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Magnesium in PDB 3lm8: Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677

Enzymatic activity of Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677

All present enzymatic activity of Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677:
2.7.6.2;

Protein crystallography data

The structure of Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677, PDB code: 3lm8 was solved by A.Kuzin, M.Abashidze, J.Seetharaman, M.Mao, R.Xiao, E.L.Foote, C.Ciccosanti, H.Wang, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomicsconsortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.943, 62.153, 84.161, 82.89, 82.02, 87.61
R / Rfree (%) 21.3 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677 (pdb code 3lm8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677, PDB code: 3lm8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3lm8

Go back to Magnesium Binding Sites List in 3lm8
Magnesium binding site 1 out of 5 in the Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677


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 Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg225

b:52.3
occ:1.00
 OD2 A:ASP51 3.6 49.7 1.0
OD1 A:ASP53 3.8 57.9 1.0
OD1 A:ASP51 4.3 36.9 1.0
CG A:ASP51 4.4 45.8 1.0
OD2 A:ASP81 4.5 67.1 1.0
OD2 A:ASP53 4.5 46.7 1.0
CG A:ASP53 4.6 49.1 1.0
C6 C:VIB223 4.7 36.6 1.0
C7 C:VIB223 5.0 53.6 1.0

Magnesium binding site 2 out of 5 in 3lm8

Go back to Magnesium Binding Sites List in 3lm8
Magnesium binding site 2 out of 5 in the Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677


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 Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg226

b:43.3
occ:1.00
 O A:LYS12 3.7 26.5 1.0
O A:ILE15 4.1 26.0 1.0
C A:LYS12 4.6 36.0 1.0
CB A:LYS12 4.6 31.3 1.0
CE A:LYS12 4.6 51.2 1.0
O A:PRO16 4.6 30.3 1.0

Magnesium binding site 3 out of 5 in 3lm8

Go back to Magnesium Binding Sites List in 3lm8
Magnesium binding site 3 out of 5 in the Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677


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 Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg226

b:46.8
occ:1.00
 OD2 B:ASP51 3.7 38.4 1.0
C6 D:VIB223 4.4 52.3 1.0
OD1 B:ASP53 4.4 52.4 1.0
CG B:ASP51 4.6 37.4 1.0
OD1 B:ASP51 4.7 44.6 1.0

Magnesium binding site 4 out of 5 in 3lm8

Go back to Magnesium Binding Sites List in 3lm8
Magnesium binding site 4 out of 5 in the Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677


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 Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg227

b:40.6
occ:1.00
 OD1 B:ASP53 4.1 52.4 1.0
OD2 B:ASP53 4.3 54.5 1.0
O4 B:PO4225 4.4 87.9 1.0
CG B:ASP53 4.6 42.8 1.0
OD2 B:ASP51 4.7 38.4 1.0
NE2 B:GLN74 5.0 71.1 1.0

Magnesium binding site 5 out of 5 in 3lm8

Go back to Magnesium Binding Sites List in 3lm8
Magnesium binding site 5 out of 5 in the Crystal Structure of Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677


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 Thiamine Pyrophosphokinase From Bacillus Subtilis, Northeast Structural Genomics Consortium Target SR677 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg228

b:40.3
occ:1.00
 OD1 B:ASP23 4.0 67.0 1.0
CD2 B:HIS25 4.2 61.2 1.0
OD2 B:ASP23 4.2 44.4 1.0
OE1 B:GLU24 4.3 71.1 1.0
CG B:ASP23 4.6 60.1 1.0
CB B:GLU24 4.7 55.3 1.0
NE2 B:HIS25 4.7 59.9 1.0
CD B:GLU24 5.0 68.6 1.0

Reference:

A.Kuzin, M.Abashidze, J.Seetharaman, M.Mao, R.Xiao, E.L.Foote, C.Ciccosanti, H.Wang, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong. Northeast Structural Genomics Consortium Target SR677 To Be Published.
Page generated: Wed Aug 14 18:34:38 2024

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