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Magnesium in PDB 1jyx: E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with Iptg, PDB code: 1jyx was solved by D.H.Juers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.770, 161.190, 202.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 24.4

Other elements in 1jyx:

The structure of E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg (pdb code 1jyx). 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 in Complex with Iptg, PDB code: 1jyx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1jyx

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Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:18.9
occ:1.00
OE2 A:GLU416 2.0 15.7 1.0
O A:HOH8616 2.0 15.3 1.0
O A:HOH8680 2.1 16.9 1.0
O A:HOH8758 2.1 19.2 1.0
OE1 A:GLU461 2.2 14.8 1.0
ND1 A:HIS418 2.2 18.7 1.0
CD A:GLU416 3.1 14.7 1.0
CE1 A:HIS418 3.1 14.6 1.0
CD A:GLU461 3.2 23.2 1.0
CG A:HIS418 3.4 21.4 1.0
OE1 A:GLU416 3.5 14.5 1.0
CB A:HIS418 3.7 13.0 1.0
ND2 A:ASN102 4.0 14.7 1.0
CB A:GLU461 4.0 12.2 1.0
OE2 A:GLU461 4.1 21.2 1.0
CG A:GLU461 4.1 12.6 1.0
CB A:ASP201 4.2 16.0 1.0
N A:ASP201 4.2 19.3 1.0
O A:ASP199 4.2 17.4 1.0
O A:HOH8603 4.3 20.3 1.0
ND2 A:ASN460 4.3 17.6 1.0
CG A:GLU416 4.3 10.6 1.0
NE2 A:HIS418 4.3 20.5 1.0
O4 A:IPT2001 4.4 17.1 0.9
O A:HOH8893 4.5 36.0 1.0
CD2 A:HIS418 4.5 15.6 1.0
O A:ASN102 4.7 19.1 1.0
CA A:ASP201 4.7 18.5 1.0
C2 A:IPT2001 4.8 18.7 0.9
O3 A:IPT2001 4.9 23.5 0.9
C A:GLN200 4.9 17.7 1.0
CG2 A:VAL103 4.9 18.8 1.0
CA A:GLN200 4.9 11.6 1.0

Magnesium binding site 2 out of 9 in 1jyx

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Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:21.1
occ:1.00
O A:ASN18 2.1 21.7 1.0
O A:VAL21 2.1 22.4 1.0
OE1 A:GLN163 2.3 27.1 1.0
O A:ASP15 2.3 23.1 1.0
OD2 A:ASP193 2.4 19.8 1.0
OD1 A:ASP193 3.0 26.4 1.0
CG A:ASP193 3.0 39.5 1.0
C A:ASN18 3.1 25.0 1.0
CD A:GLN163 3.2 20.7 1.0
C A:VAL21 3.3 18.5 1.0
C A:ASP15 3.5 22.8 1.0
NE2 A:GLN163 3.5 16.6 1.0
N A:ASN18 3.6 24.3 1.0
CA A:ASN18 3.8 27.8 1.0
CA A:VAL21 4.0 13.2 1.0
N A:PRO19 4.0 20.1 1.0
CB A:VAL21 4.1 25.9 1.0
CA A:TRP16 4.1 16.4 1.0
N A:VAL21 4.1 21.1 1.0
OH A:TYR161 4.1 25.8 1.0
N A:TRP16 4.3 20.8 1.0
CB A:ASN18 4.3 21.5 1.0
N A:THR22 4.3 22.6 1.0
CA A:PRO19 4.3 29.0 1.0
C A:TRP16 4.3 24.4 1.0
CB A:ASP193 4.5 20.4 1.0
N A:GLU17 4.5 24.6 1.0
CG A:GLN163 4.5 20.3 1.0
CE2 A:TYR161 4.6 20.9 1.0
CA A:THR22 4.6 23.1 1.0
CA A:ASP15 4.7 30.9 1.0
CG1 A:VAL21 4.7 21.7 1.0
C A:GLU17 4.8 24.5 1.0
C A:PRO19 4.8 26.9 1.0
CZ A:TYR161 4.8 19.4 1.0
O A:TRP16 4.9 25.6 1.0

