Atomistry » Magnesium » PDB 3s8c-3si7 » 3sep
Atomistry »
  Magnesium »
    PDB 3s8c-3si7 »
      3sep »

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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Go back to Magnesium Binding Sites List in 3sep
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy