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Magnesium in PDB 1n5j: Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution)

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution)

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution):
2.7.4.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution), PDB code: 1n5j was solved by E.Fioravanti, A.Haouz, T.Ursby, H.Munier-Lehmann, M.Delarue, D.Bourgeois, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.96 / 1.85
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.248, 76.248, 135.114, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution) (pdb code 1n5j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution), PDB code: 1n5j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1n5j

Go back to Magnesium Binding Sites List in 1n5j
Magnesium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution)


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 Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg217

b:11.9
occ:0.54
 MG A:MG217 0.0 11.9 0.5
MG A:MG217 0.2 19.2 0.5
O A:HOH1009 2.0 12.3 0.5
O2B A:TYD218 2.0 12.0 0.5
O2A A:TYD218 2.1 12.3 0.5
O A:HOH1018 2.2 12.1 0.5
O2B A:TTP219 2.2 19.8 0.5
OE1 A:GLU166 2.2 15.3 1.0
OD1 A:ASP9 2.4 16.7 1.0
O2A A:TTP219 2.5 19.2 0.5
O A:HOH1018 2.5 12.8 0.5
O A:HOH1009 2.6 14.3 0.5
CD A:GLU166 3.2 15.8 1.0
PB A:TYD218 3.3 12.1 0.5
PA A:TYD218 3.3 12.4 0.5
CG A:ASP9 3.4 14.4 1.0
PB A:TTP219 3.5 21.1 0.5
O3A A:TYD218 3.6 12.4 0.5
PA A:TTP219 3.7 20.1 0.5
CG A:GLU166 3.8 12.8 1.0
C5' A:TTP219 3.9 13.5 0.5
O3A A:TTP219 3.9 20.1 0.5
C3' A:TYD218 4.0 12.2 0.5
O A:HOH1119 4.0 22.0 1.0
OE2 A:GLU166 4.0 15.5 1.0
O A:HOH1014 4.1 13.6 1.0
O1B A:TYD218 4.1 14.1 0.5
CB A:ASP9 4.1 15.5 1.0
O3' A:TYD218 4.1 14.2 0.5
OD2 A:ASP163 4.1 17.7 1.0
O A:HOH1036 4.2 36.8 1.0
C3' A:TTP219 4.2 12.9 0.5
O5' A:TYD218 4.2 12.6 0.5
C5' A:TYD218 4.2 12.7 0.5
OD2 A:ASP9 4.2 13.6 1.0
O3B A:TYD218 4.3 12.8 0.5
O5' A:TTP219 4.4 17.0 0.5
C4' A:TYD218 4.4 12.5 0.5
O3B A:TTP219 4.4 22.1 0.5
O1G A:TTP219 4.5 24.1 0.5
C4' A:TTP219 4.5 12.9 0.5
O3' A:TTP219 4.5 11.7 0.5
O1A A:TYD218 4.5 12.5 0.5
O1B A:TTP219 4.6 19.9 0.5
O2G A:TTP219 4.6 23.0 0.5
PG A:TTP219 4.7 24.4 0.5
O1A A:TTP219 4.9 21.1 0.5
CA A:ASP9 4.9 14.5 1.0
O A:HOH1151 5.0 30.8 1.0

Magnesium binding site 2 out of 2 in 1n5j

Go back to Magnesium Binding Sites List in 1n5j
Magnesium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution)


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 Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine Diphosphate (Tdp) and Thymidine Triphosphate (Ttp) at pH 5.4 (1.85 A Resolution) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg217

b:19.2
occ:0.45
 MG A:MG217 0.0 19.2 0.5
MG A:MG217 0.2 11.9 0.5
O A:HOH1009 1.9 12.3 0.5
O2A A:TYD218 2.0 12.3 0.5
OD1 A:ASP9 2.2 16.7 1.0
O2B A:TYD218 2.2 12.0 0.5
O A:HOH1018 2.2 12.1 0.5
OE1 A:GLU166 2.3 15.3 1.0
O2B A:TTP219 2.4 19.8 0.5
O2A A:TTP219 2.4 19.2 0.5
O A:HOH1009 2.5 14.3 0.5
O A:HOH1018 2.6 12.8 0.5
CG A:ASP9 3.2 14.4 1.0
CD A:GLU166 3.2 15.8 1.0
PA A:TYD218 3.4 12.4 0.5
PB A:TYD218 3.5 12.1 0.5
O3A A:TYD218 3.7 12.4 0.5
PB A:TTP219 3.7 21.1 0.5
PA A:TTP219 3.7 20.1 0.5
CG A:GLU166 3.8 12.8 1.0
C3' A:TYD218 3.8 12.2 0.5
CB A:ASP9 3.9 15.5 1.0
C5' A:TTP219 3.9 13.5 0.5
O3' A:TYD218 4.0 14.2 0.5
O A:HOH1014 4.0 13.6 1.0
OD2 A:ASP9 4.0 13.6 1.0
C3' A:TTP219 4.0 12.9 0.5
O3A A:TTP219 4.0 20.1 0.5
OE2 A:GLU166 4.1 15.5 1.0
O5' A:TYD218 4.2 12.6 0.5
OD2 A:ASP163 4.2 17.7 1.0
C5' A:TYD218 4.2 12.7 0.5
O A:HOH1119 4.2 22.0 1.0
O A:HOH1036 4.2 36.8 1.0
O1B A:TYD218 4.3 14.1 0.5
O3' A:TTP219 4.3 11.7 0.5
C4' A:TYD218 4.3 12.5 0.5
O5' A:TTP219 4.4 17.0 0.5
C4' A:TTP219 4.4 12.9 0.5
O3B A:TYD218 4.5 12.8 0.5
O1A A:TYD218 4.5 12.5 0.5
O3B A:TTP219 4.6 22.1 0.5
O1G A:TTP219 4.7 24.1 0.5
CA A:ASP9 4.8 14.5 1.0
O1B A:TTP219 4.8 19.9 0.5
O2G A:TTP219 4.8 23.0 0.5
O1A A:TTP219 4.9 21.1 0.5
PG A:TTP219 5.0 24.4 0.5
NH1 A:ARG95 5.0 12.1 1.0

Reference:

E.Fioravanti, A.Haouz, T.Ursby, H.Munier-Lehmann, M.Delarue, D.Bourgeois. Mycobacterium Tuberculosis Thymidylate Kinase: Structural Studies of Intermediates Along the Reaction Pathway J.Mol.Biol. V. 327 1077 2003.
ISSN: ISSN 0022-2836
PubMed: 12662932
DOI: 10.1016/S0022-2836(03)00202-X
Page generated: Sun Aug 10 01:18:29 2025

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