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Magnesium in PDB 1jz2: E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic), PDB code: 1jz2 was solved by D.H.Juers, J.D.Mccarter, L.Mackenzie, S.G.Withers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.60 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.500, 167.700, 201.600, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 27

Other elements in 1jz2:

The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Sodium (Na) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) (pdb code 1jz2). 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 (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic), PDB code: 1jz2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1jz2

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:26.8
occ:1.00
 OE2 A:GLU416 2.0 18.5 1.0
OE1 A:GLU461 2.1 22.0 1.0
ND1 A:HIS418 2.2 25.3 1.0
O A:HOH8517 2.2 14.0 1.0
O A:HOH8656 2.2 23.0 1.0
O A:HOH8580 2.3 15.9 1.0
CE1 A:HIS418 3.0 21.2 1.0
CD A:GLU416 3.1 19.8 1.0
CD A:GLU461 3.2 33.0 1.0
CG A:HIS418 3.3 25.3 1.0
OE1 A:GLU416 3.4 13.2 1.0
CB A:HIS418 3.8 19.5 1.0
ND2 A:ASN460 4.0 21.2 1.0
N A:ASP201 4.0 23.7 1.0
OE2 A:GLU461 4.0 15.7 1.0
CB A:GLU461 4.0 17.3 1.0
OD1 A:ASN102 4.1 19.1 1.0
CB A:ASP201 4.1 18.4 1.0
O A:ASP199 4.1 19.6 1.0
CG A:GLU461 4.1 17.9 1.0
NE2 A:HIS418 4.2 21.6 1.0
O4 A:2FG2001 4.2 14.7 1.0
O3 A:2FG2001 4.2 29.4 1.0
CG A:GLU416 4.3 14.2 1.0
CD2 A:HIS418 4.4 23.8 1.0
C2 A:2FG2001 4.6 26.8 1.0
CA A:ASP201 4.6 22.8 1.0
O A:ASN102 4.7 18.6 1.0
C A:GLN200 4.7 22.1 1.0
O A:HOH8975 4.7 23.0 1.0
CA A:GLN200 4.8 15.1 1.0
F2 A:2FG2001 4.9 28.6 1.0
C3 A:2FG2001 4.9 23.0 1.0

Magnesium binding site 2 out of 8 in 1jz2

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:27.5
occ:1.00
 OE1 A:GLN163 2.1 24.6 1.0
O A:ASN18 2.2 29.8 1.0
O A:VAL21 2.2 18.1 1.0
OD2 A:ASP193 2.3 22.7 1.0
O A:ASP15 2.3 26.8 1.0
OD1 A:ASP193 2.9 25.1 1.0
CG A:ASP193 2.9 28.7 1.0
CD A:GLN163 3.0 34.9 1.0
C A:ASN18 3.0 22.4 1.0
NE2 A:GLN163 3.3 26.3 1.0
C A:VAL21 3.4 20.4 1.0
C A:ASP15 3.5 26.4 1.0
N A:ASN18 3.6 30.4 1.0
CA A:ASN18 3.8 27.3 1.0
OH A:TYR161 3.8 24.9 1.0
N A:PRO19 3.9 22.4 1.0
CA A:TRP16 4.1 27.2 1.0
N A:TRP16 4.2 25.4 1.0
CA A:VAL21 4.2 18.2 1.0
N A:VAL21 4.2 27.0 1.0
CA A:PRO19 4.2 23.0 1.0
CE2 A:TYR161 4.3 26.4 1.0
CB A:VAL21 4.3 27.5 1.0
CB A:ASN18 4.3 20.3 1.0
CG A:GLN163 4.3 15.6 1.0
C A:TRP16 4.3 27.9 1.0
N A:GLU17 4.4 28.9 1.0
N A:THR22 4.4 20.6 1.0
CB A:ASP193 4.4 15.1 1.0
CA A:THR22 4.4 14.3 1.0
CZ A:TYR161 4.5 37.6 1.0
CA A:ASP15 4.6 25.7 1.0
C A:GLU17 4.8 36.7 1.0
CG1 A:VAL21 4.8 26.8 1.0
C A:PRO19 4.8 28.5 1.0
CG2 A:THR22 4.8 19.1 1.0
O A:TRP16 5.0 24.5 1.0