Magnesium binding site 3 out of 9 in 1jyx

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Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:18.9
occ:1.00
OE2 B:GLU416 2.0 14.1 1.0
OE1 B:GLU461 2.1 16.4 1.0
ND1 B:HIS418 2.1 10.5 1.0
O B:HOH8593 2.2 14.1 1.0
O B:HOH8670 2.2 14.4 1.0
O B:HOH8529 2.2 12.9 1.0
CE1 B:HIS418 3.0 13.5 1.0
CD B:GLU461 3.1 32.8 1.0
CD B:GLU416 3.2 19.7 1.0
CG B:HIS418 3.3 17.8 1.0
CB B:HIS418 3.6 16.4 1.0
OE1 B:GLU416 3.7 13.2 1.0
OE2 B:GLU461 3.9 18.8 1.0
CB B:GLU461 4.0 15.0 1.0
ND2 B:ASN102 4.1 11.2 1.0
CG B:GLU461 4.1 22.2 1.0
NE2 B:HIS418 4.2 15.6 1.0
O B:HOH8517 4.2 18.0 1.0
N B:ASP201 4.2 14.6 1.0
CB B:ASP201 4.2 18.1 1.0
O B:ASP199 4.3 17.4 1.0
ND2 B:ASN460 4.3 11.3 1.0
CD2 B:HIS418 4.4 13.9 1.0
CG B:GLU416 4.4 17.8 1.0
O4 B:IPT2001 4.4 16.1 1.0
O B:HOH8805 4.5 26.4 1.0
O B:ASN102 4.6 17.6 1.0
CA B:ASP201 4.8 16.5 1.0
C2 B:IPT2001 4.9 20.4 1.0
C B:GLN200 4.9 22.1 1.0
O3 B:IPT2001 4.9 19.0 1.0
CG2 B:VAL103 4.9 17.1 1.0
CA B:GLN200 5.0 13.8 1.0

Magnesium binding site 4 out of 9 in 1jyx

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Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:22.2
occ:1.00
OD2 B:ASP193 2.3 21.9 1.0
OE1 B:GLN163 2.3 18.6 1.0
O B:ASP15 2.3 18.6 1.0
O B:ASN18 2.3 19.4 1.0
O B:VAL21 2.4 19.0 1.0
OD1 B:ASP193 2.8 19.9 1.0
CG B:ASP193 2.9 18.7 1.0
CD B:GLN163 3.2 28.8 1.0
C B:ASN18 3.3 23.6 1.0
NE2 B:GLN163 3.4 17.8 1.0
C B:ASP15 3.5 19.1 1.0
C B:VAL21 3.5 19.2 1.0
N B:ASN18 3.7 18.7 1.0
CA B:ASN18 3.9 17.0 1.0
CA B:TRP16 4.1 15.1 1.0
OH B:TYR161 4.1 18.6 1.0
N B:PRO19 4.1 19.2 1.0
CB B:ASN18 4.2 20.7 1.0
N B:TRP16 4.2 14.8 1.0
CA B:VAL21 4.2 20.8 1.0
C B:TRP16 4.3 26.4 1.0
N B:VAL21 4.3 20.8 1.0
CA B:PRO19 4.3 18.1 1.0
CE2 B:TYR161 4.3 22.7 1.0
CB B:ASP193 4.4 13.2 1.0
N B:GLU17 4.4 28.1 1.0
CG B:GLN163 4.5 20.6 1.0
CB B:VAL21 4.5 18.6 1.0
N B:THR22 4.6 17.9 1.0
CZ B:TYR161 4.7 24.7 1.0
CA B:ASP15 4.7 19.1 1.0
CA B:THR22 4.7 16.6 1.0
C B:PRO19 4.8 27.8 1.0
O B:TRP16 4.9 19.2 1.0
C B:GLU17 4.9 26.8 1.0
CG1 B:VAL21 4.9 22.1 1.0

Magnesium binding site 5 out of 9 in 1jyx

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Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:24.1
occ:1.00
O B:HOH9431 1.9 20.7 1.0
O B:HOH9350 2.0 23.3 1.0
O B:HOH9412 2.0 36.0 1.0
O B:HOH9411 2.1 49.0 1.0
O B:HOH9266 2.1 23.9 1.0
O B:HOH9392 2.3 30.2 1.0
OE2 B:GLU369 3.8 21.9 1.0
OE1 B:GLU369 4.1 26.7 1.0
O B:HOH9370 4.1 24.4 1.0
O B:HOH9428 4.2 23.0 1.0
O B:HOH9380 4.3 24.0 1.0
O B:HOH9268 4.3 30.1 1.0
CD B:GLU369 4.4 23.4 1.0
O B:HOH9382 4.4 29.6 1.0

