Magnesium in PDB 2hdn: Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution

The structure of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution, PDB code: 2hdn was solved by S.Mui, S.E.Heffron, A.Aorora, K.Abel, E.Bergmann, F.Jurnak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.710, 156.060, 134.830, 90.00, 95.38, 90.00
R / Rfree (%)	18 / 22.3

The binding sites of Magnesium atom in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution (pdb code 2hdn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution, PDB code: 2hdn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1998 b:32.2 occ:1.00 O B:HOH1002 2.1 53.1 1.0 O2B B:GDP1999 2.1 16.9 1.0 O12 B:TAC1888 2.1 49.3 0.7 O B:HOH1001 2.2 26.9 1.0 OG1 A:THR25 2.3 34.2 1.0 O11 B:TAC1888 2.4 38.4 0.7 PB B:GDP1999 3.2 30.5 1.0 O1B B:GDP1999 3.3 27.0 1.0 C12 B:TAC1888 3.3 48.5 0.7 C11 B:TAC1888 3.4 40.3 0.7 CB A:THR25 3.6 32.3 1.0 O B:CYS81 3.8 15.3 1.0 C1B B:TAC1888 3.8 42.9 0.7 O3B B:GDP1999 4.0 21.4 1.0 O B:PRO82 4.0 25.1 1.0 CA B:PRO82 4.1 17.4 1.0 N A:THR25 4.2 25.0 1.0 OD2 B:ASP80 4.3 16.3 1.0 O3A B:GDP1999 4.5 35.4 1.0 O10 B:TAC1888 4.5 38.1 0.7 O1 B:TAC1888 4.5 55.4 0.7 CE A:LYS24 4.5 18.6 1.0 CA A:THR25 4.5 29.6 1.0 O2A B:GDP1999 4.5 24.5 1.0 C B:PRO82 4.5 21.1 1.0 OD1 B:ASP80 4.5 17.5 1.0 C1C B:TAC1888 4.6 53.2 0.7 CG2 A:THR25 4.6 28.1 1.0 C B:CYS81 4.6 19.4 1.0 O1C B:TAC1888 4.6 51.7 0.7 CB A:LYS24 4.7 26.3 1.0 C1A B:TAC1888 4.7 37.6 0.7 O B:HOH1006 4.7 41.9 1.0 CG B:ASP80 4.8 16.6 1.0 NZ A:LYS24 4.8 25.1 1.0 N B:PRO82 4.8 18.0 1.0 PA B:GDP1999 4.9 36.8 1.0 O1A B:GDP1999 5.0 34.5 1.0

Magnesium binding site 2 out of 6 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2998 b:30.7 occ:1.00 O12 D:TAC2888 1.9 48.8 0.6 O D:HOH2002 2.1 49.2 1.0 O2B D:GDP2999 2.2 18.8 1.0 O11 D:TAC2888 2.2 44.0 0.6 O D:HOH2001 2.2 26.5 1.0 OG1 C:THR25 2.2 35.9 1.0 C12 D:TAC2888 3.1 52.1 0.6 C11 D:TAC2888 3.2 44.7 0.6 PB D:GDP2999 3.3 32.7 1.0 O1B D:GDP2999 3.4 35.6 1.0 CB C:THR25 3.6 28.8 1.0 C1B D:TAC2888 3.6 47.8 0.6 O D:CYS81 3.9 22.4 1.0 O D:PRO82 4.0 19.7 1.0 CA D:PRO82 4.1 22.9 1.0 O3B D:GDP2999 4.1 28.2 1.0 OD2 D:ASP80 4.1 28.2 1.0 N C:THR25 4.2 30.4 1.0 O1 D:TAC2888 4.3 56.2 0.6 C1C D:TAC2888 4.4 54.6 0.6 O10 D:TAC2888 4.4 37.6 0.6 O1C D:TAC2888 4.4 54.3 0.6 O2A D:GDP2999 4.5 27.2 1.0 CG2 C:THR25 4.5 29.7 1.0 CA C:THR25 4.5 31.3 1.0 C1A D:TAC2888 4.5 39.5 0.6 C D:PRO82 4.5 22.3 1.0 O3A D:GDP2999 4.6 34.7 1.0 C D:CYS81 4.6 21.7 1.0 OD1 D:ASP80 4.6 32.0 1.0 CE C:LYS24 4.7 30.1 1.0 N D:PRO82 4.8 22.6 1.0 CG D:ASP80 4.8 22.1 1.0 NZ C:LYS24 4.9 24.0 1.0 C1 D:TAC2888 4.9 55.9 0.6 PA D:GDP2999 4.9 41.4 1.0 CB D:PRO82 4.9 21.1 1.0 O D:HOH2006 5.0 15.9 1.0 C10 D:TAC2888 5.0 39.2 0.6

