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Magnesium in PDB 3sep: E. Coli (Lacz) Beta-Galactosidase (S796A)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A), PDB code: 3sep was solved by L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.342, 163.165, 203.401, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.1

Other elements in 3sep:

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) 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 (S796A) (pdb code 3sep). 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 (S796A), PDB code: 3sep:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3sep

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Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:24.7
occ:1.00
 ND1 A:HIS418 2.0 21.8 1.0
OE1 A:GLU461 2.1 23.2 1.0
O A:HOH4846 2.1 21.0 1.0
OE2 A:GLU416 2.1 21.5 1.0
O A:HOH4796 2.1 20.7 1.0
O A:HOH4152 2.2 18.9 1.0
CE1 A:HIS418 2.9 23.8 1.0
CD A:GLU461 3.1 28.2 1.0
CG A:HIS418 3.2 21.8 1.0
CD A:GLU416 3.2 18.5 1.0
CB A:HIS418 3.6 20.5 1.0
OE1 A:GLU416 3.7 24.5 1.0
OE2 A:GLU461 3.8 23.4 1.0
NE2 A:HIS418 4.1 19.0 1.0
CB A:GLU461 4.1 19.8 1.0
CG A:GLU461 4.2 25.4 1.0
OD1 A:ASN102 4.2 26.3 1.0
CB A:ASP201 4.2 22.7 1.0
CD2 A:HIS418 4.2 21.8 1.0
O A:ASP199 4.2 24.4 1.0
N A:ASP201 4.3 26.8 1.0
O A:HOH4693 4.3 35.6 1.0
ND2 A:ASN460 4.3 18.7 1.0
CG A:GLU416 4.4 21.1 1.0
O A:HOH4001 4.5 24.2 1.0
O A:ASN102 4.6 25.6 1.0
O A:HOH4283 4.6 36.8 1.0
CA A:ASP201 4.8 24.3 1.0
CG2 A:VAL103 4.9 24.7 1.0
C A:GLN200 4.9 26.6 1.0
CA A:GLN200 5.0 24.2 1.0

Magnesium binding site 2 out of 9 in 3sep

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Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:33.0
occ:1.00
 OD2 A:ASP193 2.1 45.1 1.0
O A:ASP15 2.1 42.1 1.0
O A:ASN18 2.2 36.7 1.0
OE1 A:GLN163 2.3 38.4 1.0
O A:VAL21 2.3 38.6 1.0
CG A:ASP193 2.9 42.7 1.0
OD1 A:ASP193 3.1 42.0 1.0
CD A:GLN163 3.2 34.6 1.0
C A:ASN18 3.2 38.8 1.0
C A:ASP15 3.3 41.0 1.0
C A:VAL21 3.5 36.7 1.0
NE2 A:GLN163 3.5 31.3 1.0
N A:ASN18 3.6 39.4 1.0
OH A:TYR161 3.8 36.9 1.0
CA A:ASN18 3.8 40.6 1.0
CA A:TRP16 4.0 39.3 1.0
N A:TRP16 4.1 41.3 1.0
CB A:ASN18 4.1 39.4 1.0
C A:TRP16 4.2 37.8 1.0
CE2 A:TYR161 4.3 40.5 1.0
N A:PRO19 4.3 38.0 1.0
CA A:VAL21 4.3 37.5 1.0
N A:GLU17 4.3 36.9 1.0
CB A:ASP193 4.4 34.9 1.0
N A:VAL21 4.4 38.2 1.0
CA A:ASP15 4.4 42.7 1.0
CB A:VAL21 4.4 38.6 1.0
N A:THR22 4.5 38.4 1.0
CZ A:TYR161 4.5 37.6 1.0
CG A:GLN163 4.6 33.0 1.0
CA A:PRO19 4.6 39.5 1.0
CA A:THR22 4.6 36.9 1.0
C A:GLU17 4.8 39.0 1.0
CB A:ASP15 4.8 41.1 1.0
CG1 A:VAL21 4.8 34.3 1.0
O A:TRP16 4.9 37.7 1.0
C A:PRO19 5.0 41.3 1.0

