Magnesium in PDB 6czf: The Structure of E. Coli Purf in Complex with Ppgpp-Mg

All present enzymatic activity of The Structure of E. Coli Purf in Complex with Ppgpp-Mg:
2.4.2.14;

The structure of The Structure of E. Coli Purf in Complex with Ppgpp-Mg, PDB code: 6czf was solved by B.Wang, R.A.Grant, M.T.Laub, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.64 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.293, 115.339, 156.066, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.1

The binding sites of Magnesium atom in the The Structure of E. Coli Purf in Complex with Ppgpp-Mg (pdb code 6czf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structure of E. Coli Purf in Complex with Ppgpp-Mg, PDB code: 6czf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Structure of E. Coli Purf in Complex with Ppgpp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of E. Coli Purf in Complex with Ppgpp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:36.7 occ:0.56 MG A:MG501 0.0 36.7 0.6 H3' A:G4P502 1.3 44.1 0.5 O1D A:G4P502 1.6 33.7 0.5 O2C A:G4P502 1.8 33.8 0.5 PC A:G4P502 1.9 39.8 0.5 O1B A:G4P502 1.9 35.7 0.5 O3C A:G4P502 2.0 29.3 0.5 C3' A:G4P502 2.0 36.8 0.5 PD A:G4P502 2.0 34.5 0.5 O3' A:G4P502 2.1 28.5 0.5 O2C A:G4P502 2.2 31.4 0.5 O1D A:G4P502 2.2 34.0 0.5 O2A A:G4P502 2.2 35.5 0.5 MG A:MG501 2.6 38.5 0.4 O3D A:G4P502 2.7 42.0 0.5 O2A A:G4P502 2.8 35.3 0.5 C2' A:G4P502 3.1 36.3 0.5 H3' A:G4P502 3.2 42.9 0.5 C4' A:G4P502 3.2 36.9 0.5 H4' A:G4P502 3.3 44.3 0.5 O1C A:G4P502 3.4 35.3 0.5 PB A:G4P502 3.4 33.2 0.5 HH12 C:ARG45 3.4 47.0 1.0 H2' A:G4P502 3.4 43.6 0.5 O2' A:G4P502 3.4 41.5 0.5 O2D A:G4P502 3.4 40.0 0.5 PC A:G4P502 3.5 35.8 0.5 PD A:G4P502 3.5 34.6 0.5 PA A:G4P502 3.5 30.5 0.5 HH12 A:ARG45 3.5 55.2 1.0 O3C A:G4P502 3.8 31.8 0.5 O3A A:G4P502 3.8 36.0 0.5 O1B A:G4P502 3.9 34.3 0.5 H5'' A:G4P502 3.9 42.3 0.5 C5' A:G4P502 4.0 35.3 0.5 PA A:G4P502 4.0 32.7 0.5 O5' A:G4P502 4.0 34.4 0.5 O2D A:G4P502 4.1 38.5 0.5 C3' A:G4P502 4.1 35.8 0.5 NH1 A:ARG45 4.1 46.0 1.0 HH22 C:ARG45 4.2 54.1 1.0 NH1 C:ARG45 4.2 39.2 1.0 O2B A:G4P502 4.3 32.9 0.5 O5' A:G4P502 4.3 34.7 0.5 O3' A:G4P502 4.3 28.0 0.5 HO2' A:G4P502 4.3 49.8 0.5 O3B A:G4P502 4.3 30.7 0.5 HE2 A:HIS59 4.3 66.7 1.0 C1' A:G4P502 4.3 34.1 0.5 O4' A:G4P502 4.4 32.9 0.5 HH11 A:ARG45 4.4 55.2 1.0 H4' A:G4P502 4.4 43.8 0.5 HH21 A:ARG58 4.6 71.9 1.0 HH22 A:ARG45 4.6 59.7 1.0 O3D A:G4P502 4.6 38.7 0.5 O1C A:G4P502 4.7 34.0 0.5 O1A A:G4P502 4.7 34.8 0.5 HH11 C:ARG45 4.7 47.0 1.0 C4' A:G4P502 4.7 36.5 0.5 H1' A:G4P502 4.9 40.9 0.5 H5'' A:G4P502 4.9 45.9 0.5 C5' A:G4P502 4.9 38.3 0.5 NH2 C:ARG45 4.9 45.1 1.0 O3A A:G4P502 5.0 35.1 0.5

