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Magnesium in PDB 3ihk: Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83

Protein crystallography data

The structure of Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83, PDB code: 3ihk was solved by A.Kuzin, M.Abashidze, J.Seetharaman, S.Vorobiev, M.Mao, R.Xiao, C.Ciccosanti, M.Maglaqui, E.L.Foote, L.Zhao, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structuralgenomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.157, 105.157, 121.383, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83 (pdb code 3ihk). 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 Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83, PDB code: 3ihk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ihk

Go back to Magnesium Binding Sites List in 3ihk
Magnesium binding site 1 out of 6 in the Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83


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 Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg219

b:19.1
occ:1.00
O3A A:TPP902 2.5 62.4 1.0
OD2 A:ASP47 2.5 49.1 1.0
OD2 A:ASP45 2.7 43.5 1.0
O3B A:TPP902 2.9 66.0 1.0
OD1 A:ASP45 3.1 40.8 1.0
CG A:ASP45 3.1 40.8 1.0
MG A:MG220 3.2 22.1 1.0
CG A:ASP47 3.3 46.9 1.0
PB A:TPP902 3.3 66.3 1.0
OD1 A:ASP47 3.5 48.2 1.0
O2A A:TPP902 3.6 62.1 1.0
PA A:TPP902 3.6 61.2 1.0
C7 A:TPP902 4.0 50.1 1.0
NZ A:LYS71 4.2 44.4 1.0
O7 A:TPP902 4.2 56.7 1.0
O1B A:TPP902 4.3 63.7 1.0
O2B A:TPP902 4.4 64.8 1.0
CB A:ASP45 4.4 40.7 1.0
CB A:ASP47 4.5 43.3 1.0
O A:ALA69 4.5 55.6 1.0
OD2 A:ASP75 4.6 43.0 1.0
O1A A:TPP902 4.8 60.6 1.0

Magnesium binding site 2 out of 6 in 3ihk

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Magnesium binding site 2 out of 6 in the Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83


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 Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg220

b:22.1
occ:1.00
OD2 A:ASP75 2.4 43.0 1.0
OD1 A:ASP45 2.6 40.8 1.0
OD1 A:ASP47 2.8 48.2 1.0
OD2 A:ASP26 2.9 49.7 1.0
MG A:MG219 3.2 19.1 1.0
CG A:ASP26 3.2 48.6 1.0
CG A:ASP45 3.3 40.8 1.0
OD2 A:ASP45 3.3 43.5 1.0
OD1 A:ASP26 3.3 50.5 1.0
O3A A:TPP902 3.3 62.4 1.0
OG A:SER48 3.6 47.9 1.0
CG A:ASP75 3.6 41.4 1.0
CG A:ASP47 3.7 46.9 1.0
O2A A:TPP902 3.9 62.1 1.0
OD2 A:ASP47 3.9 49.1 1.0
PA A:TPP902 4.1 61.2 1.0
O2B A:TPP902 4.3 64.8 1.0
PB A:TPP902 4.3 66.3 1.0
CB A:ASP26 4.3 44.3 1.0
OD1 A:ASP75 4.3 40.8 1.0
O1A A:TPP902 4.5 60.6 1.0
O3B A:TPP902 4.5 66.0 1.0
N A:ASP45 4.6 37.8 1.0
CB A:ASP75 4.6 40.1 1.0
N A:ASP47 4.6 40.1 1.0
N A:PHE46 4.7 39.5 1.0
CB A:ASP45 4.7 40.7 1.0
CB A:SER48 4.9 47.6 1.0
CB A:ASP47 5.0 43.3 1.0

Magnesium binding site 3 out of 6 in 3ihk

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Magnesium binding site 3 out of 6 in the Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83


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 Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg219

b:2.2
occ:1.00
OD1 B:ASP47 2.4 39.7 1.0
OD2 B:ASP75 2.5 37.1 1.0
OD1 B:ASP26 2.6 41.5 1.0
OD1 B:ASP45 2.6 39.7 1.0
O2A C:TPP902 2.8 50.8 1.0
CG B:ASP26 3.1 40.9 1.0
OG B:SER48 3.4 37.1 1.0
O3A C:TPP902 3.4 52.9 1.0
CG B:ASP47 3.4 40.6 1.0
MG B:MG220 3.5 18.8 1.0
OD2 B:ASP26 3.6 43.9 1.0
CG B:ASP75 3.7 37.7 1.0
CG B:ASP45 3.7 38.4 1.0
PA C:TPP902 3.7 52.7 1.0
OD2 B:ASP47 3.8 41.6 1.0
CB B:ASP26 3.9 37.7 1.0
OD2 B:ASP45 4.1 39.1 1.0
N B:ASP47 4.3 35.7 1.0
CB B:SER48 4.5 35.7 1.0
OD1 B:ASP75 4.5 39.0 1.0
N B:SER48 4.5 35.4 1.0
N B:PHE46 4.6 37.0 1.0
CB B:ASP75 4.7 35.2 1.0
O7 C:TPP902 4.7 51.3 1.0
N B:ASP45 4.7 33.4 1.0
CB B:ASP47 4.7 37.8 1.0
O1A C:TPP902 4.9 51.8 1.0
PB C:TPP902 4.9 54.6 1.0
CA B:ASP47 4.9 36.3 1.0
CB B:ASP45 5.0 36.8 1.0

