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Magnesium in PDB 3vd4: E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg, PDB code: 3vd4 was solved by R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.90 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.762, 162.446, 203.360, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.2

Other elements in 3vd4:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg also contains other interesting chemical elements:

Sodium (Na) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg (pdb code 3vd4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg, PDB code: 3vd4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3vd4

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Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:25.9
occ:1.00
 O A:HOH4074 2.0 27.0 1.0
O A:HOH4012 2.0 18.1 1.0
OE2 A:GLU416 2.1 23.1 1.0
OE1 A:GLU461 2.1 23.6 1.0
O A:HOH4149 2.2 19.0 1.0
ND1 A:HIS418 2.4 17.2 1.0
CD A:GLU416 3.2 22.6 1.0
CD A:GLU461 3.2 29.7 1.0
CE1 A:HIS418 3.2 22.7 1.0
CG A:HIS418 3.4 20.4 1.0
OE1 A:GLU416 3.6 22.5 1.0
CB A:HIS418 3.8 17.4 1.0
OE2 A:GLU461 3.9 28.1 1.0
CB A:ASP201 4.1 20.5 1.0
OD1 A:ASN102 4.1 22.5 1.0
N A:ASP201 4.1 23.1 1.0
OD1 A:ASP460 4.2 22.1 1.0
CG A:GLU461 4.2 22.6 1.0
O A:HOH4001 4.2 26.1 1.0
CB A:GLU461 4.2 19.4 1.0
O A:HOH4272 4.2 24.3 1.0
O A:ASP199 4.2 23.8 1.0
NE2 A:HIS418 4.4 21.5 1.0
CG A:GLU416 4.4 17.9 1.0
O4 A:IPT2001 4.4 20.3 0.9
CD2 A:HIS418 4.5 17.4 1.0
O A:ASN102 4.7 25.5 1.0
CA A:ASP201 4.7 20.8 1.0
O3 A:IPT2001 4.7 23.8 0.9
C2 A:IPT2001 4.8 23.8 0.9
C A:GLN200 4.9 26.3 1.0
CA A:GLN200 5.0 24.3 1.0

Magnesium binding site 2 out of 9 in 3vd4

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Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:31.3
occ:1.00
 OD2 A:ASP193 2.1 42.7 1.0
O A:ASP15 2.1 33.2 1.0
O A:ASN18 2.3 28.7 1.0
OE1 A:GLN163 2.3 33.3 1.0
O A:VAL21 2.3 34.4 1.0
CG A:ASP193 3.0 39.1 1.0
OD1 A:ASP193 3.1 40.5 1.0
CD A:GLN163 3.2 29.9 1.0
C A:ASN18 3.3 30.1 1.0
C A:ASP15 3.3 33.9 1.0
C A:VAL21 3.5 31.8 1.0
NE2 A:GLN163 3.6 27.7 1.0
N A:ASN18 3.7 31.5 1.0
OH A:TYR161 3.8 35.8 1.0
CA A:ASN18 3.9 32.1 1.0
CA A:TRP16 3.9 33.0 1.0
N A:TRP16 4.0 34.2 1.0
C A:TRP16 4.2 32.8 1.0
CB A:ASN18 4.2 29.3 1.0
CA A:VAL21 4.2 30.4 1.0
CE2 A:TYR161 4.3 34.3 1.0
CB A:VAL21 4.3 32.4 1.0
N A:PRO19 4.3 30.0 1.0
CB A:ASP193 4.4 31.6 1.0
N A:GLU17 4.4 30.4 1.0
N A:VAL21 4.4 32.5 1.0
CA A:ASP15 4.4 35.7 1.0
CG A:GLN163 4.5 28.3 1.0
N A:THR22 4.5 31.8 1.0
CZ A:TYR161 4.5 30.4 1.0
CA A:PRO19 4.6 32.0 1.0
CA A:THR22 4.6 33.5 1.0
CG1 A:VAL21 4.7 26.5 1.0
CB A:ASP15 4.8 33.3 1.0
O A:TRP16 4.8 32.8 1.0
C A:GLU17 4.9 32.8 1.0

