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Magnesium in PDB 3i3b: E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on

Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on

All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on:
3.2.1.23;

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on, PDB code: 3i3b was solved by M.L.Dugdale, D.Dymianiw, B.Minhas, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.18 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.600, 168.420, 201.310, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.4

Other elements in 3i3b:

The structure of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on (pdb code 3i3b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on, PDB code: 3i3b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 3i3b

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Magnesium binding site 1 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:17.5
occ:1.00
 OE1 A:GLU461 2.0 16.7 1.0
OE2 A:GLU416 2.1 15.4 1.0
O A:HOH4154 2.1 11.0 1.0
O A:HOH4076 2.2 10.6 1.0
ND1 A:HIS418 2.3 17.8 1.0
O A:HOH4012 2.3 8.5 1.0
CD A:GLU461 3.1 18.4 1.0
CE1 A:HIS418 3.1 16.9 1.0
CD A:GLU416 3.2 14.0 1.0
CG A:HIS418 3.3 16.0 1.0
CB A:HIS418 3.7 15.8 1.0
OE1 A:GLU416 3.7 15.1 1.0
OE2 A:GLU461 3.9 16.5 1.0
CG A:GLU461 4.1 16.1 1.0
C2 A:1492001 4.1 15.3 1.0
N A:ASP201 4.2 15.1 1.0
CB A:GLU461 4.2 12.9 1.0
CB A:ASP201 4.2 15.8 1.0
O A:ASP199 4.2 15.6 1.0
OD1 A:ASN102 4.2 16.1 1.0
NE2 A:HIS418 4.3 16.3 1.0
O4 A:1492001 4.3 18.0 1.0
ND2 A:ASN460 4.3 15.3 1.0
CG A:GLU416 4.4 13.3 1.0
CD2 A:HIS418 4.4 16.4 1.0
O3 A:1492001 4.5 11.9 1.0
O2 A:1492001 4.5 12.3 1.0
O A:ASN102 4.6 15.7 1.0
CA A:ASP201 4.8 15.0 1.0
C3 A:1492001 4.8 13.8 1.0
CA A:GLN200 4.9 13.0 1.0
C A:GLN200 4.9 13.6 1.0
CG2 A:VAL103 5.0 15.2 1.0

Magnesium binding site 2 out of 11 in 3i3b

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Magnesium binding site 2 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:19.2
occ:1.00
 NE2 A:GLN163 2.2 15.9 1.0
OD2 A:ASP193 2.2 20.1 1.0
O A:VAL21 2.2 24.3 1.0
O A:ASN18 2.3 25.9 1.0
O A:ASP15 2.3 29.5 1.0
CG A:ASP193 3.0 21.9 1.0
OD1 A:ASP193 3.1 23.5 1.0
CD A:GLN163 3.1 18.1 1.0
C A:ASN18 3.3 25.0 1.0
OE1 A:GLN163 3.3 21.7 1.0
C A:VAL21 3.4 23.2 1.0
C A:ASP15 3.5 27.3 1.0
N A:ASN18 3.7 24.7 1.0
CA A:ASN18 4.0 25.6 1.0
OH A:TYR161 4.0 21.1 1.0
CA A:TRP16 4.1 25.8 1.0
CA A:VAL21 4.2 23.0 1.0
N A:TRP16 4.2 26.9 1.0
CE2 A:TYR161 4.2 22.2 1.0
CB A:ASN18 4.3 26.3 1.0
CB A:VAL21 4.3 23.0 1.0
C A:TRP16 4.3 25.1 1.0
N A:PRO19 4.3 23.1 1.0
N A:VAL21 4.3 23.0 1.0
N A:THR22 4.4 22.5 1.0
N A:GLU17 4.4 23.1 1.0
CB A:ASP193 4.4 19.4 1.0
CG A:GLN163 4.5 16.9 1.0
CA A:PRO19 4.5 22.9 1.0
CA A:THR22 4.5 23.0 1.0
CA A:ASP15 4.6 27.3 1.0
CZ A:TYR161 4.6 21.9 1.0
O A:TRP16 4.8 25.2 1.0
CG1 A:VAL21 4.9 22.4 1.0
CB A:ASP15 4.9 25.7 1.0
C A:PRO19 4.9 22.4 1.0
C A:GLU17 4.9 23.9 1.0

