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Magnesium in PDB 1gtv: Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine-5'-Diphosphate (Tdp)

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine-5'-Diphosphate (Tdp)

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine-5'-Diphosphate (Tdp):
2.7.4.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine-5'-Diphosphate (Tdp), PDB code: 1gtv was solved by T.Ursby, M.Weik, E.Fioravanti, M.Delarue, M.Goeldner, D.Bourgeois, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.27 / 1.55
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.353, 76.353, 134.815, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine-5'-Diphosphate (Tdp) (pdb code 1gtv). 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-5'-Diphosphate (Tdp), PDB code: 1gtv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1gtv

Go back to Magnesium Binding Sites List in 1gtv
Magnesium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine-5'-Diphosphate (Tdp)


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-5'-Diphosphate (Tdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:16.5
occ:0.48
MG B:MG301 0.3 11.2 0.5
O A:HOH2244 1.8 19.3 0.5
O2B A:TYD302 1.9 20.3 0.5
O A:HOH2193 2.0 16.9 1.0
O2A A:TYD302 2.0 16.3 0.5
OE1 A:GLU166 2.0 18.2 0.5
OE1 B:GLU166 2.1 15.9 0.5
O1P B:TMP302 2.1 15.6 0.5
O B:HOH2029 2.2 16.6 1.0
OD1 A:ASP9 2.2 13.7 0.5
OD1 B:ASP9 2.2 13.7 0.5
CD B:GLU166 3.1 18.6 0.5
CD A:GLU166 3.1 18.9 0.5
PB A:TYD302 3.2 15.9 0.5
PA A:TYD302 3.3 14.1 0.5
CG A:ASP9 3.3 12.4 0.5
CG B:ASP9 3.3 12.4 0.5
P B:TMP302 3.3 14.4 0.5
O3A A:TYD302 3.5 18.3 0.5
O3P B:TMP302 3.7 12.4 0.5
CG B:GLU166 3.8 15.5 0.5
CG A:GLU166 3.8 16.2 0.5
OE2 B:GLU166 3.9 16.5 0.5
C3' A:TYD302 3.9 16.3 0.5
C3' B:TMP302 4.0 8.6 0.5
O5' B:TMP302 4.0 12.7 0.5
O B:HOH2031 4.0 16.4 1.0
OD2 B:ASP163 4.0 17.4 0.5
O1B A:TYD302 4.0 19.7 0.5
OE2 A:GLU166 4.0 17.5 0.5
O3' B:TMP302 4.0 10.3 0.5
C5' B:TMP302 4.0 11.7 0.5
OD2 A:ASP163 4.0 20.4 0.5
CB A:ASP9 4.1 12.3 0.5
CB B:ASP9 4.1 12.3 0.5
O5' A:TYD302 4.1 13.8 0.5
O3' A:TYD302 4.1 19.4 0.5
C5' A:TYD302 4.2 16.4 0.5
OD2 A:ASP9 4.2 13.1 0.5
OD2 B:ASP9 4.2 13.1 0.5
O B:HOH2027 4.2 28.6 1.0
O A:HOH2246 4.2 38.0 1.0
O3B A:TYD302 4.3 18.7 0.5
O A:HOH2177 4.3 23.9 1.0
C4' B:TMP302 4.3 13.0 0.5
O B:HOH2022 4.4 54.6 0.5
C4' A:TYD302 4.4 17.2 0.5
O B:HOH2028 4.4 53.3 1.0
O1A A:TYD302 4.5 17.5 0.5
O B:HOH2023 4.5 48.6 0.5
O2P B:TMP302 4.5 15.7 0.5
O A:HOH2243 4.7 52.0 0.5
O A:HOH2247 4.8 49.8 1.0
CA A:ASP9 4.9 11.0 0.5
CA B:ASP9 4.9 11.0 0.5
CG B:ASP163 4.9 14.8 0.5

Magnesium binding site 2 out of 2 in 1gtv

Go back to Magnesium Binding Sites List in 1gtv
Magnesium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase Complexed with Thymidine-5'-Diphosphate (Tdp)


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-5'-Diphosphate (Tdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:11.2
occ:0.52
MG A:MG301 0.3 16.5 0.5
OD1 A:ASP9 2.0 13.7 0.5
OD1 B:ASP9 2.0 13.7 0.5
O B:HOH2029 2.0 16.6 1.0
O2A A:TYD302 2.0 16.3 0.5
OE1 B:GLU166 2.0 15.9 0.5
OE1 A:GLU166 2.1 18.2 0.5
O A:HOH2244 2.1 19.3 0.5
O1P B:TMP302 2.1 15.6 0.5
O A:HOH2193 2.1 16.9 1.0
O2B A:TYD302 2.2 20.3 0.5
CG A:ASP9 3.1 12.4 0.5
CG B:ASP9 3.1 12.4 0.5
CD B:GLU166 3.1 18.6 0.5
CD A:GLU166 3.1 18.9 0.5
PA A:TYD302 3.4 14.1 0.5
P B:TMP302 3.4 14.4 0.5
PB A:TYD302 3.5 15.9 0.5
O3A A:TYD302 3.7 18.3 0.5
CG B:GLU166 3.7 15.5 0.5
CG A:GLU166 3.8 16.2 0.5
CB A:ASP9 3.8 12.3 0.5
CB B:ASP9 3.8 12.3 0.5
O B:HOH2031 3.8 16.4 1.0
O3P B:TMP302 3.8 12.4 0.5
C3' A:TYD302 3.9 16.3 0.5
C3' B:TMP302 4.0 8.6 0.5
OD2 A:ASP9 4.0 13.1 0.5
OD2 B:ASP9 4.0 13.1 0.5
OE2 B:GLU166 4.0 16.5 0.5
O3' B:TMP302 4.0 10.3 0.5
O5' B:TMP302 4.1 12.7 0.5
O3' A:TYD302 4.1 19.4 0.5
OE2 A:GLU166 4.1 17.5 0.5
O A:HOH2177 4.2 23.9 1.0
O B:HOH2027 4.2 28.6 1.0
C5' B:TMP302 4.2 11.7 0.5
O A:HOH2246 4.2 38.0 1.0
O5' A:TYD302 4.2 13.8 0.5
O1B A:TYD302 4.2 19.7 0.5
OD2 B:ASP163 4.3 17.4 0.5
OD2 A:ASP163 4.3 20.4 0.5
C5' A:TYD302 4.3 16.4 0.5
C4' B:TMP302 4.4 13.0 0.5
C4' A:TYD302 4.5 17.2 0.5
O1A A:TYD302 4.5 17.5 0.5
O2P B:TMP302 4.5 15.7 0.5
O3B A:TYD302 4.6 18.7 0.5
CA A:ASP9 4.6 11.0 0.5
CA B:ASP9 4.6 11.0 0.5
O B:HOH2022 4.6 54.6 0.5
O B:HOH2028 4.6 53.3 1.0
O B:HOH2023 4.8 48.6 0.5
O A:HOH2247 4.8 49.8 1.0
O A:HOH2243 4.8 52.0 0.5
NH1 A:ARG95 5.0 13.6 0.5
NH1 B:ARG95 5.0 13.6 0.5

Reference:

T.Ursby, M.Weik, E.Fioravanti, M.Delarue, M.Goeldner, D.Bourgeois. Cryophotolysis of Caged Compounds: A Technique For Trapping Intermediate States in Protein Crystals Acta Crystallogr.,Sect.D V. 58 607 2002.
ISSN: ISSN 0907-4449
PubMed: 11914484
DOI: 10.1107/S0907444902002135
Page generated: Mon Dec 14 05:58:24 2020

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