Magnesium binding site 2 out of 4 in the The Structure of E. Coli Purf in Complex with Ppgpp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of E. Coli Purf in Complex with Ppgpp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:38.5 occ:0.44 MG A:MG501 0.0 38.5 0.4 H3' A:G4P502 1.2 42.9 0.5 O2C A:G4P502 1.6 31.4 0.5 PC A:G4P502 1.6 35.8 0.5 O3' A:G4P502 1.8 28.0 0.5 C3' A:G4P502 1.8 35.8 0.5 O1D A:G4P502 2.0 34.0 0.5 O1B A:G4P502 2.0 34.3 0.5 O2A A:G4P502 2.1 35.3 0.5 O3C A:G4P502 2.2 31.8 0.5 O1D A:G4P502 2.2 33.7 0.5 PD A:G4P502 2.4 34.6 0.5 O2C A:G4P502 2.5 33.8 0.5 MG A:MG501 2.6 36.7 0.6 O2A A:G4P502 2.7 35.5 0.5 H4' A:G4P502 2.8 43.8 0.5 C4' A:G4P502 2.9 36.5 0.5 O3D A:G4P502 3.0 38.7 0.5 C2' A:G4P502 3.1 39.0 0.5 O1C A:G4P502 3.1 34.0 0.5 H3' A:G4P502 3.2 44.1 0.5 HH12 A:ARG45 3.2 55.2 1.0 PB A:G4P502 3.4 34.3 0.5 PA A:G4P502 3.4 32.7 0.5 O2' A:G4P502 3.4 38.0 0.5 H2' A:G4P502 3.5 46.9 0.5 PD A:G4P502 3.5 34.5 0.5 HH12 C:ARG45 3.7 47.0 1.0 C5' A:G4P502 3.7 38.3 0.5 O3A A:G4P502 3.7 35.1 0.5 H5'' A:G4P502 3.7 45.9 0.5 PC A:G4P502 3.7 39.8 0.5 O2D A:G4P502 3.8 38.5 0.5 O5' A:G4P502 3.9 34.7 0.5 O1B A:G4P502 3.9 35.7 0.5 PA A:G4P502 3.9 30.5 0.5 O3C A:G4P502 4.0 29.3 0.5 O4' A:G4P502 4.1 35.2 0.5 NH1 A:ARG45 4.1 46.0 1.0 HH22 A:ARG45 4.1 59.7 1.0 C1' A:G4P502 4.2 35.6 0.5 C3' A:G4P502 4.2 36.8 0.5 O5' A:G4P502 4.2 34.4 0.5 O2B A:G4P502 4.2 37.8 0.5 O2D A:G4P502 4.3 40.0 0.5 NH1 C:ARG45 4.3 39.2 1.0 O3B A:G4P502 4.4 35.4 0.5 HO2' A:G4P502 4.4 45.6 0.5 O3' A:G4P502 4.5 28.5 0.5 HH11 A:ARG45 4.5 55.2 1.0 HH11 C:ARG45 4.5 47.0 1.0 O1A A:G4P502 4.6 34.7 0.5 HB2 A:ALA47 4.6 55.8 1.0 O3D A:G4P502 4.6 42.0 0.5 H4' A:G4P502 4.6 44.3 0.5 HE2 C:HIS59 4.6 55.9 1.0 H1' A:G4P502 4.6 42.8 0.5 H5' A:G4P502 4.7 45.9 0.5 HH21 C:ARG58 4.8 62.6 1.0 HB1 A:ALA47 4.8 55.8 1.0 C4' A:G4P502 4.8 36.9 0.5 NH2 A:ARG45 4.8 49.8 1.0 H5'' A:G4P502 4.9 42.3 0.5 O3A A:G4P502 4.9 36.0 0.5 C5' A:G4P502 4.9 35.3 0.5 PB A:G4P502 5.0 33.2 0.5 CZ A:ARG45 5.0 54.1 1.0 HH22 C:ARG45 5.0 54.1 1.0 O1A A:G4P502 5.0 34.8 0.5 O1C A:G4P502 5.0 35.3 0.5

