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Magnesium in PDB 3dym: E. Coli (Lacz) Beta-Galactosidase (H418E)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (H418E)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (H418E):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (H418E), PDB code: 3dym was solved by D.H.Juers, R.E.Huber, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.50 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.340, 167.160, 200.350, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3dym:

The structure of E. Coli (Lacz) Beta-Galactosidase (H418E) also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (H418E) (pdb code 3dym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (H418E), PDB code: 3dym:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3dym

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Magnesium binding site 1 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:30.8
occ:1.00
 O A:HOH4153 2.1 20.2 1.0
OE2 A:GLU418 2.1 24.4 1.0
O A:HOH4014 2.1 32.8 1.0
OE2 A:GLU416 2.1 25.1 1.0
O A:HOH4077 2.2 14.7 1.0
OE1 A:GLU461 2.3 29.8 1.0
CD A:GLU416 3.2 29.5 1.0
CD A:GLU418 3.2 57.0 1.0
CD A:GLU461 3.3 67.4 1.0
OE1 A:GLU416 3.6 17.1 1.0
CB A:GLU418 4.0 23.9 1.0
O A:HOH4816 4.0 36.5 1.0
OE2 A:GLU461 4.0 29.5 1.0
OE1 A:GLU418 4.0 30.5 1.0
OD1 A:ASN102 4.1 37.1 1.0
CG A:GLU418 4.1 34.3 1.0
CB A:GLU461 4.2 12.3 1.0
N A:ASP201 4.2 23.6 1.0
CB A:ASP201 4.2 22.6 1.0
O A:ASP199 4.2 21.1 1.0
O A:HOH4290 4.3 45.0 1.0
CG A:GLU461 4.3 13.0 1.0
ND2 A:ASN460 4.3 15.4 1.0
O A:HOH4001 4.4 48.7 1.0
CG A:GLU416 4.4 13.4 1.0
O A:HOH4279 4.5 48.1 1.0
O A:ASN102 4.6 28.6 1.0
CG2 A:VAL103 4.6 30.2 1.0
CA A:ASP201 4.7 16.8 1.0
CA A:GLN200 4.9 18.5 1.0
C A:GLN200 4.9 18.5 1.0

Magnesium binding site 2 out of 10 in 3dym

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Magnesium binding site 2 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:23.3
occ:1.00
 OE1 A:GLN163 2.2 28.5 1.0
O A:ASN18 2.2 25.4 1.0
O A:ASP15 2.3 20.2 1.0
O A:VAL21 2.3 20.8 1.0
OD2 A:ASP193 2.4 30.8 1.0
OD1 A:ASP193 2.8 26.2 1.0
CG A:ASP193 3.0 25.8 1.0
C A:ASN18 3.0 28.0 1.0
CD A:GLN163 3.1 21.8 1.0
C A:VAL21 3.4 20.9 1.0
NE2 A:GLN163 3.4 23.4 1.0
C A:ASP15 3.5 24.4 1.0
N A:ASN18 3.6 34.5 1.0
CA A:ASN18 3.8 25.2 1.0
N A:PRO19 3.9 22.9 1.0
OH A:TYR161 4.0 24.7 1.0
CB A:ASN18 4.0 28.9 1.0
CA A:TRP16 4.0 14.2 1.0
CA A:VAL21 4.1 18.8 1.0
N A:VAL21 4.1 20.5 1.0
CB A:VAL21 4.2 23.0 1.0
C A:TRP16 4.2 21.0 1.0
N A:TRP16 4.2 16.4 1.0
N A:GLU17 4.4 22.3 1.0
CE2 A:TYR161 4.4 22.8 1.0
CA A:PRO19 4.4 22.0 1.0
N A:THR22 4.4 13.2 1.0
CB A:ASP193 4.4 15.2 1.0
CG A:GLN163 4.5 16.3 1.0
CA A:ASP15 4.6 24.6 1.0
CA A:THR22 4.6 22.5 1.0
CZ A:TYR161 4.7 24.7 1.0
C A:PRO19 4.8 22.9 1.0
O A:TRP16 4.8 21.4 1.0
C A:GLU17 4.8 27.9 1.0
CG1 A:VAL21 4.8 17.0 1.0
CB A:ASP15 4.9 20.4 1.0
CG A:ASN18 5.0 31.3 1.0
N A:GLY20 5.0 19.4 1.0