Magnesium binding site 3 out of 6 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg3998 b:25.5 occ:1.00 O F:HOH3002 2.1 59.8 1.0 O F:HOH3001 2.1 36.6 1.0 O12 F:TAC3888 2.1 46.6 0.6 O2B F:GDP3999 2.2 32.0 1.0 O11 F:TAC3888 2.3 36.9 0.6 OG1 E:THR25 2.4 39.5 1.0 C12 F:TAC3888 3.3 47.3 0.6 PB F:GDP3999 3.3 40.3 1.0 O1B F:GDP3999 3.4 40.5 1.0 C11 F:TAC3888 3.4 40.0 0.6 CB E:THR25 3.8 31.6 1.0 C1B F:TAC3888 3.8 42.5 0.6 O F:CYS81 3.8 26.1 1.0 O F:PRO82 3.8 26.1 1.0 CA F:PRO82 4.0 23.8 1.0 O3B F:GDP3999 4.1 32.8 1.0 N E:THR25 4.3 25.1 1.0 OD2 F:ASP80 4.3 28.1 1.0 C F:PRO82 4.4 22.8 1.0 O10 F:TAC3888 4.4 32.5 0.6 O1 F:TAC3888 4.4 52.9 0.6 NZ E:LYS24 4.4 20.2 1.0 O2A F:GDP3999 4.5 36.6 1.0 C1C F:TAC3888 4.5 50.7 0.6 C F:CYS81 4.6 21.4 1.0 O3A F:GDP3999 4.6 40.5 1.0 CE E:LYS24 4.6 18.2 1.0 C1A F:TAC3888 4.6 36.4 0.6 CA E:THR25 4.6 28.8 1.0 O1C F:TAC3888 4.7 51.5 0.6 CG2 E:THR25 4.7 26.3 1.0 N F:PRO82 4.7 23.8 1.0 OD1 F:ASP80 4.8 25.0 1.0 O F:HOH3006 4.8 14.6 1.0 CB F:PRO82 4.9 24.5 1.0 CG F:ASP80 4.9 19.9 1.0 CB E:LYS24 4.9 27.7 1.0 PA F:GDP3999 5.0 42.8 1.0

Magnesium binding site 4 out of 6 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg4998 b:43.1 occ:1.00 O H:HOH4002 2.0 54.9 1.0 O H:HOH4001 2.1 34.6 1.0 O12 H:TAC4888 2.1 41.5 0.8 O11 H:TAC4888 2.2 35.9 0.8 O2B H:GDP4999 2.3 19.1 1.0 OG1 G:THR25 2.4 29.4 1.0 C12 H:TAC4888 3.3 43.5 0.8 C11 H:TAC4888 3.3 37.0 0.8 PB H:GDP4999 3.4 32.8 1.0 O1B H:GDP4999 3.5 32.2 1.0 O H:CYS81 3.6 13.8 1.0 O H:PRO82 3.7 26.2 1.0 C1B H:TAC4888 3.8 40.6 0.8 CB G:THR25 3.8 23.8 1.0 CA H:PRO82 3.8 24.5 1.0 O3B H:GDP4999 4.1 26.4 1.0 C H:PRO82 4.3 23.8 1.0 O10 H:TAC4888 4.3 25.5 0.8 OD2 H:ASP80 4.3 19.2 1.0 N G:THR25 4.4 28.0 1.0 C H:CYS81 4.4 17.2 1.0 NZ G:LYS24 4.5 18.0 1.0 O1 H:TAC4888 4.5 52.0 0.8 N H:PRO82 4.6 22.2 1.0 C1A H:TAC4888 4.6 30.7 0.8 O G:HOH4006 4.6 23.4 1.0 CE G:LYS24 4.6 20.9 1.0 OD1 H:ASP80 4.6 28.4 1.0 C1C H:TAC4888 4.6 45.6 0.8 CG2 G:THR25 4.7 10.7 1.0 O3A H:GDP4999 4.7 38.9 1.0 O2A H:GDP4999 4.7 44.1 1.0 CA G:THR25 4.7 26.6 1.0 O1C H:TAC4888 4.8 47.4 0.8 CB H:PRO82 4.8 24.8 1.0 CG H:ASP80 4.8 14.8 1.0 C10 H:TAC4888 4.9 30.4 0.8 CB G:LYS24 5.0 26.8 1.0