Magnesium binding site 3 out of 8 in 1jz2

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:21.4
occ:1.00
 O B:HOH8599 1.8 13.8 1.0
OE1 B:GLU461 1.9 31.0 1.0
OE2 B:GLU416 2.0 22.6 1.0
O B:HOH8674 2.1 20.8 1.0
ND1 B:HIS418 2.2 19.0 1.0
O B:HOH8535 2.4 16.0 1.0
CD B:GLU461 2.9 14.7 1.0
CE1 B:HIS418 3.1 18.7 1.0
CD B:GLU416 3.2 30.6 1.0
CG B:HIS418 3.3 18.3 1.0
CB B:HIS418 3.7 19.3 1.0
OE1 B:GLU416 3.7 14.9 1.0
OE2 B:GLU461 3.7 16.4 1.0
O4 B:2FG2001 3.9 28.0 1.0
CG B:GLU461 4.0 17.4 1.0
OD1 B:ASN102 4.0 18.9 1.0
CB B:GLU461 4.1 11.2 1.0
CB B:ASP201 4.1 13.9 1.0
ND2 B:ASN460 4.2 17.8 1.0
NE2 B:HIS418 4.2 18.0 1.0
CD2 B:HIS418 4.4 16.8 1.0
N B:ASP201 4.4 23.2 1.0
O B:ASP199 4.4 13.5 1.0
CG B:GLU416 4.4 26.2 1.0
O3 B:2FG2001 4.4 17.6 1.0
O6 B:BTB2002 4.5 21.5 1.0
C2 B:2FG2001 4.5 21.2 1.0
F2 B:2FG2001 4.7 29.8 1.0
O B:ASN102 4.8 19.8 1.0
CA B:ASP201 4.8 20.3 1.0
C3 B:2FG2001 4.9 24.6 1.0
CG2 B:VAL103 5.0 17.1 1.0

Magnesium binding site 4 out of 8 in 1jz2

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:27.6
occ:1.00
 O B:VAL21 2.1 25.1 1.0
O B:ASP15 2.2 24.4 1.0
OE1 B:GLN163 2.3 17.6 1.0
O B:ASN18 2.3 23.5 1.0
OD2 B:ASP193 2.4 22.6 1.0
C B:ASN18 3.1 23.0 1.0
CG B:ASP193 3.2 33.3 1.0
OD1 B:ASP193 3.2 27.6 1.0
C B:VAL21 3.2 24.8 1.0
CD B:GLN163 3.3 39.6 1.0
C B:ASP15 3.4 28.2 1.0
N B:ASN18 3.6 32.7 1.0
NE2 B:GLN163 3.7 21.1 1.0
CA B:ASN18 3.8 19.7 1.0
CA B:TRP16 4.0 23.0 1.0
OH B:TYR161 4.0 32.2 1.0
CA B:VAL21 4.0 32.5 1.0
N B:PRO19 4.0 26.7 1.0
N B:TRP16 4.1 23.6 1.0
C B:TRP16 4.1 31.4 1.0
CB B:VAL21 4.2 39.7 1.0
CB B:ASN18 4.2 22.2 1.0
N B:VAL21 4.2 22.9 1.0
N B:THR22 4.3 29.6 1.0
N B:GLU17 4.3 30.0 1.0
CE2 B:TYR161 4.4 15.3 1.0
CA B:PRO19 4.5 26.0 1.0
CA B:ASP15 4.5 25.9 1.0
CG B:GLN163 4.5 20.2 1.0
CG1 B:VAL21 4.6 38.5 1.0
CA B:THR22 4.6 28.4 1.0
CB B:ASP193 4.6 25.9 1.0
CZ B:TYR161 4.7 47.8 1.0
O B:TRP16 4.7 22.9 1.0
C B:GLU17 4.8 34.0 1.0
C B:PRO19 4.9 37.9 1.0
CB B:ASP15 5.0 18.0 1.0