Magnesium binding site 3 out of 10 in 3dym

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Magnesium binding site 3 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:44.4
occ:1.00
 O A:HOH4716 2.3 35.7 1.0
O A:HOH4573 2.5 31.6 1.0
O A:HOH4767 2.7 37.9 1.0
C1 A:DMS8406 3.1 35.8 1.0
O A:HOH4612 4.4 48.0 1.0
S A:DMS8406 4.5 78.1 1.0
O A:DMS8406 4.5 53.6 1.0
OE2 A:GLU314 4.7 32.7 1.0
O A:HOH4790 4.8 24.2 1.0
OE1 A:GLU314 4.8 21.3 1.0

Magnesium binding site 4 out of 10 in 3dym

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Magnesium binding site 4 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3105

b:32.1
occ:1.00
 O A:HOH4698 4.3 42.8 1.0
OE1 A:GLU136 4.3 52.0 1.0
CB A:GLN135 4.9 36.6 1.0

Magnesium binding site 5 out of 10 in 3dym

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Magnesium binding site 5 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:22.0
occ:1.00
 OE2 B:GLU416 2.0 17.4 1.0
OE1 B:GLU461 2.0 28.3 1.0
O B:HOH4027 2.0 19.4 1.0
O B:HOH4168 2.0 21.9 1.0
O B:HOH4091 2.1 19.5 1.0
OE2 B:GLU418 2.1 27.2 1.0
CD B:GLU461 3.0 30.4 1.0
CD B:GLU416 3.1 18.0 1.0
CD B:GLU418 3.4 38.6 1.0
OE1 B:GLU416 3.5 16.2 1.0
O B:HOH4817 3.7 34.4 1.0
OE2 B:GLU461 3.8 27.2 1.0
CB B:GLU418 4.0 18.8 1.0
OD1 B:ASN102 4.0 28.3 1.0
O B:HOH4303 4.0 44.7 1.0
CG B:GLU461 4.1 10.7 1.0
CB B:GLU461 4.2 11.2 1.0
ND2 B:ASN460 4.2 16.1 1.0
CG B:GLU418 4.2 29.5 1.0
CB B:ASP201 4.2 30.4 1.0
O B:ASP199 4.3 19.7 1.0
OE1 B:GLU418 4.3 31.4 1.0
N B:ASP201 4.3 22.0 1.0
CG B:GLU416 4.3 14.6 1.0
O B:HOH4290 4.6 42.2 1.0
O B:ASN102 4.6 29.4 1.0
O B:HOH4530 4.7 48.1 1.0
CA B:ASP201 4.8 26.1 1.0
CG2 B:VAL103 4.8 36.1 1.0

Magnesium binding site 6 out of 10 in 3dym

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Magnesium binding site 6 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:18.2
occ:1.00
 OE1 B:GLN163 2.1 26.4 1.0
OD2 B:ASP193 2.2 22.0 1.0
O B:ASN18 2.2 15.4 1.0
O B:ASP15 2.3 22.5 1.0
O B:VAL21 2.4 18.7 1.0
CG B:ASP193 2.9 17.0 1.0
OD1 B:ASP193 3.0 20.3 1.0
CD B:GLN163 3.1 31.5 1.0
C B:ASN18 3.2 25.1 1.0
C B:ASP15 3.4 28.8 1.0
NE2 B:GLN163 3.5 18.2 1.0
C B:VAL21 3.5 24.2 1.0
N B:ASN18 3.6 28.1 1.0
CA B:ASN18 3.9 27.4 1.0
CA B:TRP16 3.9 16.9 1.0
OH B:TYR161 4.0 19.6 1.0
N B:TRP16 4.1 19.5 1.0
N B:PRO19 4.1 28.4 1.0
C B:TRP16 4.2 24.4 1.0
CA B:VAL21 4.3 27.0 1.0
CB B:ASN18 4.3 21.0 1.0
N B:GLU17 4.3 22.6 1.0
CB B:ASP193 4.3 12.2 1.0
CB B:VAL21 4.4 27.7 1.0
N B:VAL21 4.4 30.3 1.0
CE2 B:TYR161 4.4 20.8 1.0
CA B:PRO19 4.4 37.6 1.0
CG B:GLN163 4.5 16.6 1.0
N B:THR22 4.5 19.6 1.0
CA B:ASP15 4.6 27.6 1.0
CZ B:TYR161 4.6 34.8 1.0
CA B:THR22 4.7 23.8 1.0
C B:GLU17 4.8 33.4 1.0
O B:TRP16 4.8 20.0 1.0
C B:PRO19 4.9 33.9 1.0