Magnesium binding site 4 out of 6 in 3ihk

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Magnesium binding site 4 out of 6 in the Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83


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 Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg220

b:18.8
occ:1.00
OD2 B:ASP45 2.5 39.1 1.0
OD2 B:ASP47 2.8 41.6 1.0
O3A C:TPP902 2.8 52.9 1.0
O7 C:TPP902 2.9 51.3 1.0
O3B C:TPP902 2.9 54.4 1.0
CG B:ASP45 3.1 38.4 1.0
OD1 B:ASP45 3.1 39.7 1.0
PA C:TPP902 3.3 52.7 1.0
CG B:ASP47 3.5 40.6 1.0
O2A C:TPP902 3.5 50.8 1.0
PB C:TPP902 3.5 54.6 1.0
MG B:MG219 3.5 2.2 1.0
OD1 B:ASP47 3.7 39.7 1.0
O B:ALA69 3.7 49.4 1.0
NZ B:LYS71 3.8 44.0 1.0
C7 C:TPP902 3.9 47.5 1.0
C6 C:TPP902 4.3 43.8 1.0
O2B C:TPP902 4.3 54.3 1.0
CB B:ASP45 4.4 36.8 1.0
OD2 B:ASP75 4.4 37.1 1.0
CB B:ASP47 4.7 37.8 1.0
C B:ALA69 4.7 50.1 1.0
O1A C:TPP902 4.7 51.8 1.0
O1B C:TPP902 4.7 52.4 1.0
OD1 B:ASP75 5.0 39.0 1.0

Magnesium binding site 5 out of 6 in 3ihk

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Magnesium binding site 5 out of 6 in the Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83


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 Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg220

b:48.6
occ:1.00
OD2 C:ASP75 2.7 45.9 1.0
OD1 C:ASP45 2.7 66.7 1.0
OD2 C:ASP26 3.0 54.6 1.0
O3A C:TPP219 3.0 77.8 1.0
OD1 C:ASP47 3.1 70.2 1.0
O2A C:TPP219 3.1 77.5 1.0
OD2 C:ASP45 3.2 67.0 1.0
CG C:ASP45 3.3 65.9 1.0
OD2 C:ASP47 3.4 69.7 1.0
CG C:ASP47 3.6 70.0 1.0
CG C:ASP75 3.6 46.5 1.0
PA C:TPP219 3.7 78.3 1.0
CG C:ASP26 3.9 54.2 1.0
OG C:SER48 4.0 73.7 1.0
MG C:MG221 4.1 40.9 1.0
OD1 C:ASP26 4.2 55.7 1.0
O2B C:TPP219 4.3 78.3 1.0
PB C:TPP219 4.3 78.5 1.0
CB C:ASP75 4.4 45.8 1.0
OD1 C:ASP75 4.4 46.5 1.0
O7 C:TPP219 4.6 73.6 1.0
CB C:ASP45 4.8 64.2 1.0
O1A C:TPP219 4.9 77.8 1.0

Magnesium binding site 6 out of 6 in 3ihk

Go back to Magnesium Binding Sites List in 3ihk
Magnesium binding site 6 out of 6 in the Crystal Structure of Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83


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 Thiamin Pyrophosphokinase From S.Mutans, Northeast Structural Genomics Consortium Target SMR83 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg221

b:40.9
occ:1.00
OD2 C:ASP45 2.8 67.0 1.0
O3B C:TPP219 2.9 77.7 1.0
O3A C:TPP219 3.0 77.8 1.0
O7 C:TPP219 3.1 73.6 1.0
NZ C:LYS71 3.2 59.7 1.0
OD2 C:ASP47 3.2 69.7 1.0
PB C:TPP219 3.5 78.5 1.0
PA C:TPP219 3.7 78.3 1.0
CG C:ASP45 3.8 65.9 1.0
O2B C:TPP219 3.9 78.3 1.0
C7 C:TPP219 3.9 65.5 1.0
C6 C:TPP219 4.0 59.3 1.0
MG C:MG220 4.1 48.6 1.0
O C:ALA69 4.1 65.3 1.0
O2A C:TPP219 4.4 77.5 1.0
CE C:LYS71 4.4 60.5 1.0
CG C:ASP47 4.5 70.0 1.0
OD1 C:ASP45 4.5 66.7 1.0
CB C:ASP45 4.8 64.2 1.0
O1B C:TPP219 4.9 77.3 1.0
O1A C:TPP219 4.9 77.8 1.0

Reference:

A.Kuzin, M.Abashidze, J.Seetharaman, S.Vorobiev, M.Mao, R.Xiao, C.Ciccosanti, M.Maglaqui, E.L.Foote, L.Zhao, J.K.Everett, R.Nair, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong. Northeast Structural Genomics Consortium Target SMR83 To Be Published.
Page generated: Mon Dec 14 08:16:56 2020

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