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Magnesium in PDB 3vd3: E. Coli (Lacz) Beta-Galactosidase (N460D)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460D)

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460D), PDB code: 3vd3 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) 57.25 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.140, 151.650, 131.330, 90.00, 103.47, 90.00
R / Rfree (%) 20 / 28.2

Other elements in 3vd3:

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

Sodium (Na) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460D) (pdb code 3vd3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460D), PDB code: 3vd3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3vd3

Go back to Magnesium Binding Sites List in 3vd3
Magnesium binding site 1 out of 7 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:42.5
occ:1.00
 OE2 A:GLU416 2.0 30.5 1.0
ND1 A:HIS418 2.1 24.9 1.0
OE1 A:GLU461 2.1 29.5 1.0
O A:HOH4007 2.1 17.7 1.0
O A:HOH4112 2.3 33.6 1.0
O A:HOH4111 2.4 34.4 1.0
CE1 A:HIS418 2.9 26.7 1.0
CD A:GLU461 3.2 24.0 1.0
CG A:HIS418 3.2 22.3 1.0
CD A:GLU416 3.2 31.2 1.0
CB A:HIS418 3.6 18.9 1.0
OE1 A:GLU416 3.8 42.5 1.0
OD1 A:ASN102 3.9 39.1 1.0
OE2 A:GLU461 3.9 33.0 1.0
NE2 A:HIS418 4.1 26.1 1.0
CG A:GLU461 4.1 22.4 1.0
CB A:GLU461 4.1 18.3 1.0
N A:ASP201 4.2 23.7 1.0
CD2 A:HIS418 4.2 26.6 1.0
CB A:ASP201 4.2 23.8 1.0
O A:ASP199 4.3 20.7 1.0
CG A:GLU416 4.4 25.9 1.0
O A:ASN102 4.5 36.1 1.0
OD2 A:ASP460 4.6 27.5 1.0
CA A:ASP201 4.8 22.7 1.0
C A:GLN200 4.9 24.2 1.0
CA A:GLN200 5.0 24.0 1.0

Magnesium binding site 2 out of 7 in 3vd3

Go back to Magnesium Binding Sites List in 3vd3
Magnesium binding site 2 out of 7 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:45.3
occ:1.00
 OE1 B:GLU461 2.1 40.9 1.0
OE2 B:GLU416 2.1 39.6 1.0
O B:HOH4110 2.2 34.1 1.0
ND1 B:HIS418 2.2 40.1 1.0
O B:HOH4109 2.2 36.5 1.0
O B:HOH4108 2.3 33.2 1.0
CD B:GLU461 2.9 35.7 1.0
CE1 B:HIS418 3.0 38.0 1.0
CG B:HIS418 3.2 32.4 1.0
CD B:GLU416 3.2 32.7 1.0
OE2 B:GLU461 3.5 40.0 1.0
CB B:HIS418 3.6 27.0 1.0
OE1 B:GLU416 3.8 34.6 1.0
CB B:GLU461 3.9 28.6 1.0
CG B:GLU461 4.0 29.0 1.0
NE2 B:HIS418 4.1 41.1 1.0
OD1 B:ASN102 4.1 44.3 1.0
CD2 B:HIS418 4.2 35.4 1.0
CG B:GLU416 4.2 23.9 1.0
O B:ASP199 4.3 28.8 1.0
CB B:ASP201 4.3 34.7 1.0
N B:ASP201 4.4 34.2 1.0
O B:HOH4089 4.4 33.4 1.0
OD2 B:ASP460 4.4 27.5 1.0
O B:HOH4001 4.5 33.0 1.0
O B:ASN102 4.5 31.7 1.0
O B:HOH4081 4.6 19.7 1.0
CA B:ASP201 4.9 33.8 1.0
CA B:HIS418 5.0 25.4 1.0

