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Magnesium in PDB 7sf2: Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus

Protein crystallography data

The structure of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus, PDB code: 7sf2 was solved by Y.Kim, G.Joachimiak, M.Endres, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.10 / 2.75
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 335.847, 349.396, 352.108, 90, 90, 90
R / Rfree (%) 18.2 / 20.9

Other elements in 7sf2:

The structure of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus (pdb code 7sf2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus, PDB code: 7sf2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7sf2

Go back to Magnesium Binding Sites List in 7sf2
Magnesium binding site 1 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:20.3
occ:1.00
 OE1 A:GLN186 2.0 18.7 1.0
O A:VAL198 2.0 18.3 1.0
OD2 A:ASP174 2.0 19.0 1.0
O A:HOH853 2.0 16.4 1.0
OD2 A:ASP130 2.1 18.8 1.0
O A:HOH837 2.2 20.6 1.0
CD A:GLN186 3.0 18.8 1.0
CG A:ASP130 3.1 17.9 1.0
CG A:ASP174 3.1 22.6 1.0
C A:VAL198 3.1 21.9 1.0
OD1 A:ASP174 3.5 26.4 1.0
NE2 A:GLN186 3.5 16.9 1.0
CB A:ASP130 3.7 15.3 1.0
N A:VAL198 3.8 24.6 1.0
CA A:VAL198 3.9 18.9 1.0
O A:HOH882 3.9 14.6 1.0
OD1 A:ASP130 4.0 29.1 1.0
N A:THR199 4.1 22.4 1.0
OG1 A:THR199 4.3 30.8 1.0
CB A:VAL198 4.3 19.1 1.0
CA A:THR199 4.3 19.0 1.0
CG A:GLN186 4.3 19.3 1.0
CB A:ASP174 4.4 21.9 1.0
OG1 A:THR176 4.5 34.2 1.0
CB A:GLN186 4.6 17.7 1.0
CG2 A:THR176 4.8 23.4 1.0
C A:PRO197 4.9 23.7 1.0
O A:ASP130 4.9 18.8 1.0
CA A:THR176 4.9 28.8 1.0
CA A:ASP130 4.9 16.1 1.0
CB A:THR199 4.9 19.7 1.0
C A:ASP130 5.0 14.2 1.0

Magnesium binding site 2 out of 6 in 7sf2

Go back to Magnesium Binding Sites List in 7sf2
Magnesium binding site 2 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:18.4
occ:1.00
 OD2 B:ASP174 2.0 24.9 1.0
OE1 B:GLN186 2.0 23.0 1.0
O B:HOH805 2.1 20.4 1.0
OD2 B:ASP130 2.1 17.2 1.0
O B:HOH808 2.1 18.6 1.0
O B:VAL198 2.2 17.9 1.0
CG B:ASP174 2.9 22.0 1.0
CD B:GLN186 3.0 22.7 1.0
CG B:ASP130 3.2 18.1 1.0
OD1 B:ASP174 3.2 23.5 1.0
C B:VAL198 3.3 23.6 1.0
NE2 B:GLN186 3.5 13.1 1.0
N B:VAL198 3.8 23.4 1.0
CB B:ASP130 3.9 15.6 1.0
O B:HOH885 4.0 11.5 1.0
OD1 B:ASP130 4.0 28.4 1.0
CA B:VAL198 4.0 17.9 1.0
N B:THR199 4.2 21.8 1.0
CG B:GLN186 4.3 21.6 1.0
OG1 B:THR199 4.3 24.1 1.0
CB B:ASP174 4.3 17.1 1.0
OG1 B:THR176 4.4 33.9 1.0
CA B:THR199 4.4 18.9 1.0
CB B:VAL198 4.4 17.9 1.0
CB B:GLN186 4.5 25.7 1.0
CG2 B:THR176 4.5 19.4 1.0
CA B:THR176 4.8 28.7 1.0
CB B:THR176 4.9 31.6 1.0
C B:PRO197 5.0 21.8 1.0