Magnesium binding site 6 out of 9 in 1jyx

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Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:17.3
occ:1.00
O C:HOH8604 2.0 14.4 1.0
OE1 C:GLU461 2.0 15.2 1.0
OE2 C:GLU416 2.1 12.7 1.0
O C:HOH8540 2.1 13.1 1.0
ND1 C:HIS418 2.2 12.4 1.0
O C:HOH8680 2.2 15.7 1.0
CE1 C:HIS418 3.0 13.7 1.0
CD C:GLU461 3.1 18.4 1.0
CD C:GLU416 3.2 14.8 1.0
CG C:HIS418 3.3 15.2 1.0
OE1 C:GLU416 3.6 13.8 1.0
CB C:HIS418 3.7 12.8 1.0
OE2 C:GLU461 3.9 18.7 1.0
CB C:GLU461 4.0 11.9 1.0
CG C:GLU461 4.1 12.1 1.0
ND2 C:ASN102 4.2 11.7 1.0
CB C:ASP201 4.2 10.6 1.0
O C:HOH8528 4.2 14.4 1.0
N C:ASP201 4.2 13.6 1.0
NE2 C:HIS418 4.3 15.5 1.0
ND2 C:ASN460 4.3 12.0 1.0
O C:ASP199 4.3 14.5 1.0
CG C:GLU416 4.4 11.6 1.0
CD2 C:HIS418 4.4 16.7 1.0
O C:HOH8818 4.5 25.7 1.0
O4 C:IPT2001 4.5 17.5 1.0
O C:ASN102 4.7 19.5 1.0
C2 C:IPT2001 4.7 16.5 1.0
CA C:ASP201 4.8 14.1 1.0
O3 C:IPT2001 4.8 16.7 1.0
CA C:GLN200 4.9 10.7 1.0
C C:GLN200 4.9 17.7 1.0

Magnesium binding site 7 out of 9 in 1jyx

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Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:17.4
occ:1.00
OE1 C:GLN163 2.2 15.4 1.0
OD2 C:ASP193 2.2 19.0 1.0
O C:VAL21 2.2 25.0 1.0
O C:ASP15 2.4 21.6 1.0
O C:ASN18 2.4 22.9 1.0
OD1 C:ASP193 2.8 17.2 1.0
CG C:ASP193 2.9 18.1 1.0
CD C:GLN163 3.1 25.3 1.0
C C:ASN18 3.3 23.8 1.0
NE2 C:GLN163 3.4 17.3 1.0
C C:VAL21 3.4 22.4 1.0
C C:ASP15 3.6 26.7 1.0
N C:ASN18 3.7 23.1 1.0
OH C:TYR161 3.9 17.3 1.0
CA C:TRP16 4.0 14.0 1.0
CA C:ASN18 4.1 22.1 1.0
CA C:VAL21 4.2 18.5 1.0
N C:PRO19 4.2 16.8 1.0
C C:TRP16 4.3 19.8 1.0
N C:TRP16 4.3 19.4 1.0
N C:VAL21 4.3 19.5 1.0
CE2 C:TYR161 4.4 14.8 1.0
CB C:ASP193 4.4 18.2 1.0
CB C:VAL21 4.4 25.0 1.0
CG C:GLN163 4.4 19.2 1.0
CA C:PRO19 4.4 29.0 1.0
N C:THR22 4.4 18.3 1.0
CB C:ASN18 4.5 21.7 1.0
N C:GLU17 4.5 17.3 1.0
CA C:THR22 4.6 15.2 1.0
CZ C:TYR161 4.6 17.7 1.0
CA C:ASP15 4.7 19.5 1.0
O C:TRP16 4.7 20.4 1.0
CG1 C:VAL21 4.8 22.3 1.0
C C:GLU17 4.9 23.0 1.0
C C:PRO19 4.9 34.2 1.0