Magnesium binding site 3 out of 9 in 3sep

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Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:17.1
occ:1.00
 ND1 B:HIS418 2.1 18.4 1.0
OE2 B:GLU416 2.1 16.4 1.0
OE1 B:GLU461 2.1 13.1 1.0
O B:HOH5038 2.1 14.7 1.0
O B:HOH4967 2.1 16.5 1.0
O B:HOH4030 2.4 17.1 1.0
CE1 B:HIS418 2.9 21.4 1.0
CG B:HIS418 3.2 21.9 1.0
CD B:GLU416 3.2 18.2 1.0
CD B:GLU461 3.2 19.7 1.0
CB B:HIS418 3.6 14.7 1.0
OE1 B:GLU416 3.7 15.4 1.0
OE2 B:GLU461 3.9 14.2 1.0
OD1 B:ASN102 4.0 21.4 1.0
NE2 B:HIS418 4.1 21.1 1.0
CB B:ASP201 4.1 14.9 1.0
CB B:GLU461 4.2 16.6 1.0
N B:ASP201 4.2 14.4 1.0
O B:HOH4821 4.2 26.1 1.0
CD2 B:HIS418 4.2 17.5 1.0
CG B:GLU461 4.3 9.1 1.0
O B:ASP199 4.3 17.2 1.0
O B:HOH4018 4.4 15.4 1.0
CG B:GLU416 4.4 14.8 1.0
ND2 B:ASN460 4.4 14.6 1.0
O B:ASN102 4.6 22.3 1.0
O B:HOH4299 4.7 22.6 1.0
CA B:ASP201 4.7 13.8 1.0
C B:GLN200 5.0 16.6 1.0
CG2 B:VAL103 5.0 15.0 1.0

Magnesium binding site 4 out of 9 in 3sep

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Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:21.3
occ:1.00
 O B:ASP15 2.1 19.9 1.0
OD2 B:ASP193 2.1 21.4 1.0
O B:ASN18 2.3 19.0 1.0
OE1 B:GLN163 2.3 23.2 1.0
O B:VAL21 2.3 22.1 1.0
CG B:ASP193 2.9 20.2 1.0
OD1 B:ASP193 3.0 20.6 1.0
CD B:GLN163 3.1 27.7 1.0
C B:ASN18 3.2 20.9 1.0
C B:ASP15 3.3 17.0 1.0
NE2 B:GLN163 3.4 13.9 1.0
C B:VAL21 3.4 20.9 1.0
N B:ASN18 3.7 21.8 1.0
CA B:ASN18 3.9 19.6 1.0
CA B:TRP16 4.0 20.7 1.0
OH B:TYR161 4.1 18.2 1.0
N B:TRP16 4.1 18.3 1.0
N B:PRO19 4.2 22.2 1.0
CA B:VAL21 4.2 23.4 1.0
CB B:ASN18 4.2 21.6 1.0
C B:TRP16 4.3 21.6 1.0
N B:VAL21 4.3 24.0 1.0
CB B:VAL21 4.3 23.8 1.0
CB B:ASP193 4.3 17.4 1.0
CE2 B:TYR161 4.4 16.6 1.0
CA B:PRO19 4.4 22.7 1.0
N B:GLU17 4.4 20.9 1.0
CA B:ASP15 4.5 20.3 1.0
N B:THR22 4.5 17.4 1.0
CG B:GLN163 4.5 24.2 1.0
CA B:THR22 4.7 18.6 1.0
CZ B:TYR161 4.7 16.6 1.0
O B:TRP16 4.8 22.0 1.0
C B:GLU17 4.8 21.5 1.0
CB B:ASP15 4.9 21.4 1.0
C B:PRO19 4.9 25.1 1.0
CG1 B:VAL21 5.0 24.0 1.0

Magnesium binding site 5 out of 9 in 3sep

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Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:46.3
occ:1.00
 O B:HOH5039 2.1 38.2 1.0
O B:HOH4976 2.1 32.1 1.0
O B:HOH5123 2.2 42.2 1.0
O B:HOH4718 2.4 37.2 1.0
OE1 B:GLU369 3.8 24.5 1.0
O B:HOH4954 4.0 45.8 1.0
O B:HOH4791 4.1 32.1 1.0
OE2 B:GLU369 4.3 30.6 1.0
CD B:GLU369 4.5 25.4 1.0

