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Magnesium in PDB 1f4h: E. Coli (Lacz) Beta-Galactosidase (Orthorhombic)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (Orthorhombic)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (Orthorhombic):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (Orthorhombic), PDB code: 1f4h 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) 25.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 153.400, 173.400, 204.400, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (Orthorhombic) (pdb code 1f4h). 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 (Orthorhombic), PDB code: 1f4h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1f4h

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:28.1
occ:1.00
 OE2 A:GLU461 2.3 47.9 1.0
O A:HOH4008 2.4 27.9 1.0
ND1 A:HIS418 2.5 29.6 1.0
OE1 A:GLU416 2.6 5.9 1.0
ND2 A:ASN102 3.1 31.8 1.0
CE1 A:HIS418 3.4 26.0 1.0
CD A:GLU461 3.4 42.9 1.0
CG A:HIS418 3.5 25.2 1.0
CD A:GLU416 3.7 24.1 1.0
CB A:HIS418 3.8 17.1 1.0
CB A:ASP201 3.9 41.7 1.0
OE1 A:GLU461 3.9 11.8 1.0
O A:ASN102 3.9 37.1 1.0
N A:ASP201 3.9 18.4 1.0
OE2 A:GLU416 4.2 14.8 1.0
O A:ASP199 4.3 5.8 1.0
CA A:ASP201 4.3 30.1 1.0
C A:ASN102 4.4 33.8 1.0
O A:HOH4001 4.4 33.4 1.0
CG A:ASN102 4.5 71.2 1.0
CG A:GLU461 4.6 16.9 1.0
NE2 A:HIS418 4.6 26.3 1.0
CD2 A:HIS418 4.7 31.2 1.0
N A:VAL103 4.7 19.2 1.0
CA A:VAL103 4.7 16.5 1.0
C A:GLN200 4.7 23.6 1.0
CG2 A:VAL103 4.8 13.5 1.0
CG A:GLU416 4.9 20.4 1.0
CA A:GLN200 4.9 18.4 1.0
CG A:ASP201 5.0 59.8 1.0

Magnesium binding site 2 out of 8 in 1f4h

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:31.4
occ:1.00
 O A:VAL21 2.1 29.4 1.0
NE2 A:GLN163 2.2 1.0 1.0
O A:ASN18 2.3 20.8 1.0
O A:ASP15 2.3 27.9 1.0
OD2 A:ASP193 2.3 5.0 1.0
CD A:GLN163 3.1 27.3 1.0
C A:ASN18 3.1 23.2 1.0
CG A:ASP193 3.1 25.2 1.0
OD1 A:ASP193 3.1 9.3 1.0
OE1 A:GLN163 3.3 27.3 1.0
C A:VAL21 3.3 16.2 1.0
C A:ASP15 3.5 21.8 1.0
N A:ASN18 3.7 18.2 1.0
CA A:ASN18 3.7 13.2 1.0
CB A:VAL21 3.9 18.9 1.0
CA A:VAL21 3.9 15.9 1.0
N A:VAL21 3.9 23.1 1.0
N A:PRO19 4.1 20.0 1.0
CB A:ASN18 4.1 9.8 1.0
CE2 A:TYR161 4.2 16.2 1.0
OH A:TYR161 4.2 30.9 1.0
CA A:TRP16 4.3 24.7 1.0
N A:THR22 4.3 6.6 1.0
CG1 A:VAL21 4.3 15.3 1.0
N A:TRP16 4.3 19.3 1.0
CG A:GLN163 4.4 17.7 1.0
C A:TRP16 4.5 20.2 1.0
CA A:PRO19 4.5 16.6 1.0
CA A:ASP15 4.5 28.6 1.0
CB A:ASP193 4.5 5.3 1.0
CA A:THR22 4.6 10.4 1.0
N A:GLU17 4.6 4.4 1.0
CZ A:TYR161 4.7 22.4 1.0
C A:PRO19 4.7 19.7 1.0
CB A:ASP15 4.8 37.6 1.0
CG A:ASN18 4.8 46.5 1.0
N A:GLY20 4.9 8.2 1.0
O A:TRP16 5.0 28.8 1.0
C A:GLU17 5.0 29.0 1.0