Magnesium binding site 3 out of 6 in 7sf2

Go back to Magnesium Binding Sites List in 7sf2
Magnesium binding site 3 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:21.5
occ:1.00
 OD2 C:ASP174 2.0 18.7 1.0
OE1 C:GLN186 2.0 21.9 1.0
O C:VAL198 2.1 24.2 1.0
OD2 C:ASP130 2.1 17.6 1.0
O C:HOH824 2.1 18.1 1.0
O C:HOH874 2.3 26.0 1.0
CG C:ASP174 3.0 24.5 1.0
CG C:ASP130 3.1 21.3 1.0
CD C:GLN186 3.1 21.9 1.0
C C:VAL198 3.2 21.7 1.0
OD1 C:ASP174 3.4 18.9 1.0
NE2 C:GLN186 3.6 15.7 1.0
N C:VAL198 3.8 28.4 1.0
CB C:ASP130 3.9 17.4 1.0
CA C:VAL198 4.0 23.6 1.0
OD1 C:ASP130 4.0 30.8 1.0
O C:HOH816 4.0 14.4 1.0
N C:THR199 4.1 19.7 1.0
OG1 C:THR199 4.1 36.3 1.0
CA C:THR199 4.3 21.4 1.0
CB C:ASP174 4.3 17.8 1.0
CG C:GLN186 4.4 18.9 1.0
CB C:VAL198 4.4 22.4 1.0
OG1 C:THR176 4.5 28.9 1.0
CB C:GLN186 4.6 20.5 1.0
CG2 C:THR176 4.8 27.5 1.0
CB C:THR199 4.9 24.4 1.0
O C:ASP130 4.9 17.2 1.0
C C:PRO197 4.9 27.8 1.0
CA C:THR176 4.9 32.0 1.0
C C:ASP130 5.0 19.9 1.0

Magnesium binding site 4 out of 6 in 7sf2

Go back to Magnesium Binding Sites List in 7sf2
Magnesium binding site 4 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:19.2
occ:1.00
 OE1 D:GLN186 2.0 19.3 1.0
OD2 D:ASP130 2.0 19.5 1.0
O D:HOH829 2.1 16.2 1.0
O D:VAL198 2.1 17.3 1.0
OD2 D:ASP174 2.1 21.7 1.0
O D:HOH826 2.2 21.4 1.0
CG D:ASP130 3.0 22.8 1.0
CD D:GLN186 3.1 22.1 1.0
CG D:ASP174 3.1 17.5 1.0
C D:VAL198 3.2 19.5 1.0
OD1 D:ASP174 3.4 23.6 1.0
NE2 D:GLN186 3.5 14.1 1.0
CB D:ASP130 3.7 15.8 1.0
N D:VAL198 3.7 23.8 1.0
CA D:VAL198 3.9 20.0 1.0
OD1 D:ASP130 4.0 22.4 1.0
O D:HOH861 4.1 21.5 1.0
N D:THR199 4.1 17.5 1.0
OG1 D:THR199 4.2 26.3 1.0
CA D:THR199 4.3 16.3 1.0
CB D:VAL198 4.3 18.3 1.0
CG D:GLN186 4.4 16.0 1.0
CB D:ASP174 4.4 21.7 1.0
CB D:GLN186 4.6 17.5 1.0
OG1 D:THR176 4.6 34.8 1.0
CG2 D:THR176 4.9 22.0 1.0
C D:PRO197 4.9 20.7 1.0
CA D:ASP130 4.9 16.2 1.0
CB D:THR199 4.9 23.8 1.0
CA D:THR176 5.0 22.8 1.0
O D:ASP130 5.0 24.3 1.0
C D:ASP130 5.0 18.7 1.0

