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Sodium in PDB 5etp: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution:
2.7.6.3;

Protein crystallography data

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution, PDB code: 5etp was solved by M.L.Dennis, T.S.Peat, J.D.Swarbrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.70 / 1.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.950, 57.770, 38.640, 90.00, 116.11, 90.00
R / Rfree (%) 10.7 / 12.5

Other elements in 5etp:

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution also contains other interesting chemical elements:

Bromine (Br) 1 atom
Calcium (Ca) 4 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution (pdb code 5etp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution, PDB code: 5etp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5etp

Go back to Sodium Binding Sites List in 5etp
Sodium binding site 1 out of 3 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:20.4
occ:1.00
 O A:HOH409 2.2 30.0 1.0
O A:HOH539 2.2 19.4 1.0
OD2 A:ASP139 2.3 9.1 1.0
O A:HOH406 2.3 10.7 1.0
O A:HOH528 2.5 12.2 1.0
O A:HOH465 2.6 18.8 1.0
O A:HOH321 2.7 21.4 1.0
CG A:ASP139 3.5 6.1 1.0
CB A:ASP139 4.0 5.7 1.0
NZ A:LYS119 4.1 7.4 1.0
O A:HOH545 4.3 16.1 1.0
O A:HOH322 4.4 14.7 1.0
OD1 A:ASP139 4.5 5.8 1.0
OE1 A:GLU141 4.9 9.6 1.0

Sodium binding site 2 out of 3 in 5etp

Go back to Sodium Binding Sites List in 5etp
Sodium binding site 2 out of 3 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:29.5
occ:1.00
 O A:HOH509 2.2 30.0 1.0
O A:MET0 2.2 10.4 0.5
O A:MET0 2.2 10.4 0.5
O A:HOH327 2.2 30.0 1.0
O A:HOH454 3.0 24.2 1.0
C A:MET0 3.4 7.4 0.5
C A:MET0 3.4 7.4 0.5
N A:MET0 4.1 11.2 0.5
N A:MET0 4.1 11.2 0.5
CA A:MET0 4.2 9.4 0.5
CA A:MET0 4.2 9.4 0.5
N A:THR1 4.4 5.6 1.0
O A:HOH533 4.5 23.8 1.0
CB A:MET0 4.5 11.9 0.5
CB A:MET0 4.5 11.9 0.5
CA A:THR1 4.6 5.9 1.0
O A:HOH490 4.8 15.5 1.0
O A:HOH440 4.8 19.1 1.0

Sodium binding site 3 out of 3 in 5etp

Go back to Sodium Binding Sites List in 5etp
Sodium binding site 3 out of 3 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:8.1
occ:1.00
 O A:HOH511 2.4 17.5 1.0
O A:HOH480 2.4 10.4 1.0
O A:HOH430 2.4 19.5 1.0
O A:HOH313 2.4 15.0 1.0
OE1 A:GLU30 2.4 10.5 1.0
O A:SER63 2.7 8.3 1.0
CD A:GLU30 3.5 8.8 1.0
C A:SER63 3.6 5.1 1.0
OE2 A:GLU30 3.8 10.7 1.0
OG A:SER63 4.0 7.9 1.0
CB A:SER63 4.0 6.3 1.0
O A:HOH426 4.2 11.2 1.0
O A:HOH341 4.3 13.4 1.0
O A:HOH447 4.3 15.5 1.0
N A:LEU64 4.3 4.3 1.0
CA A:LEU64 4.4 4.1 1.0
CA A:SER63 4.5 4.7 1.0
O A:HOH508 4.7 13.8 1.0
CG A:GLU30 4.8 7.6 1.0
C A:LEU64 5.0 4.2 1.0

Reference:

M.L.Dennis, N.P.Pitcher, M.D.Lee, A.J.Debono, Z.C.Wang, J.R.Harjani, R.Rahmani, B.Cleary, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structural Basis For the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase From Staphylococcus Aureus and Escherichia Coli. J.Med.Chem. V. 59 5248 2016.
ISSN: ISSN 0022-2623
PubMed: 27094768
DOI: 10.1021/ACS.JMEDCHEM.6B00002
Page generated: Mon Oct 7 20:51:15 2024

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