Magnesium binding site 8 out of 9 in 1jyx

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Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:17.9
occ:1.00
OE1 D:GLU461 2.0 17.8 1.0
O D:HOH8813 2.1 14.8 1.0
OE2 D:GLU416 2.1 17.0 1.0
ND1 D:HIS418 2.1 20.2 1.0
O D:HOH8889 2.2 16.2 1.0
O D:HOH8749 2.2 18.2 1.0
CE1 D:HIS418 3.0 24.3 1.0
CD D:GLU461 3.0 23.9 1.0
CD D:GLU416 3.1 21.0 1.0
CG D:HIS418 3.2 17.9 1.0
OE1 D:GLU416 3.6 16.6 1.0
CB D:HIS418 3.6 15.3 1.0
OE2 D:GLU461 3.8 25.1 1.0
CB D:GLU461 4.0 13.2 1.0
O D:HOH8736 4.1 17.6 1.0
CG D:GLU461 4.1 15.9 1.0
CB D:ASP201 4.1 17.7 1.0
ND2 D:ASN102 4.1 14.0 1.0
NE2 D:HIS418 4.1 22.7 1.0
N D:ASP201 4.2 16.8 1.0
ND2 D:ASN460 4.3 16.3 1.0
O D:ASP199 4.3 20.5 1.0
CD2 D:HIS418 4.4 18.0 1.0
CG D:GLU416 4.4 14.9 1.0
O4 D:IPT2001 4.4 20.9 1.0
CA D:ASP201 4.7 14.8 1.0
O D:ASN102 4.7 23.6 1.0
C2 D:IPT2001 4.7 17.1 1.0
O D:HOH9022 4.8 32.2 1.0
O3 D:IPT2001 4.9 23.2 1.0
CA D:GLN200 4.9 16.7 1.0
C D:GLN200 4.9 17.3 1.0

Magnesium binding site 9 out of 9 in 1jyx

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Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase 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 in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:23.8
occ:1.00
O D:ASN18 2.1 26.8 1.0
O D:VAL21 2.2 22.7 1.0
OE1 D:GLN163 2.3 27.4 1.0
O D:ASP15 2.4 26.3 1.0
OD2 D:ASP193 2.4 23.7 1.0
OD1 D:ASP193 2.9 22.0 1.0
CG D:ASP193 3.0 30.9 1.0
C D:ASN18 3.1 22.3 1.0
CD D:GLN163 3.2 26.4 1.0
C D:VAL21 3.4 21.6 1.0
NE2 D:GLN163 3.5 23.8 1.0
C D:ASP15 3.5 25.9 1.0
N D:ASN18 3.7 17.7 1.0
CA D:ASN18 3.9 20.1 1.0
N D:PRO19 4.1 23.0 1.0
OH D:TYR161 4.1 22.8 1.0
CA D:VAL21 4.1 19.9 1.0
CA D:TRP16 4.1 28.0 1.0
N D:VAL21 4.1 21.5 1.0
CB D:ASN18 4.2 19.2 1.0
CB D:VAL21 4.2 29.6 1.0
N D:TRP16 4.2 22.7 1.0
CA D:PRO19 4.3 29.8 1.0
C D:TRP16 4.4 31.9 1.0
N D:THR22 4.4 24.0 1.0
CE2 D:TYR161 4.4 25.5 1.0
CB D:ASP193 4.5 18.8 1.0
N D:GLU17 4.5 27.9 1.0
CG D:GLN163 4.6 21.8 1.0
CG1 D:VAL21 4.6 30.4 1.0
CA D:THR22 4.6 19.8 1.0
CA D:ASP15 4.7 28.6 1.0
C D:PRO19 4.7 26.0 1.0
CZ D:TYR161 4.8 20.4 1.0
C D:GLU17 4.9 19.0 1.0
O D:TRP16 4.9 22.3 1.0
N D:GLY20 4.9 28.3 1.0
CG D:ASN18 5.0 29.4 1.0

Reference:

D.H.Juers, T.D.Heightman, A.Vasella, J.D.Mccarter, L.Mackenzie, S.G.Withers, B.W.Matthews. A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Biochemistry V. 40 14781 2001.
ISSN: ISSN 0006-2960
PubMed: 11732897
DOI: 10.1021/BI011727I
Page generated: Mon Dec 14 06:12:06 2020

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