Magnesium binding site 3 out of 8 in 1f4h

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:20.7
occ:1.00
 O B:HOH4014 2.0 7.1 1.0
O B:HOH4156 2.2 21.6 1.0
ND1 B:HIS418 2.3 31.7 1.0
OE2 B:GLU461 2.5 44.7 1.0
CE1 B:HIS418 2.6 27.3 1.0
ND2 B:ASN102 2.8 52.8 1.0
OE1 B:GLU416 3.0 1.0 1.0
CD B:GLU461 3.2 26.2 1.0
OE1 B:GLU461 3.3 28.9 1.0
O B:HOH4568 3.3 23.6 1.0
O B:HOH4001 3.5 41.5 1.0
CG B:HIS418 3.6 33.7 1.0
O B:HOH4298 3.6 45.2 1.0
CB B:ASP201 3.8 26.4 1.0
NE2 B:HIS418 3.9 24.1 1.0
CG B:ASN102 4.0 39.8 1.0
CG2 B:VAL103 4.1 32.3 1.0
CD B:GLU416 4.1 54.2 1.0
N B:ASP201 4.3 20.0 1.0
OD1 B:ASN102 4.4 51.5 1.0
CD2 B:HIS418 4.4 29.5 1.0
CB B:HIS418 4.4 31.4 1.0
CA B:ASP201 4.6 21.9 1.0
CG B:GLU461 4.6 1.0 1.0
OE2 B:GLU416 4.6 1.0 1.0
O B:ASN102 4.7 27.4 1.0
CG B:ASP201 4.9 56.5 1.0
C B:ASN102 4.9 37.5 1.0
CB B:GLU461 5.0 18.4 1.0
O B:ASP199 5.0 24.3 1.0

Magnesium binding site 4 out of 8 in 1f4h

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:36.5
occ:1.00
 O B:ASN18 2.0 31.4 1.0
O B:VAL21 2.1 41.8 1.0
OD2 B:ASP193 2.2 8.5 1.0
O B:ASP15 2.4 39.0 1.0
NE2 B:GLN163 2.6 79.7 1.0
C B:ASN18 2.9 24.5 1.0
CG B:ASP193 3.0 37.1 1.0
OE1 B:GLN163 3.1 44.0 1.0
OD1 B:ASP193 3.1 42.7 1.0
CD B:GLN163 3.1 35.3 1.0
C B:VAL21 3.3 38.3 1.0
N B:PRO19 3.6 29.0 1.0
C B:ASP15 3.6 32.8 1.0
N B:ASN18 3.7 16.8 1.0
CA B:PRO19 3.8 25.3 1.0
CA B:ASN18 3.8 12.1 1.0
CA B:VAL21 4.1 20.4 1.0
N B:VAL21 4.1 25.4 1.0
CB B:VAL21 4.2 15.7 1.0
CA B:TRP16 4.3 22.2 1.0
N B:THR22 4.3 27.5 1.0
CB B:ASP193 4.4 11.9 1.0
C B:PRO19 4.4 32.5 1.0
CG1 B:VAL21 4.4 16.4 1.0
N B:TRP16 4.4 14.9 1.0
C B:TRP16 4.4 31.5 1.0
CE2 B:TYR161 4.5 22.3 1.0
CB B:ASN18 4.5 35.1 1.0
CG B:GLN163 4.5 29.9 1.0
CA B:THR22 4.5 24.4 1.0
N B:GLY20 4.5 31.8 1.0
N B:GLU17 4.6 21.2 1.0
CA B:ASP15 4.7 40.0 1.0
OH B:TYR161 4.7 18.9 1.0
C B:GLU17 4.9 33.3 1.0
CG B:ASN18 4.9 48.2 1.0
O B:TRP16 4.9 33.7 1.0
CB B:ASP15 5.0 43.0 1.0
N B:ASP193 5.0 11.4 1.0

