334 2.5 40.7 1.0
CD C:GLN718 3.1 31.3 1.0
NE2 C:GLN718 3.4 20.1 1.0
NE2 C:HIS622 3.9 14.1 1.0
O C:THR911 4.0 15.0 1.0
O C:HOH8912 4.3 31.9 1.0
O C:HOH9056 4.4 27.8 1.0
O C:HOH9527 4.5 43.1 1.0
CG C:GLN718 4.5 18.6 1.0
C1 C:DMS8427 4.5 46.0 1.0
CE1 C:HIS622 4.5 15.4 1.0
N C:GLN719 4.6 15.8 1.0
O C:GLN719 4.6 15.3 1.0
O C:HOH8711 4.7 15.5 1.0
O C:HOH8886 4.7 16.0 1.0
O C:DMS8427 4.8 60.1 1.0
O C:HOH8872 4.9 45.6 1.0
CA C:GLN718 5.0 10.8 1.0
C C:THR911 5.0 18.4 1.0

Reference:

D.H.Juers, R.H.Jacobson, D.Wigley, X.J.Zhang, R.E.Huber, D.E.Tronrud, B.W.Matthews. High Resolution Refinement of Beta-Galactosidase in A New Crystal Form Reveals Multiple Metal-Binding Sites and Provides A Structural Basis For Alpha-Complementation. Protein Sci. V. 9 1685 2000.
ISSN: ISSN 0961-8368
PubMed: 11045615
Page generated: Tue Aug 13 02:42:05 2024

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