Magnesium binding site 3 out of 4 in the The Structure of E. Coli Purf in Complex with Ppgpp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of E. Coli Purf in Complex with Ppgpp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:37.1 occ:0.54 MG D:MG501 0.0 37.1 0.5 H3' D:G4P502 1.3 43.7 0.5 O2C D:G4P502 1.5 36.5 0.5 O1D D:G4P502 1.7 34.6 0.5 PC D:G4P502 1.9 34.1 0.5 O1D D:G4P502 2.0 33.7 0.5 O2A D:G4P502 2.0 32.1 0.5 O1B D:G4P502 2.1 32.9 0.5 C3' D:G4P502 2.1 36.4 0.5 MG D:MG501 2.2 37.9 0.5 O2C D:G4P502 2.2 32.0 0.5 O3' D:G4P502 2.3 28.2 0.5 O3C D:G4P502 2.3 28.2 0.5 PD D:G4P502 2.3 29.0 0.5 O2A D:G4P502 2.4 33.2 0.5 H3' D:G4P502 2.9 40.7 0.5 O3D D:G4P502 3.0 37.8 0.5 HH12 D:ARG45 3.1 43.1 1.0 C4' D:G4P502 3.2 36.1 0.5 H4' D:G4P502 3.2 43.4 0.5 C2' D:G4P502 3.3 34.7 0.5 HH12 B:ARG45 3.3 35.9 1.0 PD D:G4P502 3.3 26.8 0.5 PA D:G4P502 3.4 27.2 0.5 O1C D:G4P502 3.4 34.2 0.5 PC D:G4P502 3.4 34.9 0.5 PB D:G4P502 3.5 30.9 0.5 O1B D:G4P502 3.5 33.7 0.5 H2' D:G4P502 3.5 41.7 0.5 O3C D:G4P502 3.7 29.1 0.5 O2' D:G4P502 3.7 41.1 0.5 O2D D:G4P502 3.7 38.6 0.5 H5'' D:G4P502 3.7 43.6 0.5 PA D:G4P502 3.7 25.9 0.5 C5' D:G4P502 3.8 36.4 0.5 O3A D:G4P502 3.8 34.3 0.5 C3' D:G4P502 3.9 33.9 0.5 O5' D:G4P502 3.9 34.8 0.5 NH1 D:ARG45 3.9 35.9 1.0 NH1 B:ARG45 4.0 29.9 1.0 O2D D:G4P502 4.1 37.1 0.5 HH22 D:ARG45 4.1 41.8 1.0 O5' D:G4P502 4.1 34.8 0.5 O3' D:G4P502 4.2 26.7 0.5 HH11 B:ARG45 4.2 35.9 1.0 H4' D:G4P502 4.3 43.5 0.5 HH11 D:ARG45 4.3 43.1 1.0 O4' D:G4P502 4.4 30.9 0.5 O2B D:G4P502 4.4 35.6 0.5 O3B D:G4P502 4.4 28.8 0.5 C1' D:G4P502 4.4 32.0 0.5 O3D D:G4P502 4.4 33.8 0.5 C4' D:G4P502 4.5 36.3 0.5 O1A D:G4P502 4.5 34.2 0.5 HO2' D:G4P502 4.5 49.3 0.5 H5'' D:G4P502 4.6 45.2 0.5 PB D:G4P502 4.6 36.3 0.5 C5' D:G4P502 4.6 37.6 0.5 O1C D:G4P502 4.7 32.6 0.5 HH22 B:ARG45 4.7 39.8 1.0 O3A D:G4P502 4.7 33.6 0.5 NH2 D:ARG45 4.8 34.9 1.0 HH21 B:ARG58 4.8 69.5 1.0 HE2 B:HIS59 4.8 44.2 1.0 CZ D:ARG45 4.8 36.8 1.0 H5' D:G4P502 4.9 43.6 0.5 O1A D:G4P502 4.9 33.5 0.5 H1' D:G4P502 5.0 38.4 0.5