Magnesium binding site 5 out of 8 in 1f4h

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Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:15.7
occ:1.00
 O C:HOH4156 2.2 10.2 1.0
ND1 C:HIS418 2.5 32.2 1.0
O C:HOH4014 2.5 6.8 1.0
OE2 C:GLU461 2.6 68.2 1.0
CE1 C:HIS418 2.9 30.5 1.0
CD C:GLU461 2.9 45.2 1.0
OE1 C:GLU461 3.2 16.9 1.0
ND2 C:ASN102 3.3 28.0 1.0
OE1 C:GLU416 3.4 8.0 1.0
O C:HOH4001 3.5 38.0 1.0
O C:HOH4568 3.6 20.2 1.0
O C:HOH7520 3.7 34.1 1.0
CG C:GLU461 3.7 7.5 1.0
CB C:ASP201 3.7 26.9 1.0
CG C:HIS418 3.8 28.8 1.0
NE2 C:HIS418 4.2 30.2 1.0
CD C:GLU416 4.5 29.4 1.0
N C:ASP201 4.5 16.8 1.0
CG C:ASN102 4.5 49.4 1.0
CB C:HIS418 4.5 24.4 1.0
CD2 C:HIS418 4.7 29.8 1.0
CA C:ASP201 4.7 21.8 1.0
CG C:ASP201 4.7 38.8 1.0
ND2 C:ASN460 4.7 17.7 1.0
CG2 C:VAL103 4.8 21.9 1.0
OE2 C:GLU416 4.8 13.7 1.0
OD2 C:ASP201 4.9 63.8 1.0
OD1 C:ASN102 4.9 39.4 1.0
O C:ASN102 4.9 50.1 1.0

Magnesium binding site 6 out of 8 in 1f4h

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:31.8
occ:1.00
 O C:ASN18 2.2 28.1 1.0
OD2 C:ASP193 2.3 11.9 1.0
NE2 C:GLN163 2.4 38.7 1.0
O C:VAL21 2.5 43.7 1.0
O C:ASP15 2.6 45.3 1.0
CD C:GLN163 2.8 19.6 1.0
OE1 C:GLN163 2.9 35.9 1.0
CG C:ASP193 3.2 29.3 1.0
C C:ASN18 3.3 27.9 1.0
C C:VAL21 3.3 34.9 1.0
OD1 C:ASP193 3.4 46.9 1.0
C C:ASP15 3.7 39.0 1.0
N C:ASN18 3.9 22.9 1.0
CG C:GLN163 4.0 5.0 1.0
CA C:ASN18 4.1 19.6 1.0
CA C:VAL21 4.1 13.3 1.0
N C:THR22 4.1 35.5 1.0
OH C:TYR161 4.1 34.2 1.0
N C:VAL21 4.2 21.5 1.0
CE2 C:TYR161 4.2 12.0 1.0
N C:PRO19 4.2 30.4 1.0
CA C:PRO19 4.3 30.5 1.0
CA C:THR22 4.3 25.9 1.0
CA C:TRP16 4.3 25.2 1.0
CB C:VAL21 4.4 13.9 1.0
N C:TRP16 4.5 33.3 1.0
CB C:ASN18 4.5 17.8 1.0
CB C:ASP193 4.6 18.6 1.0
C C:TRP16 4.6 35.8 1.0
CZ C:TYR161 4.6 15.0 1.0
N C:GLU17 4.7 25.7 1.0
CA C:ASP15 4.8 30.9 1.0
C C:PRO19 4.8 46.0 1.0
CG1 C:VAL21 4.9 13.1 1.0
N C:GLY20 5.0 42.3 1.0