Magnesium binding site 5 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:23.0
occ:1.00
 O C:HOH8592 2.0 19.2 1.0
O C:HOH8670 2.0 18.2 1.0
OE2 C:GLU416 2.1 25.2 1.0
O C:HOH8528 2.1 14.3 1.0
OE1 C:GLU461 2.1 15.9 1.0
ND1 C:HIS418 2.3 23.3 1.0
CD C:GLU416 3.1 50.1 1.0
CD C:GLU461 3.2 26.1 1.0
CE1 C:HIS418 3.3 17.6 1.0
CG C:HIS418 3.4 20.0 1.0
OE1 C:GLU416 3.5 22.8 1.0
CB C:HIS418 3.7 15.4 1.0
OD1 C:ASN102 4.0 23.1 1.0
OE2 C:GLU461 4.0 20.2 1.0
CB C:ASP201 4.0 32.3 1.0
N C:ASP201 4.1 32.8 1.0
O C:ASP199 4.1 22.8 1.0
CG C:GLU461 4.2 18.7 1.0
CB C:GLU461 4.2 17.1 1.0
O4 C:2FG2001 4.2 19.7 1.0
ND2 C:ASN460 4.2 16.3 1.0
O3 C:2FG2001 4.3 20.9 1.0
CG C:GLU416 4.4 11.0 1.0
NE2 C:HIS418 4.5 19.1 1.0
CD2 C:HIS418 4.5 21.4 1.0
O C:ASN102 4.5 25.5 1.0
C2 C:2FG2001 4.6 24.1 1.0
CA C:ASP201 4.7 29.0 1.0
F2 C:2FG2001 4.8 24.7 1.0
CA C:GLN200 4.8 20.0 1.0
C C:GLN200 4.9 31.7 1.0
CG2 C:VAL103 4.9 23.8 1.0
C3 C:2FG2001 5.0 22.2 1.0
O C:HOH8983 5.0 19.6 1.0

Magnesium binding site 6 out of 8 in 1jz2

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:26.3
occ:1.00
 O C:ASN18 2.2 23.9 1.0
O C:VAL21 2.2 15.8 1.0
OE1 C:GLN163 2.2 23.0 1.0
OD2 C:ASP193 2.4 25.4 1.0
O C:ASP15 2.5 39.0 1.0
C C:ASN18 3.1 32.1 1.0
OD1 C:ASP193 3.1 28.2 1.0
CG C:ASP193 3.1 26.0 1.0
CD C:GLN163 3.2 33.6 1.0
C C:VAL21 3.4 29.6 1.0
NE2 C:GLN163 3.5 15.6 1.0
C C:ASP15 3.6 40.8 1.0
N C:ASN18 3.7 24.4 1.0
CA C:ASN18 3.9 26.8 1.0
N C:PRO19 4.0 34.0 1.0
OH C:TYR161 4.1 24.8 1.0
CA C:VAL21 4.2 30.1 1.0
N C:VAL21 4.2 28.2 1.0
CA C:TRP16 4.2 27.5 1.0
CB C:VAL21 4.2 37.8 1.0
C C:TRP16 4.3 30.2 1.0
CB C:ASN18 4.3 15.7 1.0
CA C:PRO19 4.3 32.1 1.0
CE2 C:TYR161 4.3 14.4 1.0
N C:TRP16 4.4 26.7 1.0
N C:THR22 4.4 24.2 1.0
CG C:GLN163 4.4 23.5 1.0
CA C:THR22 4.5 24.6 1.0
N C:GLU17 4.5 20.1 1.0
CB C:ASP193 4.6 19.5 1.0
CA C:ASP15 4.7 29.8 1.0
O C:TRP16 4.7 28.2 1.0
CZ C:TYR161 4.7 28.2 1.0
C C:PRO19 4.8 42.2 1.0
CG1 C:VAL21 4.8 33.1 1.0
C C:GLU17 4.8 35.9 1.0
CB C:ASP15 4.9 37.4 1.0