Magnesium binding site 6 out of 9 in 3sep

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Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:17.3
occ:1.00
 ND1 C:HIS418 2.1 18.2 1.0
OE1 C:GLU461 2.1 11.5 1.0
OE2 C:GLU416 2.1 21.9 1.0
O C:HOH4959 2.1 15.4 1.0
O C:HOH5027 2.1 14.2 1.0
O C:HOH4044 2.3 11.6 1.0
CE1 C:HIS418 2.9 15.2 1.0
CD C:GLU461 3.2 15.7 1.0
CG C:HIS418 3.2 18.9 1.0
CD C:GLU416 3.2 19.3 1.0
CB C:HIS418 3.6 16.2 1.0
OE1 C:GLU416 3.7 18.8 1.0
OE2 C:GLU461 3.9 13.8 1.0
OD1 C:ASN102 4.0 26.9 1.0
NE2 C:HIS418 4.1 19.2 1.0
CB C:GLU461 4.1 9.6 1.0
CB C:ASP201 4.2 14.4 1.0
CG C:GLU461 4.2 9.8 1.0
CD2 C:HIS418 4.2 15.1 1.0
O C:HOH4851 4.2 37.1 1.0
N C:ASP201 4.2 16.3 1.0
O C:ASP199 4.3 16.6 1.0
CG C:GLU416 4.4 12.3 1.0
O C:HOH4032 4.4 18.5 1.0
ND2 C:ASN460 4.4 15.0 1.0
O C:HOH4319 4.6 27.5 1.0
O C:ASN102 4.6 18.0 1.0
CA C:ASP201 4.8 16.3 1.0
C C:GLN200 4.9 17.8 1.0
CG2 C:VAL103 4.9 14.4 1.0
CA C:GLN200 5.0 18.4 1.0

Magnesium binding site 7 out of 9 in 3sep

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Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:21.2
occ:1.00
 OD2 C:ASP193 2.1 23.1 1.0
O C:ASP15 2.1 23.6 1.0
OE1 C:GLN163 2.3 23.6 1.0
O C:ASN18 2.3 22.4 1.0
O C:VAL21 2.3 23.8 1.0
CG C:ASP193 2.9 19.0 1.0
OD1 C:ASP193 3.0 23.9 1.0
CD C:GLN163 3.2 20.1 1.0
C C:ASN18 3.2 21.8 1.0
C C:ASP15 3.3 21.7 1.0
C C:VAL21 3.4 24.7 1.0
NE2 C:GLN163 3.5 18.1 1.0
N C:ASN18 3.6 25.3 1.0
CA C:ASN18 3.9 23.3 1.0
CA C:TRP16 4.0 19.2 1.0
OH C:TYR161 4.1 17.6 1.0
N C:TRP16 4.1 20.4 1.0
CA C:VAL21 4.2 26.8 1.0
N C:PRO19 4.2 19.1 1.0
C C:TRP16 4.2 21.3 1.0
CB C:ASN18 4.3 22.7 1.0
N C:VAL21 4.3 27.6 1.0
CB C:VAL21 4.3 27.4 1.0
CB C:ASP193 4.3 17.2 1.0
CE2 C:TYR161 4.4 17.6 1.0
CA C:ASP15 4.4 23.6 1.0
N C:GLU17 4.5 17.7 1.0
CA C:PRO19 4.5 22.7 1.0
N C:THR22 4.5 21.5 1.0
CG C:GLN163 4.5 21.2 1.0
CZ C:TYR161 4.7 20.5 1.0
CA C:THR22 4.7 19.7 1.0
O C:TRP16 4.8 20.0 1.0
C C:GLU17 4.8 23.3 1.0
CG1 C:VAL21 4.8 25.9 1.0
CB C:ASP15 4.9 19.8 1.0