Magnesium binding site 3 out of 9 in 3vd4

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Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:21.1
occ:1.00
 OE1 B:GLU461 2.1 18.9 1.0
OE2 B:GLU416 2.1 16.0 1.0
O B:HOH4087 2.1 17.5 1.0
O B:HOH4164 2.2 17.3 1.0
O B:HOH4024 2.2 15.8 1.0
ND1 B:HIS418 2.4 15.3 1.0
CD B:GLU461 3.2 26.4 1.0
CD B:GLU416 3.2 13.6 1.0
CE1 B:HIS418 3.3 14.5 1.0
CG B:HIS418 3.4 16.8 1.0
OE1 B:GLU416 3.7 15.6 1.0
CB B:HIS418 3.7 11.9 1.0
OE2 B:GLU461 3.9 18.8 1.0
OD1 B:ASN102 4.0 18.1 1.0
CB B:GLU461 4.2 16.5 1.0
O B:HOH4012 4.2 18.7 1.0
CB B:ASP201 4.2 10.4 1.0
OD1 B:ASP460 4.2 17.4 1.0
CG B:GLU461 4.2 15.7 1.0
N B:ASP201 4.2 13.0 1.0
O B:ASP199 4.3 17.4 1.0
O B:HOH4298 4.4 18.7 1.0
CG B:GLU416 4.4 14.0 1.0
NE2 B:HIS418 4.4 19.4 1.0
O4 B:IPT2001 4.5 15.6 1.0
CD2 B:HIS418 4.5 16.7 1.0
O B:ASN102 4.6 20.9 1.0
O3 B:IPT2001 4.7 17.6 1.0
C2 B:IPT2001 4.8 22.9 1.0
CA B:ASP201 4.8 12.7 1.0
C B:GLN200 4.9 16.6 1.0
CA B:GLN200 5.0 14.4 1.0

Magnesium binding site 4 out of 9 in 3vd4

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Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:17.8
occ:1.00
 OD2 B:ASP193 2.1 19.8 1.0
O B:ASP15 2.1 16.4 1.0
O B:ASN18 2.3 18.2 1.0
OE1 B:GLN163 2.3 18.8 1.0
O B:VAL21 2.3 17.7 1.0
CG B:ASP193 2.9 21.4 1.0
OD1 B:ASP193 3.1 24.4 1.0
CD B:GLN163 3.2 25.8 1.0
C B:ASN18 3.2 20.3 1.0
C B:ASP15 3.3 15.3 1.0
C B:VAL21 3.5 19.7 1.0
NE2 B:GLN163 3.5 20.0 1.0
N B:ASN18 3.6 20.9 1.0
CA B:ASN18 3.9 21.0 1.0
OH B:TYR161 4.0 21.9 1.0
CA B:TRP16 4.0 21.5 1.0
N B:TRP16 4.1 18.0 1.0
N B:PRO19 4.2 21.0 1.0
CA B:VAL21 4.2 20.8 1.0
CB B:ASN18 4.2 19.9 1.0
C B:TRP16 4.3 21.8 1.0
CB B:VAL21 4.3 24.5 1.0
N B:VAL21 4.3 23.5 1.0
CB B:ASP193 4.4 18.4 1.0
CE2 B:TYR161 4.4 29.2 1.0
N B:GLU17 4.4 21.8 1.0
CA B:PRO19 4.4 22.6 1.0
CA B:ASP15 4.5 18.7 1.0
CG B:GLN163 4.5 20.9 1.0
N B:THR22 4.5 19.0 1.0
CZ B:TYR161 4.6 28.4 1.0
CA B:THR22 4.7 20.1 1.0
CG1 B:VAL21 4.8 20.3 1.0
C B:GLU17 4.8 21.5 1.0
O B:TRP16 4.9 23.3 1.0
CB B:ASP15 4.9 16.1 1.0
C B:PRO19 4.9 24.5 1.0

Magnesium binding site 5 out of 9 in 3vd4

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Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:35.9
occ:1.00
 O B:HOH4807 2.0 26.4 1.0
O B:HOH4770 2.0 28.2 1.0
O B:HOH4798 2.1 35.7 1.0
O B:HOH4856 2.1 32.2 1.0
O B:HOH4709 2.1 29.3 1.0
OE1 B:GLU369 3.9 25.9 1.0
O B:HOH4783 4.1 23.2 1.0
OE2 B:GLU369 4.1 29.9 1.0
O B:HOH4846 4.2 22.5 1.0
CD B:GLU369 4.4 27.8 1.0