Magnesium binding site 7 out of 8 in 1f4h

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Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:40.2
occ:1.00
 OE2 D:GLU461 1.6 64.4 1.0
O D:HOH4014 2.0 28.9 1.0
O D:HOH4156 2.0 35.5 1.0
OE1 D:GLU416 2.8 9.2 1.0
ND1 D:HIS418 2.8 26.8 1.0
CD D:GLU461 2.9 46.4 1.0
CE1 D:HIS418 3.3 23.6 1.0
ND2 D:ASN102 3.6 34.2 1.0
OE1 D:GLU461 3.6 18.4 1.0
CD D:GLU416 3.7 20.4 1.0
CG D:GLU461 3.8 25.6 1.0
OE2 D:GLU416 3.9 1.0 1.0
O D:HOH4298 3.9 26.8 1.0
CB D:ASP201 3.9 35.2 1.0
CG D:HIS418 4.0 24.5 1.0
N D:ASP201 4.1 24.9 1.0
ND2 D:ASN460 4.3 37.2 1.0
O D:HOH4568 4.3 48.9 1.0
O D:ASN102 4.6 58.9 1.0
CA D:ASP201 4.6 28.9 1.0
CB D:HIS418 4.6 17.8 1.0
NE2 D:HIS418 4.6 22.6 1.0
O D:ASP199 4.8 17.5 1.0
CG D:ASN102 4.9 40.2 1.0
CB D:GLU461 4.9 11.8 1.0
CD2 D:HIS418 5.0 25.1 1.0

Magnesium binding site 8 out of 8 in 1f4h

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Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (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 (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:25.4
occ:1.00
 OD2 D:ASP193 2.0 2.7 1.0
O D:ASN18 2.1 25.1 1.0
NE2 D:GLN163 2.2 1.0 1.0
O D:VAL21 2.5 6.0 1.0
O D:ASP15 2.6 28.2 1.0
CG D:ASP193 2.8 18.6 1.0
C D:ASN18 2.8 25.6 1.0
OD1 D:ASP193 2.9 26.0 1.0
CD D:GLN163 3.0 23.9 1.0
OE1 D:GLN163 3.0 20.5 1.0
N D:PRO19 3.6 14.5 1.0
N D:ASN18 3.6 21.9 1.0
C D:VAL21 3.7 10.5 1.0
CA D:ASN18 3.7 18.2 1.0
C D:ASP15 3.8 23.4 1.0
CA D:PRO19 3.9 5.5 1.0
CB D:ASP193 4.1 6.8 1.0
OH D:TYR161 4.2 17.3 1.0
CA D:TRP16 4.2 24.1 1.0
C D:TRP16 4.4 16.6 1.0
N D:GLU17 4.4 12.5 1.0
N D:TRP16 4.4 23.6 1.0
O D:HOH4147 4.4 26.7 1.0
CG D:GLN163 4.4 16.1 1.0
CB D:ASN18 4.5 3.4 1.0
N D:THR22 4.5 1.5 1.0
CA D:THR22 4.5 3.8 1.0
C D:PRO19 4.6 21.4 1.0
CE2 D:TYR161 4.7 14.8 1.0
CA D:VAL21 4.8 9.1 1.0
N D:GLY20 4.8 21.9 1.0
N D:VAL21 4.8 12.7 1.0
C D:GLU17 4.8 27.8 1.0
CB D:VAL21 4.8 13.0 1.0
N D:ASP193 4.9 17.6 1.0
CD D:PRO19 4.9 11.0 1.0
CG D:ASN18 4.9 39.8 1.0
CG2 D:THR22 4.9 20.0 1.0
CZ D:TYR161 4.9 1.0 1.0
CA D:ASP15 5.0 15.6 1.0
CA D:ASP193 5.0 8.3 1.0
N D:GLY194 5.0 6.2 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 03:07:05 2024

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