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Magnesium in PDB 2dft: Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution

Enzymatic activity of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution

All present enzymatic activity of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution:
2.7.1.71;

Protein crystallography data

The structure of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution, PDB code: 2dft was solved by M.V.Dias, L.M.Faim, I.B.Vasconcelos, J.S.De Oliveira, L.A.Basso, D.S.Santos, W.F.De Azevedo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.17 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.619, 62.203, 170.633, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 28.2

Other elements in 2dft:

The structure of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution (pdb code 2dft). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution, PDB code: 2dft:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2dft

Go back to Magnesium Binding Sites List in 2dft
Magnesium binding site 1 out of 4 in the Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg190

b:22.4
occ:1.00
 O2B A:ADP180 2.2 22.4 1.0
O3B A:ADP180 2.6 23.1 1.0
OG A:SER16 2.8 30.8 1.0
PB A:ADP180 2.8 19.0 1.0
O1A A:ADP180 3.3 17.1 1.0
O3A A:ADP180 3.6 14.2 1.0
PA A:ADP180 4.1 15.1 1.0
CB A:SER16 4.2 15.6 1.0
O1B A:ADP180 4.3 20.2 1.0
N A:SER16 4.4 17.3 1.0
O2A A:ADP180 4.6 15.1 1.0
O A:HOH449 4.6 41.3 1.0
O A:HOH343 4.7 28.6 1.0
CA A:SER16 4.9 15.5 1.0
CE A:LYS15 4.9 11.1 1.0
NZ A:LYS15 5.0 14.6 1.0
OD2 A:ASP32 5.0 36.4 1.0

Magnesium binding site 2 out of 4 in 2dft

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Magnesium binding site 2 out of 4 in the Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg196

b:15.3
occ:1.00
 O B:HOH312 2.0 2.0 1.0
O B:HOH254 2.5 13.4 1.0
O2B B:ADP181 2.5 10.5 1.0
OG B:SER16 2.6 21.9 1.0
O3B B:ADP181 3.0 17.9 1.0
O B:HOH251 3.0 15.9 1.0
PB B:ADP181 3.2 16.1 1.0
OD2 B:ASP34 3.7 27.8 1.0
CB B:SER16 4.0 15.3 1.0
CE B:LYS15 4.2 14.8 1.0
N B:SER16 4.2 20.2 1.0
O1B B:ADP181 4.3 15.6 1.0
CB B:LYS15 4.3 11.8 1.0
O1A B:ADP181 4.5 21.9 1.0
O3A B:ADP181 4.6 23.4 1.0
CG B:ASP34 4.6 29.4 1.0
CL B:CL199 4.6 26.6 1.0
NZ B:LYS15 4.6 20.5 1.0
CA B:SER16 4.6 20.3 1.0
OD2 B:ASP32 4.8 15.9 1.0
CB B:ASP34 4.9 24.4 1.0
OD1 B:ASP32 4.9 25.9 1.0
C B:LYS15 5.0 19.6 1.0

Magnesium binding site 3 out of 4 in 2dft

Go back to Magnesium Binding Sites List in 2dft
Magnesium binding site 3 out of 4 in the Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:29.4
occ:1.00
 O2B C:ADP182 2.1 43.0 1.0
OG C:SER16 2.4 26.4 1.0
PB C:ADP182 3.1 33.4 1.0
O1B C:ADP182 3.3 38.1 1.0
CB C:SER16 3.4 27.1 1.0
OD2 A:ASP47 3.4 60.5 1.0
O1A C:ADP182 3.7 32.8 1.0
O3A C:ADP182 4.2 35.6 1.0
O3B C:ADP182 4.2 54.2 1.0
CG A:ASP47 4.3 53.3 1.0
N C:SER16 4.4 35.0 1.0
OD1 A:ASP47 4.4 58.7 1.0
CA C:SER16 4.4 26.4 1.0
PA C:ADP182 4.5 28.0 1.0
O C:HOH233 4.8 20.9 1.0
CG C:LYS15 4.9 24.9 1.0

Magnesium binding site 4 out of 4 in 2dft

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Magnesium binding site 4 out of 4 in the Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Shikimate Kinase From Mycobacterium Tuberculosis Complexed with Adp and Mg at 2.8 Angstrons of Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg208

b:41.5
occ:1.00
 O2B D:ADP183 1.8 27.8 1.0
OG D:SER16 2.2 38.0 1.0
CB D:SER16 3.1 34.4 1.0
PB D:ADP183 3.1 32.9 1.0
O3B D:ADP183 3.5 37.0 1.0
OD2 D:ASP32 3.7 34.4 1.0
N D:SER16 3.9 37.0 1.0
O1A D:ADP183 4.0 35.1 1.0
O1B D:ADP183 4.0 33.9 1.0
CA D:SER16 4.1 29.2 1.0
CG D:LYS15 4.1 32.0 1.0
O3A D:ADP183 4.3 34.3 1.0
PA D:ADP183 4.5 30.8 1.0
OD1 D:ASP32 4.5 33.7 1.0
O2A D:ADP183 4.5 29.6 1.0
CG D:ASP32 4.5 38.9 1.0
NZ D:LYS15 4.7 27.6 1.0
NH1 D:ARG117 4.8 27.6 1.0
OD2 D:ASP34 4.8 14.1 1.0
C D:LYS15 4.9 29.6 1.0
CE D:LYS15 4.9 37.1 1.0
CB D:LYS15 5.0 23.8 1.0
N D:LYS15 5.0 23.4 1.0

Reference:

M.V.Dias, L.M.Faim, I.B.Vasconcelos, J.S.De Oliveira, L.A.Basso, D.S.Santos, W.F.De Azevedo. Effects of the Magnesium and Chloride Ions and Shikimate on the Structure of Shikimate Kinase From Mycobacterium Tuberculosis Acta Crystallogr.,Sect.F V. 63 1 2007.
ISSN: ESSN 1744-3091
PubMed: 17183161
DOI: 10.1107/S1744309106046823
Page generated: Sun Aug 10 10:27:05 2025

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