Magnesium binding site 6 out of 9 in 3vd4

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Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:19.1
occ:1.00
 O C:HOH4092 2.0 16.6 1.0
OE2 C:GLU416 2.1 21.0 1.0
OE1 C:GLU461 2.1 16.4 1.0
O C:HOH4169 2.1 14.1 1.0
O C:HOH4028 2.2 14.1 1.0
ND1 C:HIS418 2.4 14.9 1.0
CD C:GLU461 3.2 25.9 1.0
CD C:GLU416 3.2 15.8 1.0
CE1 C:HIS418 3.3 15.8 1.0
CG C:HIS418 3.4 19.7 1.0
CB C:HIS418 3.7 13.7 1.0
OE1 C:GLU416 3.7 19.2 1.0
OE2 C:GLU461 3.9 19.3 1.0
CB C:GLU461 4.1 13.6 1.0
OD1 C:ASN102 4.2 20.9 1.0
CG C:GLU461 4.2 11.9 1.0
O C:ASP199 4.2 15.3 1.0
CB C:ASP201 4.2 11.9 1.0
N C:ASP201 4.2 14.2 1.0
O C:HOH4016 4.2 20.0 1.0
OD1 C:ASP460 4.2 22.3 1.0
CG C:GLU416 4.4 14.3 1.0
O C:HOH4301 4.4 21.0 1.0
NE2 C:HIS418 4.4 17.6 1.0
CD2 C:HIS418 4.5 15.0 1.0
O4 C:IPT2001 4.6 16.0 1.0
O C:ASN102 4.6 15.8 1.0
CA C:ASP201 4.8 16.4 1.0
O3 C:IPT2001 4.8 20.4 1.0
C2 C:IPT2001 4.9 21.7 1.0
C C:GLN200 4.9 17.0 1.0
CA C:GLN200 4.9 15.8 1.0

Magnesium binding site 7 out of 9 in 3vd4

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Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:15.0
occ:1.00
 OD2 C:ASP193 2.1 20.5 1.0
O C:ASP15 2.1 20.5 1.0
OE1 C:GLN163 2.3 16.1 1.0
O C:VAL21 2.3 21.0 1.0
O C:ASN18 2.3 18.4 1.0
CG C:ASP193 2.9 19.2 1.0
OD1 C:ASP193 3.1 21.0 1.0
CD C:GLN163 3.2 18.7 1.0
C C:ASN18 3.2 20.6 1.0
C C:ASP15 3.3 20.4 1.0
C C:VAL21 3.4 22.9 1.0
NE2 C:GLN163 3.5 17.5 1.0
N C:ASN18 3.7 23.5 1.0
CA C:ASN18 3.9 21.8 1.0
CA C:TRP16 4.0 19.1 1.0
OH C:TYR161 4.0 16.4 1.0
N C:TRP16 4.1 17.6 1.0
N C:PRO19 4.2 21.5 1.0
CA C:VAL21 4.2 24.9 1.0
C C:TRP16 4.3 21.6 1.0
CB C:VAL21 4.3 27.3 1.0
N C:VAL21 4.3 28.4 1.0
CB C:ASN18 4.3 21.6 1.0
CB C:ASP193 4.4 17.5 1.0
CE2 C:TYR161 4.4 18.3 1.0
CA C:ASP15 4.4 22.5 1.0
N C:THR22 4.5 22.0 1.0
CA C:PRO19 4.5 22.5 1.0
N C:GLU17 4.5 17.4 1.0
CG C:GLN163 4.5 21.8 1.0
CZ C:TYR161 4.7 19.1 1.0
CA C:THR22 4.7 18.7 1.0
CG1 C:VAL21 4.8 23.7 1.0
O C:TRP16 4.8 20.8 1.0
C C:GLU17 4.9 22.9 1.0
CB C:ASP15 4.9 19.1 1.0
C C:PRO19 5.0 25.0 1.0