Magnesium binding site 4 out of 4 in the The Structure of E. Coli Purf in Complex with Ppgpp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of E. Coli Purf in Complex with Ppgpp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:37.9 occ:0.46 MG D:MG501 0.0 37.9 0.5 H3' D:G4P502 1.3 40.7 0.5 O2C D:G4P502 1.3 32.0 0.5 PC D:G4P502 1.6 34.9 0.5 O1D D:G4P502 1.8 33.7 0.5 C3' D:G4P502 2.0 33.9 0.5 O3' D:G4P502 2.0 26.7 0.5 O1D D:G4P502 2.1 34.6 0.5 O1B D:G4P502 2.1 33.7 0.5 O2A D:G4P502 2.2 33.2 0.5 MG D:MG501 2.2 37.1 0.5 O3C D:G4P502 2.2 29.1 0.5 PD D:G4P502 2.4 26.8 0.5 O2C D:G4P502 2.5 36.5 0.5 O2A D:G4P502 2.6 32.1 0.5 H4' D:G4P502 2.9 43.5 0.5 HH12 B:ARG45 3.0 35.9 1.0 C4' D:G4P502 3.0 36.3 0.5 H3' D:G4P502 3.0 43.7 0.5 O1C D:G4P502 3.1 32.6 0.5 O3D D:G4P502 3.2 33.8 0.5 C2' D:G4P502 3.3 37.4 0.5 PD D:G4P502 3.4 29.0 0.5 PA D:G4P502 3.5 25.9 0.5 PB D:G4P502 3.5 36.3 0.5 O1B D:G4P502 3.6 32.9 0.5 PC D:G4P502 3.6 34.1 0.5 HH12 D:ARG45 3.6 43.1 1.0 O2' D:G4P502 3.7 38.9 0.5 H2' D:G4P502 3.7 44.9 0.5 O2D D:G4P502 3.7 37.1 0.5 C5' D:G4P502 3.8 37.6 0.5 H5'' D:G4P502 3.8 45.2 0.5 O3C D:G4P502 3.8 28.2 0.5 NH1 B:ARG45 3.8 29.9 1.0 HH22 B:ARG45 3.8 39.8 1.0 O3A D:G4P502 3.8 33.6 0.5 PA D:G4P502 3.8 27.2 0.5 O5' D:G4P502 3.8 34.8 0.5 C3' D:G4P502 4.1 36.4 0.5 O2D D:G4P502 4.2 38.6 0.5 O4' D:G4P502 4.2 33.4 0.5 HH11 B:ARG45 4.3 35.9 1.0 O5' D:G4P502 4.3 34.8 0.5 NH1 D:ARG45 4.3 35.9 1.0 O2B D:G4P502 4.3 38.1 0.5 C1' D:G4P502 4.4 36.6 0.5 O3' D:G4P502 4.4 28.2 0.5 O3D D:G4P502 4.5 37.8 0.5 O3B D:G4P502 4.5 30.7 0.5 NH2 B:ARG45 4.5 33.2 1.0 HH11 D:ARG45 4.5 43.1 1.0 O1A D:G4P502 4.5 33.5 0.5 HO2' D:G4P502 4.6 46.7 0.5 H4' D:G4P502 4.6 43.4 0.5 CZ B:ARG45 4.7 32.7 1.0 H5'' D:G4P502 4.7 43.6 0.5 C4' D:G4P502 4.8 36.1 0.5 PB D:G4P502 4.8 30.9 0.5 H5' D:G4P502 4.8 45.2 0.5 O3A D:G4P502 4.8 34.3 0.5 HB2 B:ALA47 4.8 34.4 1.0 C5' D:G4P502 4.8 36.4 0.5 H1' D:G4P502 4.9 43.9 0.5 HE2 D:HIS59 4.9 45.2 1.0 O1C D:G4P502 4.9 34.2 0.5 O1A D:G4P502 5.0 34.2 0.5 HH22 D:ARG45 5.0 41.8 1.0

B.Wang, P.Dai, D.Ding, A.Del Rosario, R.A.Grant, B.L.Pentelute, M.T.Laub. Affinity-Based Capture and Identification of Protein Effectors of the Growth Regulator Ppgpp. Nat. Chem. Biol. V. 15 141 2019.
ISSN: ESSN 1552-4469
PubMed: 30559427
DOI: 10.1038/S41589-018-0183-4