Magnesium binding site 3 out of 7 in 3vd3

Go back to Magnesium Binding Sites List in 3vd3
Magnesium binding site 3 out of 7 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:33.4
occ:1.00
 OD2 B:ASP193 2.1 32.1 1.0
O B:ASP15 2.1 35.5 1.0
OE1 B:GLN163 2.3 29.7 1.0
O B:ASN18 2.3 33.1 1.0
O B:VAL21 2.3 31.5 1.0
CG B:ASP193 2.9 31.4 1.0
OD1 B:ASP193 3.1 36.1 1.0
C B:ASN18 3.2 34.0 1.0
C B:ASP15 3.3 33.3 1.0
CD B:GLN163 3.3 34.2 1.0
C B:VAL21 3.5 29.7 1.0
N B:ASN18 3.6 34.0 1.0
OH B:TYR161 3.6 21.8 1.0
NE2 B:GLN163 3.7 35.1 1.0
CA B:ASN18 3.8 34.0 1.0
CE2 B:TYR161 4.0 18.6 1.0
CB B:ASN18 4.1 34.2 1.0
CA B:TRP16 4.1 29.4 1.0
N B:TRP16 4.1 30.5 1.0
N B:PRO19 4.3 31.6 1.0
CA B:ASP15 4.3 33.7 1.0
CZ B:TYR161 4.3 18.8 1.0
C B:TRP16 4.3 29.4 1.0
CB B:ASP193 4.3 27.2 1.0
CA B:VAL21 4.3 30.5 1.0
CB B:VAL21 4.4 29.9 1.0
N B:GLU17 4.4 32.4 1.0
N B:THR22 4.5 29.7 1.0
N B:VAL21 4.5 32.6 1.0
CA B:THR22 4.6 28.3 1.0
CB B:ASP15 4.6 33.9 1.0
CG B:GLN163 4.7 30.7 1.0
CA B:PRO19 4.7 31.2 1.0
C B:GLU17 4.8 35.1 1.0
CG1 B:VAL21 5.0 25.6 1.0
O B:TRP16 5.0 30.3 1.0

Magnesium binding site 4 out of 7 in 3vd3

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Magnesium binding site 4 out of 7 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:43.7
occ:1.00
 O C:HOH4098 1.9 36.5 1.0
OE1 C:GLU461 2.0 45.8 1.0
O C:HOH4097 2.0 34.6 1.0
OE2 C:GLU416 2.1 31.1 1.0
ND1 C:HIS418 2.2 34.4 1.0
O C:HOH4096 2.3 29.5 1.0
CE1 C:HIS418 3.0 36.6 1.0
CD C:GLU461 3.1 38.2 1.0
CD C:GLU416 3.2 27.5 1.0
CG C:HIS418 3.2 31.4 1.0
CB C:HIS418 3.6 26.6 1.0
OE2 C:GLU461 3.7 40.0 1.0
OE1 C:GLU416 3.7 31.4 1.0
CB C:GLU461 4.2 25.6 1.0
OD1 C:ASN102 4.2 50.0 1.0
CG C:GLU461 4.2 31.7 1.0
NE2 C:HIS418 4.2 36.9 1.0
O C:ASP199 4.2 34.7 1.0
CB C:ASP201 4.2 33.2 1.0
O C:ASN102 4.2 45.0 1.0
CD2 C:HIS418 4.3 32.9 1.0
N C:ASP201 4.4 31.2 1.0
CG C:GLU416 4.4 27.8 1.0
OD2 C:ASP460 4.6 34.3 1.0
CA C:ASP201 4.8 31.9 1.0
O C:HOH4086 4.9 23.2 1.0

Magnesium binding site 5 out of 7 in 3vd3

Go back to Magnesium Binding Sites List in 3vd3
Magnesium binding site 5 out of 7 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:29.4
occ:1.00
 OD2 C:ASP193 2.1 30.4 1.0
O C:ASP15 2.1 31.5 1.0
O C:ASN18 2.3 31.0 1.0
OE1 C:GLN163 2.3 28.2 1.0
O C:VAL21 2.3 35.7 1.0
CG C:ASP193 3.1 24.6 1.0
CD C:GLN163 3.3 30.3 1.0
C C:ASP15 3.3 32.7 1.0
C C:ASN18 3.3 31.9 1.0
C C:VAL21 3.5 35.0 1.0
OD1 C:ASP193 3.6 32.2 1.0
NE2 C:GLN163 3.7 33.5 1.0
N C:ASN18 3.9 30.1 1.0
OH C:TYR161 4.0 32.4 1.0
CA C:ASN18 4.0 30.1 1.0
CA C:TRP16 4.2 31.4 1.0
N C:TRP16 4.2 31.7 1.0
CE2 C:TYR161 4.2 16.5 1.0
CA C:VAL21 4.3 35.3 1.0
CA C:ASP15 4.3 33.6 1.0
CB C:ASN18 4.3 27.6 1.0
N C:PRO19 4.4 34.6 1.0
N C:VAL21 4.4 34.2 1.0
CB C:ASP193 4.4 20.1 1.0
N C:THR22 4.4 33.7 1.0
CB C:VAL21 4.4 35.4 1.0
CA C:THR22 4.5 34.0 1.0
C C:TRP16 4.5 29.9 1.0
CZ C:TYR161 4.6 22.9 1.0
CB C:ASP15 4.6 31.4 1.0
CG C:GLN163 4.6 28.9 1.0
CA C:PRO19 4.6 36.0 1.0
N C:GLU17 4.7 30.1 1.0
CG1 C:VAL21 4.7 34.5 1.0