Magnesium binding site 3 out of 11 in 3i3b

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Magnesium binding site 3 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:70.5
occ:1.00
 O A:HOH4690 2.2 36.6 1.0
O A:HOH4608 3.1 39.1 1.0
O A:HOH4732 3.2 47.5 1.0
O A:DMS5006 3.7 58.2 1.0
C2 A:DMS5006 4.0 58.3 1.0
OE1 A:GLU314 4.0 20.7 1.0
OE2 A:GLU314 4.4 24.6 1.0
S A:DMS5006 4.5 59.0 1.0
CD A:GLU314 4.6 20.1 1.0
O A:HOH4600 4.6 32.8 1.0

Magnesium binding site 4 out of 11 in 3i3b

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Magnesium binding site 4 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1024

b:44.7
occ:1.00
 O A:HOH4419 2.5 43.0 1.0
OE2 A:GLU136 4.3 44.1 1.0
NE2 A:GLN135 4.4 44.9 1.0
O A:HOH4676 4.4 34.2 1.0
CB A:GLN135 4.7 37.9 1.0
CD A:GLN135 5.0 43.5 1.0

Magnesium binding site 5 out of 11 in 3i3b

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Magnesium binding site 5 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:15.2
occ:1.00
 OE1 B:GLU461 2.0 10.5 1.0
OE2 B:GLU416 2.0 13.2 1.0
O B:HOH4155 2.2 7.6 1.0
O B:HOH4014 2.2 6.1 1.0
O B:HOH4078 2.2 16.0 1.0
ND1 B:HIS418 2.4 7.0 1.0
CD B:GLU416 3.2 12.4 1.0
CD B:GLU461 3.2 9.2 1.0
CE1 B:HIS418 3.4 8.8 1.0
CG B:HIS418 3.4 7.5 1.0
OE1 B:GLU416 3.7 11.1 1.0
CB B:HIS418 3.7 8.8 1.0
OE2 B:GLU461 4.0 10.5 1.0
OD1 B:ASN102 4.1 13.5 1.0
CB B:ASP201 4.1 14.5 1.0
N B:ASP201 4.1 12.3 1.0
CG B:GLU461 4.2 10.7 1.0
O B:ASP199 4.2 12.6 1.0
C2 B:1492001 4.2 14.5 1.0
CB B:GLU461 4.3 9.8 1.0
O4 B:1492001 4.3 16.4 1.0
CG B:GLU416 4.4 11.8 1.0
ND2 B:ASN460 4.4 9.8 1.0
O3 B:1492001 4.4 13.6 1.0
NE2 B:HIS418 4.5 5.8 1.0
CD2 B:HIS418 4.6 6.8 1.0
O B:ASN102 4.6 11.3 1.0
CA B:ASP201 4.7 13.9 1.0
O2 B:1492001 4.7 14.9 1.0
C B:GLN200 4.9 12.7 1.0
CA B:GLN200 4.9 12.5 1.0
C3 B:1492001 4.9 12.9 1.0

Magnesium binding site 6 out of 11 in 3i3b

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Magnesium binding site 6 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:19.7
occ:1.00
 OD2 B:ASP193 2.1 12.7 1.0
O B:ASN18 2.2 15.6 1.0
O B:ASP15 2.3 16.5 1.0
NE2 B:GLN163 2.4 13.8 1.0
O B:VAL21 2.4 15.5 1.0
CG B:ASP193 2.9 13.3 1.0
OD1 B:ASP193 3.1 15.0 1.0
C B:ASN18 3.1 17.2 1.0
CD B:GLN163 3.4 14.8 1.0
C B:ASP15 3.5 17.9 1.0
C B:VAL21 3.5 17.2 1.0
N B:ASN18 3.6 15.4 1.0
OE1 B:GLN163 3.6 16.2 1.0
CA B:ASN18 3.8 16.5 1.0
OH B:TYR161 4.0 14.1 1.0
CA B:TRP16 4.1 15.3 1.0
N B:PRO19 4.1 19.9 1.0
CB B:ASN18 4.2 16.5 1.0
C B:TRP16 4.2 16.0 1.0
N B:TRP16 4.2 15.4 1.0
CA B:VAL21 4.2 18.2 1.0
N B:VAL21 4.2 19.9 1.0
CB B:VAL21 4.3 18.5 1.0
N B:GLU17 4.3 15.6 1.0
CB B:ASP193 4.3 13.7 1.0
CA B:PRO19 4.4 19.7 1.0
CE2 B:TYR161 4.4 13.5 1.0
N B:THR22 4.5 17.0 1.0
CA B:ASP15 4.6 18.9 1.0
CZ B:TYR161 4.7 15.2 1.0
CA B:THR22 4.7 18.0 1.0
CG B:GLN163 4.7 14.7 1.0
C B:GLU17 4.7 16.4 1.0
O B:TRP16 4.8 17.1 1.0
C B:PRO19 4.8 20.9 1.0
CG1 B:VAL21 4.8 16.1 1.0
CB B:ASP15 5.0 18.1 1.0

Magnesium binding site 7 out of 11 in 3i3b

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Magnesium binding site 7 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:59.7
occ:1.00
 O B:HOH4262 2.3 32.9 1.0
O B:HOH4574 2.3 33.0 1.0
O B:HOH4362 2.6 29.7 1.0
O B:HOH4424 2.6 34.5 1.0
OE1 B:GLN718 3.3 24.0 1.0
O B:DMS5022 3.6 90.1 1.0
O B:THR911 3.9 15.3 1.0
O B:HOH4276 4.1 22.9 1.0
CD B:GLN718 4.2 20.1 1.0
O B:HOH4252 4.3 20.0 1.0
C1 B:DMS5022 4.4 90.0 1.0
O B:HOH4622 4.4 27.0 1.0
NE2 B:GLN718 4.4 20.4 1.0
NE2 B:HIS622 4.5 12.8 1.0
S B:DMS5022 4.5 89.7 1.0
CA B:THR911 4.6 13.0 1.0
O B:HOH4080 4.6 23.9 1.0
C B:THR911 4.7 13.9 1.0
CB B:THR911 4.7 11.1 1.0
O B:HOH4409 4.8 40.8 1.0
O B:HOH4240 4.8 45.1 1.0
C2 B:DMS5022 4.9 89.9 1.0

Magnesium binding site 8 out of 11 in 3i3b

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Magnesium binding site 8 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:12.2
occ:1.00
 OE1 C:GLU461 2.0 11.3 1.0
OE2 C:GLU416 2.2 14.0 1.0
O C:HOH4158 2.2 10.4 1.0
O C:HOH4016 2.2 13.0 1.0
O C:HOH4811 2.3 9.9 1.0
ND1 C:HIS418 2.3 11.0 1.0
CD C:GLU461 3.2 12.9 1.0
CD C:GLU416 3.2 9.8 1.0
CE1 C:HIS418 3.3 13.9 1.0
CG C:HIS418 3.3 11.2 1.0
CB C:HIS418 3.6 11.7 1.0
OE1 C:GLU416 3.7 9.6 1.0
OE2 C:GLU461 4.0 16.1 1.0
N C:ASP201 4.1 10.4 1.0
CG C:GLU461 4.1 10.6 1.0
O C:ASP199 4.2 8.6 1.0
CB C:ASP201 4.2 9.9 1.0
OD1 C:ASN102 4.2 10.6 1.0
CB C:GLU461 4.2 10.8 1.0
C2 C:1492001 4.3 12.4 1.0
CG C:GLU416 4.4 7.4 1.0
O4 C:1492001 4.4 13.8 1.0
NE2 C:HIS418 4.4 11.9 1.0
CD2 C:HIS418 4.4 11.2 1.0
ND2 C:ASN460 4.4 9.8 1.0
O3 C:1492001 4.5 10.9 1.0
O C:ASN102 4.6 13.3 1.0
CA C:ASP201 4.7 12.8 1.0
O2 C:1492001 4.7 12.6 1.0
CA C:GLN200 4.8 10.3 1.0
C C:GLN200 4.8 11.4 1.0
CG2 C:VAL103 4.9 18.4 1.0
C3 C:1492001 5.0 9.6 1.0