Magnesium binding site 7 out of 10 in 3dym

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Magnesium binding site 7 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:20.3
occ:1.00
 O C:HOH4176 2.0 16.5 1.0
OE2 C:GLU418 2.0 25.4 1.0
OE2 C:GLU416 2.1 20.6 1.0
O C:HOH4034 2.1 19.6 1.0
O C:HOH4098 2.2 20.9 1.0
OE1 C:GLU461 2.3 16.3 1.0
CD C:GLU416 3.2 35.9 1.0
CD C:GLU461 3.2 38.3 1.0
CD C:GLU418 3.3 67.9 1.0
OE1 C:GLU416 3.5 14.9 1.0
O C:HOH4794 3.9 36.0 1.0
CB C:GLU418 4.0 18.5 1.0
O C:HOH4021 4.0 40.2 1.0
OE2 C:GLU461 4.0 29.9 1.0
OE1 C:GLU418 4.1 30.6 1.0
N C:ASP201 4.2 33.5 1.0
ND2 C:ASN460 4.2 14.3 1.0
CB C:ASP201 4.2 23.2 1.0
O C:HOH4308 4.2 35.9 1.0
O C:ASP199 4.2 20.6 1.0
CG C:GLU418 4.2 19.1 1.0
CG C:GLU461 4.3 11.5 1.0
OD1 C:ASN102 4.3 30.4 1.0
CB C:GLU461 4.4 8.6 1.0
O C:HOH4295 4.4 45.4 1.0
CG C:GLU416 4.4 16.0 1.0
O C:ASN102 4.5 29.9 1.0
O C:HOH4518 4.6 43.3 1.0
CA C:ASP201 4.7 25.1 1.0
C C:GLN200 4.8 41.8 1.0
CG2 C:VAL103 4.8 30.0 1.0
CA C:GLN200 4.9 17.3 1.0

Magnesium binding site 8 out of 10 in 3dym

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Magnesium binding site 8 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:17.7
occ:1.00
 O C:ASN18 2.2 23.0 1.0
O C:VAL21 2.3 16.6 1.0
OD2 C:ASP193 2.4 22.7 1.0
O C:ASP15 2.4 18.8 1.0
OE1 C:GLN163 2.4 20.4 1.0
OD1 C:ASP193 3.0 18.6 1.0
CG C:ASP193 3.1 23.9 1.0
C C:ASN18 3.1 24.6 1.0
CD C:GLN163 3.3 31.7 1.0
C C:VAL21 3.4 21.4 1.0
C C:ASP15 3.6 22.9 1.0
NE2 C:GLN163 3.6 18.6 1.0
N C:ASN18 3.7 28.0 1.0
CA C:ASN18 4.0 15.2 1.0
OH C:TYR161 4.0 27.4 1.0
N C:PRO19 4.0 22.2 1.0
CA C:TRP16 4.1 17.7 1.0
CA C:VAL21 4.1 23.6 1.0
CB C:VAL21 4.2 26.7 1.0
N C:VAL21 4.2 22.5 1.0
CB C:ASN18 4.3 19.1 1.0
N C:TRP16 4.3 17.5 1.0
C C:TRP16 4.3 26.6 1.0
CA C:PRO19 4.3 25.3 1.0
CE2 C:TYR161 4.4 13.1 1.0
N C:THR22 4.4 15.0 1.0
CA C:THR22 4.5 19.6 1.0
N C:GLU17 4.5 22.1 1.0
CB C:ASP193 4.5 10.8 1.0
CG C:GLN163 4.6 29.1 1.0
CG1 C:VAL21 4.6 23.7 1.0
CA C:ASP15 4.6 26.6 1.0
CZ C:TYR161 4.7 15.0 1.0
C C:PRO19 4.8 25.2 1.0
O C:TRP16 4.8 24.8 1.0
C C:GLU17 4.9 34.3 1.0