Magnesium binding site 5 out of 6 in 7sf2

Go back to Magnesium Binding Sites List in 7sf2
Magnesium binding site 5 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:23.2
occ:1.00
 OE1 E:GLN186 2.0 22.2 1.0
O E:VAL198 2.0 22.6 1.0
O E:HOH854 2.0 18.2 1.0
OD2 E:ASP174 2.0 26.9 1.0
OD2 E:ASP130 2.1 18.3 1.0
O E:HOH832 2.1 18.6 1.0
CD E:GLN186 3.0 24.6 1.0
CG E:ASP174 3.1 20.7 1.0
CG E:ASP130 3.1 23.8 1.0
C E:VAL198 3.1 28.4 1.0
NE2 E:GLN186 3.4 19.4 1.0
OD1 E:ASP174 3.5 19.2 1.0
N E:VAL198 3.7 23.1 1.0
CB E:ASP130 3.8 18.0 1.0
CA E:VAL198 3.9 20.9 1.0
O E:HOH927 3.9 20.7 1.0
OD1 E:ASP130 4.0 27.6 1.0
N E:THR199 4.1 23.9 1.0
OG1 E:THR199 4.2 33.8 1.0
CB E:VAL198 4.3 22.9 1.0
CA E:THR199 4.3 26.5 1.0
CG E:GLN186 4.3 23.4 1.0
CB E:ASP174 4.4 22.1 1.0
CB E:GLN186 4.6 24.9 1.0
OG1 E:THR176 4.6 30.4 1.0
CG2 E:THR176 4.8 21.2 1.0
C E:PRO197 4.9 24.3 1.0
CA E:THR176 4.9 31.0 1.0
CB E:THR199 4.9 27.9 1.0
O E:ASP130 4.9 27.7 1.0
CA E:ASP130 5.0 20.1 1.0
C E:ASP130 5.0 22.1 1.0

Magnesium binding site 6 out of 6 in 7sf2

Go back to Magnesium Binding Sites List in 7sf2
Magnesium binding site 6 out of 6 in the Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg701

b:25.1
occ:1.00
 OD2 F:ASP130 2.0 21.9 1.0
OD2 F:ASP174 2.0 20.8 1.0
OE1 F:GLN186 2.0 27.1 1.0
O F:HOH846 2.2 22.7 1.0
O F:VAL198 2.2 28.8 1.0
O F:HOH810 2.2 24.1 1.0
CG F:ASP130 2.9 29.2 1.0
CD F:GLN186 3.0 28.4 1.0
CG F:ASP174 3.0 25.5 1.0
C F:VAL198 3.3 24.6 1.0
NE2 F:GLN186 3.4 25.0 1.0
OD1 F:ASP174 3.5 34.0 1.0
CB F:ASP130 3.7 29.3 1.0
OD1 F:ASP130 3.8 28.1 1.0
N F:VAL198 3.9 21.6 1.0
O F:HOH857 3.9 21.3 1.0
CA F:VAL198 4.1 21.5 1.0
N F:THR199 4.2 21.9 1.0
OG1 F:THR199 4.2 37.7 1.0
CG F:GLN186 4.3 27.8 1.0
CB F:ASP174 4.3 24.1 1.0
CA F:THR199 4.4 23.9 1.0
CB F:VAL198 4.4 26.3 1.0
CB F:GLN186 4.6 27.0 1.0
OG1 F:THR176 4.7 35.3 1.0
CG2 F:THR176 4.7 25.8 1.0
CA F:ASP130 4.9 27.6 1.0
C F:ASP130 4.9 24.6 1.0
O F:ASP130 4.9 27.9 1.0
CA F:THR176 4.9 27.4 1.0
CB F:THR199 5.0 30.8 1.0

Reference:

Y.Kim, G.Joachimiak, M.Endres, A.Joachimiak. Crystal Structure of Beta-Galactosidase From Bacteroides Cellulosilyticus To Be Published.
Page generated: Thu Oct 3 08:43:14 2024

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