Magnesium binding site 9 out of 11 in 3i3b

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Magnesium binding site 9 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:17.4
occ:1.00
 O C:VAL21 2.2 15.2 1.0
O C:ASP15 2.2 15.6 1.0
O C:ASN18 2.3 18.9 1.0
OD2 C:ASP193 2.4 15.8 1.0
NE2 C:GLN163 2.5 10.5 1.0
CG C:ASP193 3.1 16.8 1.0
C C:ASN18 3.2 18.6 1.0
OD1 C:ASP193 3.2 16.6 1.0
C C:VAL21 3.3 16.8 1.0
C C:ASP15 3.4 16.8 1.0
CD C:GLN163 3.5 15.6 1.0
N C:ASN18 3.6 18.7 1.0
OE1 C:GLN163 3.7 17.8 1.0
CA C:ASN18 3.9 18.1 1.0
CA C:VAL21 4.0 18.2 1.0
OH C:TYR161 4.0 17.5 1.0
CA C:TRP16 4.1 15.4 1.0
CB C:VAL21 4.1 17.8 1.0
N C:VAL21 4.1 18.5 1.0
N C:PRO19 4.1 19.9 1.0
N C:TRP16 4.2 15.8 1.0
CB C:ASN18 4.2 16.9 1.0
CE2 C:TYR161 4.3 13.9 1.0
C C:TRP16 4.3 17.9 1.0
N C:THR22 4.3 15.4 1.0
N C:GLU17 4.4 18.8 1.0
CA C:PRO19 4.4 19.8 1.0
CG1 C:VAL21 4.5 18.2 1.0
CA C:ASP15 4.5 18.1 1.0
CA C:THR22 4.6 14.7 1.0
CB C:ASP193 4.6 15.3 1.0
CZ C:TYR161 4.6 15.2 1.0
CG C:GLN163 4.8 13.4 1.0
C C:PRO19 4.8 19.7 1.0
O C:TRP16 4.8 16.2 1.0
C C:GLU17 4.8 19.7 1.0
CB C:ASP15 4.9 17.9 1.0
CG C:ASN18 5.0 17.0 1.0

Magnesium binding site 10 out of 11 in 3i3b

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Magnesium binding site 10 out of 11 in the E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E.Coli (Lacz) Beta-Galactosidase (M542A) in Complex with D- Galactopyranosyl-1-on within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:13.0
occ:1.00
 OE1 D:GLU461 2.1 14.6 1.0
OE2 D:GLU416 2.1 12.9 1.0
O D:HOH4154 2.2 12.9 1.0
O D:HOH4077 2.2 8.8 1.0
ND1 D:HIS418 2.3 13.9 1.0
O D:HOH4014 2.4 10.9 1.0
CD D:GLU461 3.2 13.9 1.0
CE1 D:HIS418 3.2 13.9 1.0
CD D:GLU416 3.2 8.5 1.0
CG D:HIS418 3.3 13.1 1.0
CB D:HIS418 3.6 11.9 1.0
OE1 D:GLU416 3.8 12.2 1.0
OE2 D:GLU461 3.9 17.9 1.0
CG D:GLU461 4.2 13.6 1.0
OD1 D:ASN102 4.2 12.7 1.0
CB D:GLU461 4.2 10.8 1.0
C2 D:1492001 4.2 13.4 1.0
N D:ASP201 4.3 13.9 1.0
CB D:ASP201 4.3 16.5 1.0
O D:ASP199 4.3 12.3 1.0
NE2 D:HIS418 4.3 13.4 1.0
O4 D:1492001 4.3 15.5 1.0
CD2 D:HIS418 4.4 13.2 1.0
CG D:GLU416 4.4 9.7 1.0
ND2 D:ASN460 4.5 8.0 1.0
O3 D:1492001 4.6 13.4 1.0
O D:ASN102 4.6 15.4 1.0
O2 D:1492001 4.8 10.4 1.0
CG2 D:VAL103 4.8 17.0 1.0
CA D:ASP201 4.9 14.1 1.0
C3 D:1492001 5.0 13.3 1.0
CA D:GLN200 5.0 12.3 1.0

Reference:

M.L.Dugdale, D.L.Dymianiw, B.K.Minhas, I.D'angelo, R.E.Huber. Role of Met-542 As A Guide For the Conformational Changes of Phe-601 That Occur During the Reaction of β-Galactosidase (Escherichia Coli). Biochem.Cell Biol. V. 88 861 2010.
ISSN: ISSN 0829-8211
PubMed: 20921997
DOI: 10.1139/O10-009
Page generated: Mon Dec 14 08:15:24 2020

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