Magnesium binding site 9 out of 10 in 3dym

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Magnesium binding site 9 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:26.9
occ:1.00
 O D:HOH4050 1.9 18.0 1.0
O D:HOH4114 2.1 21.5 1.0
O D:HOH4191 2.1 28.1 1.0
OE2 D:GLU418 2.2 26.4 1.0
OE1 D:GLU461 2.2 21.0 1.0
OE2 D:GLU416 2.3 31.4 1.0
CD D:GLU461 3.3 97.0 1.0
CD D:GLU416 3.3 19.7 1.0
CD D:GLU418 3.4 46.2 1.0
OE1 D:GLU416 3.6 19.7 1.0
O D:HOH4037 3.8 40.2 1.0
O D:HOH4550 3.8 66.8 1.0
OE2 D:GLU461 4.0 20.5 1.0
CB D:ASP201 4.0 24.4 1.0
CB D:GLU418 4.1 16.1 1.0
ND2 D:ASN460 4.1 17.4 1.0
N D:ASP201 4.2 26.2 1.0
OD1 D:ASN102 4.2 34.2 1.0
O D:HOH4326 4.2 42.6 1.0
OE1 D:GLU418 4.2 36.4 1.0
CB D:GLU461 4.3 15.3 1.0
CG D:GLU461 4.3 17.3 1.0
CG D:GLU418 4.3 31.7 1.0
O D:ASP199 4.4 20.3 1.0
CG2 D:VAL103 4.4 29.6 1.0
O D:HOH4313 4.4 36.1 1.0
CG D:GLU416 4.6 9.3 1.0
CA D:ASP201 4.6 20.9 1.0
O D:ASN102 4.8 29.0 1.0
C D:GLN200 5.0 27.1 1.0

Magnesium binding site 10 out of 10 in 3dym

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Magnesium binding site 10 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (H418E)


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 (H418E) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:17.1
occ:1.00
 OE1 D:GLN163 2.1 15.7 1.0
O D:VAL21 2.2 21.3 1.0
O D:ASN18 2.2 14.8 1.0
O D:ASP15 2.3 23.5 1.0
OD2 D:ASP193 2.4 33.6 1.0
OD1 D:ASP193 2.9 26.0 1.0
CG D:ASP193 3.0 32.6 1.0
CD D:GLN163 3.0 26.7 1.0
C D:ASN18 3.1 23.5 1.0
C D:VAL21 3.3 22.9 1.0
NE2 D:GLN163 3.4 21.4 1.0
C D:ASP15 3.5 19.5 1.0
N D:ASN18 3.7 33.8 1.0
CA D:ASN18 3.9 23.8 1.0
OH D:TYR161 3.9 23.9 1.0
CA D:TRP16 4.0 21.4 1.0
N D:PRO19 4.1 27.4 1.0
CB D:ASN18 4.1 15.5 1.0
N D:TRP16 4.1 21.0 1.0
CA D:VAL21 4.2 18.2 1.0
C D:TRP16 4.3 17.3 1.0
N D:THR22 4.3 19.0 1.0
N D:VAL21 4.3 28.8 1.0
CB D:VAL21 4.3 24.8 1.0
CA D:PRO19 4.4 24.8 1.0
CG D:GLN163 4.4 18.4 1.0
CA D:THR22 4.4 18.3 1.0
CE2 D:TYR161 4.4 13.4 1.0
CB D:ASP193 4.4 17.1 1.0
N D:GLU17 4.4 14.7 1.0
CZ D:TYR161 4.6 20.6 1.0
CA D:ASP15 4.6 22.7 1.0
C D:PRO19 4.8 23.3 1.0
CG1 D:VAL21 4.8 19.6 1.0
O D:TRP16 4.8 24.9 1.0
C D:GLU17 4.9 31.6 1.0
CG2 D:THR22 5.0 24.0 1.0

Reference:

D.H.Juers, B.Rob, M.L.Dugdale, N.Rahimzadeh, C.Giang, M.Lee, B.W.Matthews, R.E.Huber. Direct and Indirect Roles of His-418 in Metal Binding and in the Activity of Beta-Galactosidase (E. Coli). Protein Sci. V. 18 1281 2009.
ISSN: ISSN 0961-8368
PubMed: 19472413
DOI: 10.1002/PRO.140
Page generated: Wed Aug 14 12:47:20 2024

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