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Magnesium in PDB 3iap: E. Coli (Lacz) Beta-Galactosidase (E416Q)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E416Q)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E416Q):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E416Q), PDB code: 3iap was solved by S.Lo, M.L.Dugdale, N.Jeerh, T.Ku, N.J.Roth, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.38 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.230, 162.340, 202.060, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22

Other elements in 3iap:

The structure of E. Coli (Lacz) Beta-Galactosidase (E416Q) 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 (E416Q) (pdb code 3iap). 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 (E416Q), PDB code: 3iap:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3iap

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:18.5
occ:1.00
 O A:ASP15 2.1 20.5 1.0
O A:VAL21 2.2 16.6 1.0
O A:ASN18 2.3 24.5 1.0
NE2 A:GLN163 2.3 11.8 1.0
OD2 A:ASP193 2.4 20.6 1.0
OD1 A:ASP193 3.0 21.8 1.0
CG A:ASP193 3.1 20.6 1.0
C A:ASN18 3.3 24.4 1.0
CD A:GLN163 3.3 15.8 1.0
C A:VAL21 3.3 17.9 1.0
C A:ASP15 3.3 21.0 1.0
OE1 A:GLN163 3.6 18.1 1.0
N A:ASN18 3.7 24.8 1.0
CA A:ASN18 4.0 24.1 1.0
OH A:TYR161 4.0 15.9 1.0
CA A:TRP16 4.1 21.9 1.0
CA A:VAL21 4.1 19.0 1.0
N A:TRP16 4.1 21.4 1.0
N A:PRO19 4.2 24.4 1.0
CB A:VAL21 4.2 19.3 1.0
CE2 A:TYR161 4.2 14.6 1.0
N A:VAL21 4.3 21.3 1.0
C A:TRP16 4.3 22.8 1.0
N A:THR22 4.4 16.5 1.0
CB A:ASN18 4.4 24.4 1.0
CA A:ASP15 4.4 21.5 1.0
N A:GLU17 4.5 22.9 1.0
CA A:PRO19 4.5 24.0 1.0
CG A:GLN163 4.5 13.6 1.0
CB A:ASP193 4.5 18.8 1.0
CZ A:TYR161 4.5 15.8 1.0
CA A:THR22 4.6 16.8 1.0
CG1 A:VAL21 4.8 18.2 1.0
CB A:ASP15 4.8 21.3 1.0
O A:TRP16 4.9 23.0 1.0
C A:GLU17 4.9 24.4 1.0
C A:PRO19 4.9 23.6 1.0

Magnesium binding site 2 out of 8 in 3iap

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:42.9
occ:1.00
 O A:HOH4941 2.7 32.9 1.0
O A:HOH4192 2.7 29.6 1.0
O A:HOH4482 3.0 17.3 1.0
O A:HOH4487 3.1 22.0 1.0
O A:HOH4771 3.3 45.8 1.0
O A:THR911 3.5 11.2 1.0
CA A:THR911 3.5 11.9 1.0
C1 A:DMS7006 3.6 0.0 1.0
O A:HOH4669 3.7 23.7 1.0
CB A:THR911 4.0 12.7 1.0
C A:THR911 4.0 11.2 1.0
O A:HOH4170 4.2 24.1 1.0
CG2 A:THR911 4.3 11.2 1.0
O A:LEU910 4.5 11.1 1.0
O A:HOH4096 4.6 29.0 1.0
O A:HOH4237 4.6 23.3 1.0
N A:THR911 4.6 11.8 1.0
OE1 A:GLN718 4.7 29.2 1.0
O A:DMS7006 4.8 0.8 1.0
S A:DMS7006 4.9 0.0 1.0
C A:LEU910 5.0 12.8 1.0
O A:HOH4387 5.0 15.4 1.0