Magnesium binding site 7 out of 8 in 1jz2

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Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:19.9
occ:1.00
 O D:HOH8546 2.0 15.9 1.0
O D:HOH8685 2.0 19.6 1.0
OE1 D:GLU461 2.1 17.7 1.0
OE2 D:GLU416 2.1 19.0 1.0
O D:HOH8610 2.2 16.7 1.0
ND1 D:HIS418 2.2 18.6 1.0
CE1 D:HIS418 3.0 18.0 1.0
CD D:GLU461 3.2 22.8 1.0
CD D:GLU416 3.2 37.2 1.0
CG D:HIS418 3.3 21.8 1.0
OE1 D:GLU416 3.5 21.7 1.0
CB D:HIS418 3.7 16.9 1.0
CB D:GLU461 4.0 12.2 1.0
OE2 D:GLU461 4.0 15.5 1.0
OD1 D:ASN102 4.1 25.8 1.0
ND2 D:ASN460 4.1 13.5 1.0
CG D:GLU461 4.1 15.6 1.0
N D:ASP201 4.2 24.1 1.0
CB D:ASP201 4.2 22.9 1.0
NE2 D:HIS418 4.2 16.9 1.0
O4 D:2FG2001 4.2 18.5 1.0
O3 D:2FG2001 4.3 23.8 1.0
O D:ASP199 4.3 23.4 1.0
CD2 D:HIS418 4.3 20.2 1.0
CG D:GLU416 4.4 13.9 1.0
C2 D:2FG2001 4.5 23.8 1.0
CA D:ASP201 4.7 25.7 1.0
O D:ASN102 4.8 22.7 1.0
O D:HOH9001 4.8 16.5 1.0
C3 D:2FG2001 4.8 24.3 1.0
CA D:GLN200 4.9 15.6 1.0
F2 D:2FG2001 4.9 22.4 1.0
C D:GLN200 4.9 23.6 1.0

Magnesium binding site 8 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:26.6
occ:1.00
 O D:ASN18 2.1 20.5 1.0
O D:VAL21 2.3 20.5 1.0
OD2 D:ASP193 2.3 15.1 1.0
OE1 D:GLN163 2.3 34.2 1.0
O D:ASP15 2.5 29.3 1.0
OD1 D:ASP193 2.8 15.3 1.0
CG D:ASP193 2.9 29.2 1.0
C D:ASN18 3.0 25.5 1.0
CD D:GLN163 3.2 28.3 1.0
C D:VAL21 3.4 24.4 1.0
NE2 D:GLN163 3.4 21.6 1.0
N D:ASN18 3.6 30.6 1.0
C D:ASP15 3.7 27.5 1.0
CA D:ASN18 3.8 27.4 1.0
N D:PRO19 3.9 25.5 1.0
CA D:PRO19 4.0 34.0 1.0
N D:VAL21 4.1 16.6 1.0
CA D:VAL21 4.1 13.7 1.0
OH D:TYR161 4.2 30.1 1.0
CA D:TRP16 4.2 22.4 1.0
CB D:VAL21 4.3 18.6 1.0
CB D:ASN18 4.3 21.9 1.0
CB D:ASP193 4.4 18.4 1.0
N D:THR22 4.4 20.5 1.0
C D:TRP16 4.4 22.7 1.0
N D:TRP16 4.4 23.0 1.0
CA D:THR22 4.4 23.9 1.0
CG D:GLN163 4.5 20.6 1.0
N D:GLU17 4.5 25.0 1.0
C D:PRO19 4.5 31.0 1.0
CE2 D:TYR161 4.6 30.6 1.0
CA D:ASP15 4.8 29.7 1.0
CG1 D:VAL21 4.8 17.3 1.0
N D:GLY20 4.8 22.1 1.0
C D:GLU17 4.8 35.6 1.0
O D:TRP16 4.8 26.1 1.0
CG2 D:THR22 4.8 19.6 1.0
CZ D:TYR161 4.9 49.9 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 06:12:09 2020

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