Magnesium binding site 8 out of 9 in 3sep

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Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:20.5
occ:1.00
 O D:HOH4904 2.0 17.6 1.0
ND1 D:HIS418 2.0 19.6 1.0
OE1 D:GLU461 2.1 19.3 1.0
OE2 D:GLU416 2.1 23.3 1.0
O D:HOH4180 2.2 17.2 1.0
O D:HOH4040 2.2 22.7 1.0
CE1 D:HIS418 3.0 21.8 1.0
CG D:HIS418 3.1 25.7 1.0
CD D:GLU461 3.2 27.5 1.0
CD D:GLU416 3.2 20.8 1.0
CB D:HIS418 3.5 23.4 1.0
OE1 D:GLU416 3.7 23.6 1.0
OE2 D:GLU461 3.9 25.2 1.0
CB D:GLU461 4.0 20.3 1.0
OD1 D:ASN102 4.1 26.9 1.0
NE2 D:HIS418 4.1 24.9 1.0
CG D:GLU461 4.2 20.8 1.0
CD2 D:HIS418 4.2 20.0 1.0
CB D:ASP201 4.2 27.4 1.0
O D:ASP199 4.3 27.4 1.0
O D:HOH4748 4.3 31.6 1.0
N D:ASP201 4.3 27.2 1.0
CG D:GLU416 4.4 18.9 1.0
O D:HOH4027 4.4 25.8 1.0
ND2 D:ASN460 4.5 20.8 1.0
O D:ASN102 4.6 28.0 1.0
O D:HOH4309 4.7 33.2 1.0
CG2 D:VAL103 4.8 28.1 1.0
CA D:ASP201 4.8 24.5 1.0
CA D:HIS418 4.9 23.9 1.0

Magnesium binding site 9 out of 9 in 3sep

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Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A)


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 (S796A) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:31.6
occ:1.00
 OD2 D:ASP193 2.1 40.7 1.0
O D:ASP15 2.1 32.6 1.0
O D:ASN18 2.3 30.7 1.0
OE1 D:GLN163 2.3 33.9 1.0
O D:VAL21 2.3 31.9 1.0
CG D:ASP193 2.9 37.6 1.0
OD1 D:ASP193 3.0 38.1 1.0
CD D:GLN163 3.2 34.2 1.0
C D:ASN18 3.3 31.5 1.0
C D:ASP15 3.3 32.6 1.0
C D:VAL21 3.5 27.9 1.0
NE2 D:GLN163 3.6 25.2 1.0
N D:ASN18 3.7 34.1 1.0
OH D:TYR161 3.9 32.0 1.0
CA D:TRP16 4.0 32.5 1.0
CA D:ASN18 4.0 33.4 1.0
N D:TRP16 4.1 32.9 1.0
N D:PRO19 4.2 32.8 1.0
C D:TRP16 4.2 29.1 1.0
CE2 D:TYR161 4.3 29.9 1.0
CA D:VAL21 4.3 30.0 1.0
CB D:ASP193 4.3 32.9 1.0
CB D:ASN18 4.3 34.3 1.0
CB D:VAL21 4.4 29.4 1.0
N D:VAL21 4.4 32.3 1.0
N D:GLU17 4.4 31.5 1.0
CA D:ASP15 4.4 31.8 1.0
N D:THR22 4.4 27.6 1.0
CA D:PRO19 4.4 33.6 1.0
CG D:GLN163 4.5 28.9 1.0
CZ D:TYR161 4.5 32.0 1.0
CA D:THR22 4.6 26.2 1.0
O D:TRP16 4.8 31.7 1.0
CB D:ASP15 4.8 29.4 1.0
CG1 D:VAL21 4.9 31.0 1.0
C D:GLU17 4.9 32.9 1.0
C D:PRO19 5.0 31.8 1.0

Reference:

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Ser-796 of Beta-Galactosidase (E. Coli) Plays A Key Role in Maintaining An Optimum Balance Between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. V. 517 111 2012.
ISSN: ISSN 0003-9861
PubMed: 22155115
DOI: 10.1016/J.ABB.2011.11.017
Page generated: Thu Aug 15 10:55:14 2024

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