Magnesium binding site 3 out of 8 in 3iap

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:21.7
occ:1.00
 O B:VAL21 2.2 19.9 1.0
O B:ASN18 2.2 26.7 1.0
O B:ASP15 2.2 25.1 1.0
OD2 B:ASP193 2.2 21.5 1.0
NE2 B:GLN163 2.4 19.4 1.0
CG B:ASP193 3.0 21.8 1.0
OD1 B:ASP193 3.1 23.0 1.0
C B:ASN18 3.2 27.5 1.0
CD B:GLN163 3.3 20.2 1.0
C B:VAL21 3.3 20.4 1.0
C B:ASP15 3.4 26.8 1.0
N B:ASN18 3.6 28.7 1.0
OE1 B:GLN163 3.6 19.9 1.0
CA B:ASN18 3.8 28.0 1.0
OH B:TYR161 4.1 15.5 1.0
CA B:TRP16 4.1 27.4 1.0
CA B:VAL21 4.1 21.3 1.0
CB B:ASN18 4.2 28.1 1.0
CB B:VAL21 4.2 22.1 1.0
N B:TRP16 4.2 26.5 1.0
N B:PRO19 4.2 27.2 1.0
CE2 B:TYR161 4.3 12.7 1.0
N B:VAL21 4.3 22.8 1.0
C B:TRP16 4.3 27.9 1.0
N B:THR22 4.4 19.6 1.0
N B:GLU17 4.4 28.2 1.0
CB B:ASP193 4.5 20.1 1.0
CA B:ASP15 4.5 27.2 1.0
CA B:PRO19 4.5 26.8 1.0
CA B:THR22 4.6 19.3 1.0
CG B:GLN163 4.6 18.5 1.0
CZ B:TYR161 4.7 14.1 1.0
CG1 B:VAL21 4.7 19.9 1.0
C B:GLU17 4.8 29.3 1.0
O B:TRP16 4.9 27.2 1.0
CB B:ASP15 4.9 26.8 1.0
C B:PRO19 5.0 26.1 1.0

Magnesium binding site 4 out of 8 in 3iap

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:44.2
occ:1.00
 O B:HOH4236 2.3 29.3 1.0
O B:HOH4466 2.4 30.6 1.0
O B:HOH4594 2.6 23.5 1.0
O B:HOH4574 2.6 29.4 1.0
OE1 B:GLN718 2.8 24.7 1.0
C2 B:DMS7029 3.4 63.0 1.0
CD B:GLN718 3.8 22.0 1.0
NE2 B:GLN718 4.0 23.6 1.0
O B:THR911 4.0 12.5 1.0
O B:HOH4845 4.0 28.2 1.0
NE2 B:HIS622 4.3 11.1 1.0
O B:HOH4347 4.4 27.3 1.0
O B:HOH4837 4.4 47.8 1.0
C1 B:DMS7029 4.5 63.5 1.0
O B:HOH4227 4.5 14.3 1.0
O B:HOH4072 4.6 13.3 1.0
O B:HOH4248 4.6 30.9 1.0
S B:DMS7029 4.8 63.7 1.0
O B:GLN719 4.8 14.1 1.0
CA B:THR911 4.8 12.1 1.0
O B:HOH4785 4.8 26.2 1.0
C B:THR911 4.9 11.6 1.0
CB B:THR911 4.9 11.5 1.0
CE1 B:HIS622 5.0 11.6 1.0

Magnesium binding site 5 out of 8 in 3iap

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Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:19.4
occ:1.00
 O C:VAL21 2.1 19.3 1.0
O C:ASN18 2.2 25.7 1.0
O C:ASP15 2.3 23.8 1.0
NE2 C:GLN163 2.3 14.1 1.0
OD2 C:ASP193 2.4 19.7 1.0
OD1 C:ASP193 3.1 21.9 1.0
CG C:ASP193 3.1 20.3 1.0
C C:ASN18 3.2 26.6 1.0
CD C:GLN163 3.3 16.2 1.0
C C:VAL21 3.3 19.9 1.0
C C:ASP15 3.5 24.6 1.0
OE1 C:GLN163 3.6 14.9 1.0
N C:ASN18 3.8 28.0 1.0
CA C:ASN18 4.0 26.6 1.0
OH C:TYR161 4.0 14.1 1.0
CA C:VAL21 4.1 20.9 1.0
N C:PRO19 4.2 26.2 1.0
CA C:TRP16 4.2 26.2 1.0
CB C:VAL21 4.3 21.1 1.0
N C:TRP16 4.3 25.0 1.0
N C:VAL21 4.3 22.3 1.0
CE2 C:TYR161 4.3 14.4 1.0
N C:THR22 4.3 19.3 1.0
CA C:PRO19 4.3 26.0 1.0
C C:TRP16 4.4 26.6 1.0
CB C:ASN18 4.5 27.1 1.0
CA C:THR22 4.5 19.6 1.0
CG C:GLN163 4.6 15.0 1.0
CA C:ASP15 4.6 25.1 1.0
N C:GLU17 4.6 27.8 1.0
CB C:ASP193 4.6 19.9 1.0
CZ C:TYR161 4.6 14.3 1.0
CG1 C:VAL21 4.8 18.6 1.0
C C:PRO19 4.9 25.1 1.0
CB C:ASP15 4.9 24.9 1.0
O C:TRP16 4.9 26.6 1.0

