Magnesium in PDB 5tkv: X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase

Enzymatic activity of X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase

All present enzymatic activity of X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase:
6.3.4.2;

Protein crystallography data

The structure of X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase, PDB code: 5tkv was solved by E.P.Baldwin, J.A.Endrizzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.02 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.159, 110.675, 129.487, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase (pdb code 5tkv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase, PDB code: 5tkv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5tkv

Go back to Magnesium Binding Sites List in 5tkv
Magnesium binding site 1 out of 2 in the X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:34.4
occ:1.00
O B:HOH821 2.0 44.4 1.0
O1G B:CTP603 2.0 22.9 1.0
O1A B:CTP603 2.1 21.8 1.0
O1B B:CTP603 2.1 35.2 1.0
O B:HOH841 2.1 38.5 1.0
O B:HOH788 2.2 34.5 1.0
PB B:CTP603 3.1 25.9 1.0
PA B:CTP603 3.3 24.3 1.0
PG B:CTP603 3.3 25.2 1.0
O3A B:CTP603 3.6 31.2 1.0
O3B B:CTP603 3.6 28.9 1.0
O2G B:CTP603 4.0 26.1 1.0
NZ A:LYS223 4.1 24.7 1.0
OE2 A:GLU185 4.3 68.7 1.0
NZ A:LYS187 4.3 24.2 1.0
O2A B:CTP603 4.3 26.3 1.0
O5' B:CTP603 4.4 16.9 1.0
O2B B:CTP603 4.5 30.5 1.0
O3G B:CTP603 4.6 27.3 1.0
C5' B:CTP603 4.6 22.4 1.0
O B:HOH790 4.8 37.7 1.0
OE1 A:GLU185 4.9 67.4 1.0
CD A:GLU185 5.0 72.8 1.0

Magnesium binding site 2 out of 2 in 5tkv

Go back to Magnesium Binding Sites List in 5tkv
Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of the "Closed" Conformation of Ctp-Inhibited E. Coli Cytidine Triphosphate (Ctp) Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:40.0
occ:1.00
O2B B:CTP601 2.1 30.4 1.0
O B:HOH837 2.1 48.0 1.0
O2A B:CTP601 2.1 23.7 1.0
O B:HOH812 2.2 34.2 1.0
O3G B:CTP601 2.2 20.7 1.0
O B:HOH796 2.2 38.7 1.0
PB B:CTP601 3.2 24.6 1.0
PG B:CTP601 3.4 25.8 1.0
PA B:CTP601 3.5 23.1 1.0
O3B B:CTP601 3.7 28.7 1.0
O3A B:CTP601 3.8 32.5 1.0
O2G B:CTP601 3.9 23.7 1.0
NZ B:LYS223 4.1 33.1 1.0
NZ B:LYS187 4.3 19.8 1.0
O1A B:CTP601 4.5 24.2 1.0
O B:HOH886 4.5 36.0 1.0
OE2 B:GLU185 4.5 70.6 1.0
O5' B:CTP601 4.5 19.7 1.0
O1B B:CTP601 4.6 26.3 1.0
OE1 B:GLU185 4.6 57.0 1.0
O1G B:CTP601 4.7 22.3 1.0
C5' B:CTP601 4.8 23.6 1.0
CD B:GLU185 5.0 80.9 1.0

Reference:

E.M.Lynch, D.R.Hicks, M.Shepherd, J.A.Endrizzi, A.Maker, J.M.Hansen, R.M.Barry, Z.Gitai, E.P.Baldwin, J.M.Kollman. Human Ctp Synthase Filament Structure Reveals the Active Enzyme Conformation. Nat. Struct. Mol. Biol. V. 24 507 2017.
ISSN: ESSN 1545-9985
PubMed: 28459447
DOI: 10.1038/NSMB.3407
Page generated: Mon Dec 14 21:12:40 2020

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