Magnesium in PDB 1d8t: Crystal Structure of Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic

The structure of Crystal Structure of Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic, PDB code: 1d8t was solved by S.E.Heffron, F.Jurnak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.44 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.470, 45.170, 144.000, 90.00, 94.64, 90.00
R / Rfree (%)	20 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic (pdb code 1d8t). 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 Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic, PDB code: 1d8t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic


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 Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg998 b:11.1 occ:1.00 OG1 A:THR25 2.1 10.3 1.0 O A:HOH2064 2.1 8.2 1.0 O A:HOH2063 2.1 10.4 1.0 O2B A:GDP999 2.1 8.5 1.0 O A:HOH2018 2.2 9.8 1.0 O A:HOH2218 2.2 12.7 1.0 CB A:THR25 3.1 7.9 1.0 PB A:GDP999 3.3 10.9 1.0 O1B A:GDP999 3.4 5.2 1.0 OD1 A:ASP50 3.8 22.9 1.0 N A:THR25 3.8 9.3 1.0 O2A A:GDP999 3.9 13.1 1.0 CA A:THR25 4.1 8.5 1.0 O A:CYS81 4.1 9.2 1.0 OD2 A:ASP80 4.1 7.3 1.0 CG2 A:THR25 4.2 5.3 1.0 O3B A:GDP999 4.3 12.3 1.0 O A:HOH2062 4.3 9.8 1.0 O3A A:GDP999 4.4 14.5 1.0 O A:PRO82 4.4 12.1 1.0 PA A:GDP999 4.5 12.2 1.0 CA A:PRO82 4.5 10.9 1.0 O1A A:GDP999 4.6 14.3 1.0 OD1 A:ASP80 4.7 7.6 1.0 O A:HOH2017 4.7 11.5 1.0 C A:CYS81 4.8 9.8 1.0 CH3 A:ACT3021 4.8 54.0 1.0 O A:ACT3021 4.8 54.0 1.0 CG A:ASP80 4.8 9.8 1.0 CB A:LYS24 4.8 9.5 1.0 C A:LYS24 4.9 10.4 1.0 C A:PRO82 5.0 13.2 1.0 N A:PRO82 5.0 9.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic


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 Elongation Factor, Tu (Ef-Tu-Mggdp) Complexed with GE2270A, A Thiazolyl Peptide Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg998 b:27.3 occ:1.00 OG1 B:THR25 2.0 21.8 1.0 O B:HOH2140 2.2 17.4 1.0 O B:HOH2006 2.2 36.7 1.0 O2B B:GDP999 2.3 20.2 1.0 O B:HOH2141 2.4 38.5 1.0 O B:HOH2013 2.4 28.1 1.0 CB B:THR25 3.1 21.5 1.0 PB B:GDP999 3.4 18.3 1.0 O1B B:GDP999 3.5 19.5 1.0 OD1 B:ASP50 3.6 50.9 1.0 N B:THR25 3.9 20.5 1.0 O2A B:GDP999 3.9 18.9 1.0 CA B:THR25 4.1 20.6 1.0 OD2 B:ASP80 4.1 22.1 1.0 CG2 B:THR25 4.1 20.5 1.0 O B:CYS81 4.2 20.0 1.0 O3B B:GDP999 4.4 17.9 1.0 O B:PRO82 4.4 25.0 1.0 O3A B:GDP999 4.5 19.1 1.0 CA B:PRO82 4.5 24.2 1.0 PA B:GDP999 4.6 20.4 1.0 O1A B:GDP999 4.7 18.7 1.0 OD1 B:ASP80 4.7 19.7 1.0 O B:HOH2004 4.7 23.5 1.0 CG B:ASP50 4.8 50.3 1.0 CG B:ASP80 4.8 22.4 1.0 C B:CYS81 4.9 22.0 1.0 CB B:LYS24 4.9 16.4 1.0 C B:PRO82 5.0 23.3 1.0 N B:PRO82 5.0 23.8 1.0 C B:LYS24 5.0 19.4 1.0 NZ B:LYS24 5.0 14.1 1.0

S.E.Heffron, F.Jurnak. Structure of An Ef-Tu Complex with A Thiazolyl Peptide Antibiotic Determined at 2.35 A Resolution: Atomic Basis For GE2270A Inhibition of Ef-Tu. Biochemistry V. 39 37 2000.
ISSN: ISSN 0006-2960
PubMed: 10625477
DOI: 10.1021/BI9913597