Magnesium binding site 6 out of 7 in 3vd3

Go back to Magnesium Binding Sites List in 3vd3
Magnesium binding site 6 out of 7 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:47.6
occ:1.00
 ND1 D:HIS418 2.1 36.9 1.0
OE1 D:GLU461 2.1 40.7 1.0
O D:HOH4104 2.2 33.3 1.0
OE2 D:GLU416 2.2 37.0 1.0
O D:HOH4105 2.2 42.0 1.0
O D:HOH4094 2.3 13.2 1.0
CE1 D:HIS418 3.1 33.2 1.0
CG D:HIS418 3.1 30.8 1.0
CD D:GLU461 3.1 34.5 1.0
CB D:HIS418 3.4 26.1 1.0
CD D:GLU416 3.4 28.8 1.0
OE2 D:GLU461 3.7 39.5 1.0
CB D:GLU461 3.9 27.1 1.0
CG D:GLU461 4.1 28.0 1.0
O D:HOH4096 4.1 37.3 1.0
N D:ASP201 4.1 33.1 1.0
OE1 D:GLU416 4.1 29.7 1.0
O D:ASP199 4.1 32.4 1.0
NE2 D:HIS418 4.2 34.3 1.0
CD2 D:HIS418 4.2 33.0 1.0
CB D:ASP201 4.2 34.3 1.0
OD2 D:ASP460 4.4 27.3 1.0
CG D:GLU416 4.4 22.3 1.0
O D:ASN102 4.5 35.8 1.0
OD1 D:ASN102 4.5 40.1 1.0
CA D:ASP201 4.7 32.0 1.0
CA D:HIS418 4.8 24.4 1.0
C D:GLN200 4.8 32.6 1.0
CA D:GLN200 4.9 31.4 1.0

Magnesium binding site 7 out of 7 in 3vd3

Go back to Magnesium Binding Sites List in 3vd3
Magnesium binding site 7 out of 7 in the E. Coli (Lacz) Beta-Galactosidase (N460D)


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

b:31.0
occ:1.00
 O D:ASP15 2.1 31.2 1.0
OD2 D:ASP193 2.1 33.6 1.0
OE1 D:GLN163 2.3 29.8 1.0
O D:ASN18 2.3 29.8 1.0
O D:VAL21 2.3 26.7 1.0
CG D:ASP193 3.1 31.8 1.0
C D:ASN18 3.2 29.4 1.0
C D:ASP15 3.3 31.0 1.0
CD D:GLN163 3.3 28.6 1.0
C D:VAL21 3.5 21.8 1.0
OD1 D:ASP193 3.5 37.4 1.0
N D:ASN18 3.6 26.7 1.0
OH D:TYR161 3.7 13.8 1.0
NE2 D:GLN163 3.8 23.0 1.0
CA D:ASN18 3.8 28.3 1.0
N D:PRO19 4.2 30.4 1.0
N D:TRP16 4.2 28.3 1.0
CB D:ASN18 4.2 26.9 1.0
CA D:ASP15 4.2 32.2 1.0
CE2 D:TYR161 4.2 11.6 1.0
CA D:TRP16 4.3 26.5 1.0
CA D:VAL21 4.3 22.2 1.0
CB D:VAL21 4.3 20.4 1.0
C D:TRP16 4.4 26.1 1.0
N D:GLU17 4.4 24.1 1.0
N D:VAL21 4.4 25.4 1.0
CZ D:TYR161 4.4 15.2 1.0
CB D:ASP193 4.5 28.1 1.0
CA D:PRO19 4.5 30.7 1.0
N D:THR22 4.5 19.3 1.0
CB D:ASP15 4.6 33.3 1.0
CG D:GLN163 4.6 22.8 1.0
CA D:THR22 4.6 21.7 1.0
CG1 D:VAL21 4.7 13.8 1.0
C D:GLU17 4.8 23.3 1.0
O D:TRP16 5.0 26.6 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 12:55:19 2024

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