Magnesium binding site 8 out of 9 in 3vd4

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Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:26.8
occ:1.00
 OE2 D:GLU416 2.1 25.1 1.0
OE1 D:GLU461 2.1 20.2 1.0
O D:HOH4099 2.1 24.3 1.0
O D:HOH4175 2.2 17.8 1.0
O D:HOH4038 2.2 21.2 1.0
ND1 D:HIS418 2.4 21.6 1.0
CD D:GLU461 3.2 30.8 1.0
CD D:GLU416 3.2 20.4 1.0
CE1 D:HIS418 3.2 23.5 1.0
CG D:HIS418 3.4 19.8 1.0
CB D:HIS418 3.7 18.1 1.0
OE1 D:GLU416 3.8 24.2 1.0
OE2 D:GLU461 3.9 32.2 1.0
O D:HOH4026 4.0 27.4 1.0
OD1 D:ASN102 4.0 25.0 1.0
CB D:ASP201 4.1 20.2 1.0
CG D:GLU461 4.2 21.4 1.0
CB D:GLU461 4.2 20.6 1.0
N D:ASP201 4.2 21.5 1.0
OD1 D:ASP460 4.3 25.0 1.0
O D:ASP199 4.3 25.8 1.0
O4 D:IPT2001 4.4 27.4 1.0
O D:HOH4301 4.4 27.0 1.0
NE2 D:HIS418 4.4 22.1 1.0
CG D:GLU416 4.4 18.5 1.0
CD2 D:HIS418 4.5 19.0 1.0
O D:ASN102 4.7 26.7 1.0
O3 D:IPT2001 4.7 31.3 1.0
CA D:ASP201 4.7 20.1 1.0
C2 D:IPT2001 4.8 27.5 1.0
C D:GLN200 4.9 23.5 1.0
CG2 D:VAL103 5.0 22.7 1.0

Magnesium binding site 9 out of 9 in 3vd4

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Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460D) in Complex with Iptg


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 (N460D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:28.1
occ:1.00
 OD2 D:ASP193 2.1 32.3 1.0
O D:ASP15 2.1 26.9 1.0
O D:ASN18 2.3 26.0 1.0
OE1 D:GLN163 2.3 33.9 1.0
O D:VAL21 2.3 28.7 1.0
CG D:ASP193 2.9 30.7 1.0
OD1 D:ASP193 3.0 28.3 1.0
C D:ASN18 3.2 29.0 1.0
CD D:GLN163 3.3 35.0 1.0
C D:ASP15 3.3 27.7 1.0
C D:VAL21 3.5 25.1 1.0
N D:ASN18 3.7 31.0 1.0
NE2 D:GLN163 3.7 29.8 1.0
CA D:ASN18 3.9 30.0 1.0
OH D:TYR161 3.9 27.6 1.0
CA D:TRP16 4.0 28.7 1.0
N D:TRP16 4.1 28.2 1.0
N D:PRO19 4.2 28.6 1.0
C D:TRP16 4.2 29.5 1.0
CA D:VAL21 4.3 26.3 1.0
CE2 D:TYR161 4.3 23.5 1.0
CB D:ASP193 4.3 27.8 1.0
CB D:ASN18 4.3 31.9 1.0
CB D:VAL21 4.3 27.6 1.0
N D:GLU17 4.4 28.8 1.0
N D:VAL21 4.4 30.8 1.0
CA D:PRO19 4.4 31.3 1.0
CA D:ASP15 4.4 29.4 1.0
N D:THR22 4.5 23.8 1.0
CG D:GLN163 4.5 25.0 1.0
CZ D:TYR161 4.6 25.1 1.0
CA D:THR22 4.7 23.9 1.0
O D:TRP16 4.8 29.4 1.0
CG1 D:VAL21 4.8 26.6 1.0
C D:GLU17 4.9 31.0 1.0
CB D:ASP15 4.9 27.3 1.0
C D:PRO19 5.0 30.2 1.0

Reference:

R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber. Substitution For ASN460 Cripples {Beta}-Galactosidase (Escherichia Coli) By Increasing Substrate Affinity and Decreasing Transition State Stability. Arch.Biochem.Biophys. V. 521 51 2012.
ISSN: ISSN 0003-9861
PubMed: 22446164
DOI: 10.1016/J.ABB.2012.03.014
Page generated: Thu Aug 15 12:55:25 2024

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