Magnesium binding site 6 out of 8 in 3iap

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:55.3
occ:1.00
 O C:HOH4324 2.1 31.6 1.0
O C:HOH4235 2.2 29.4 1.0
O C:HOH4636 2.4 33.2 1.0
O C:HOH4519 2.7 35.5 1.0
OE1 C:GLN718 2.9 26.8 1.0
O C:DMS7030 3.1 68.5 1.0
O C:THR911 3.8 16.6 1.0
CD C:GLN718 3.8 22.3 1.0
NE2 C:GLN718 4.0 22.3 1.0
S C:DMS7030 4.1 68.6 1.0
O C:HOH4247 4.2 23.2 1.0
NE2 C:HIS622 4.2 13.8 1.0
O C:HOH4225 4.3 16.2 1.0
O C:HOH4358 4.4 50.4 1.0
O C:HOH4811 4.5 26.1 1.0
O C:HOH4317 4.5 36.4 1.0
O C:HOH4072 4.5 16.5 1.0
CA C:THR911 4.5 16.0 1.0
C C:THR911 4.6 16.6 1.0
CB C:THR911 4.6 15.8 1.0
CE1 C:HIS622 5.0 11.4 1.0

Magnesium binding site 7 out of 8 in 3iap

Go back to Magnesium Binding Sites List in 3iap
Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:18.8
occ:1.00
 O D:ASN18 2.2 26.3 1.0
O D:VAL21 2.2 19.7 1.0
O D:ASP15 2.3 23.6 1.0
OD2 D:ASP193 2.3 21.1 1.0
NE2 D:GLN163 2.4 12.6 1.0
OD1 D:ASP193 2.9 24.7 1.0
CG D:ASP193 3.0 22.1 1.0
C D:ASN18 3.2 26.5 1.0
CD D:GLN163 3.3 18.7 1.0
C D:VAL21 3.4 20.7 1.0
OE1 D:GLN163 3.5 20.3 1.0
C D:ASP15 3.5 23.6 1.0
N D:ASN18 3.7 27.8 1.0
CA D:ASN18 3.9 26.4 1.0
OH D:TYR161 4.0 16.5 1.0
N D:PRO19 4.1 26.3 1.0
CA D:TRP16 4.1 24.1 1.0
CA D:VAL21 4.2 21.9 1.0
N D:TRP16 4.2 23.4 1.0
N D:VAL21 4.3 23.6 1.0
CB D:ASN18 4.3 26.5 1.0
CE2 D:TYR161 4.3 16.9 1.0
C D:TRP16 4.3 24.4 1.0
N D:THR22 4.3 19.4 1.0
CB D:VAL21 4.3 21.9 1.0
CA D:PRO19 4.4 26.2 1.0
CB D:ASP193 4.5 20.0 1.0
N D:GLU17 4.5 25.3 1.0
CA D:THR22 4.5 18.6 1.0
CA D:ASP15 4.6 24.4 1.0
CG D:GLN163 4.6 18.1 1.0
CZ D:TYR161 4.6 17.5 1.0
CG1 D:VAL21 4.8 22.1 1.0
C D:PRO19 4.9 25.8 1.0
O D:TRP16 4.9 24.7 1.0
C D:GLU17 4.9 27.4 1.0
CB D:ASP15 4.9 23.3 1.0

Magnesium binding site 8 out of 8 in 3iap

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Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (E416Q)


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 (E416Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:51.5
occ:1.00
 O D:HOH4247 2.1 22.8 1.0
O D:HOH4894 2.6 44.5 1.0
O D:HOH4520 2.6 32.7 1.0
OE1 D:GLN718 2.8 30.2 1.0
C1 D:DMS7026 3.5 74.6 1.0
O D:THR911 3.7 13.6 1.0
CD D:GLN718 3.7 25.9 1.0
NE2 D:GLN718 4.0 28.7 1.0
O D:HOH4571 4.1 21.3 1.0
O D:HOH4260 4.1 27.4 1.0
NE2 D:HIS622 4.1 12.3 1.0
O D:HOH4237 4.4 15.9 1.0
C D:THR911 4.5 13.5 1.0
O D:HOH4080 4.6 13.7 1.0
CA D:THR911 4.6 14.0 1.0
O D:HOH4378 4.6 30.8 1.0
CB D:THR911 4.7 13.5 1.0
CE1 D:HIS622 4.8 13.9 1.0
O D:GLN719 5.0 18.9 1.0
N D:GLN719 5.0 18.3 1.0

Reference:

S.Lo, M.L.Dugdale, N.Jeerh, T.Ku, N.J.Roth, R.E.Huber. Studies of Glu-416 Variants of Beta-Galactosidase (E. Coli) Show That the Active Site Mg(2+) Is Not Important For Structure and Indicate That the Main Role of Mg (2+) Is to Mediate Optimization of Active Site Chemistry Protein J. V. 29 26 2010.
ISSN: ISSN 1572-3887
PubMed: 19936901
DOI: 10.1007/S10930-009-9216-X
Page generated: Wed Aug 14 16:01:03 2024

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