Magnesium binding site 5 out of 6 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg5998 b:18.4 occ:1.00 O12 J:TAC5888 2.0 49.6 0.6 O2B J:GDP5999 2.1 18.5 1.0 OG1 I:THR25 2.1 15.0 1.0 O J:HOH5001 2.1 17.1 1.0 O11 J:TAC5888 2.2 39.7 0.6 O J:HOH5002 2.3 45.4 1.0 C12 J:TAC5888 3.1 51.9 0.6 C11 J:TAC5888 3.2 41.8 0.6 PB J:GDP5999 3.3 24.5 1.0 CB I:THR25 3.4 12.2 1.0 O1B J:GDP5999 3.5 26.1 1.0 C1B J:TAC5888 3.6 47.2 0.6 O J:CYS81 3.9 13.0 1.0 O3B J:GDP5999 4.0 18.5 1.0 N I:THR25 4.1 11.3 1.0 OD2 J:ASP80 4.1 8.4 1.0 O J:PRO82 4.2 21.6 1.0 CA J:PRO82 4.2 16.1 1.0 CA I:THR25 4.3 13.2 1.0 O10 J:TAC5888 4.4 34.2 0.6 CG2 I:THR25 4.4 3.7 1.0 C1C J:TAC5888 4.4 56.5 0.6 O2A J:GDP5999 4.4 14.2 1.0 O1 J:TAC5888 4.5 60.0 0.6 O1C J:TAC5888 4.5 56.9 0.6 O3A J:GDP5999 4.5 28.7 1.0 OD1 J:ASP80 4.5 18.4 1.0 C1A J:TAC5888 4.5 37.8 0.6 CG J:ASP80 4.7 11.2 1.0 C J:CYS81 4.7 10.6 1.0 C J:PRO82 4.7 17.1 1.0 CE I:LYS24 4.7 6.5 1.0 PA J:GDP5999 4.8 21.2 1.0 CB I:LYS24 4.8 8.3 1.0 NZ I:LYS24 4.9 2.7 1.0 N J:PRO82 4.9 13.1 1.0 O1A J:GDP5999 4.9 23.4 1.0 O J:HOH5006 4.9 17.5 1.0 C1 J:TAC5888 5.0 58.4 0.6 C10 J:TAC5888 5.0 38.2 0.6

Magnesium binding site 6 out of 6 in the Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Trypsin-Modified Elongation Factor Tu in Complex with Tetracycline at 2.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg6998 b:27.6 occ:1.00 O12 L:TAC6888 2.0 42.9 0.8 O L:HOH6001 2.1 23.1 1.0 O L:HOH6002 2.2 54.6 1.0 O2B L:GDP6999 2.2 21.9 1.0 OG1 K:THR25 2.2 25.4 1.0 O11 L:TAC6888 2.2 35.2 0.8 C12 L:TAC6888 3.1 47.9 0.8 C11 L:TAC6888 3.3 38.1 0.8 PB L:GDP6999 3.4 29.1 1.0 O1B L:GDP6999 3.5 26.9 1.0 CB K:THR25 3.6 20.8 1.0 C1B L:TAC6888 3.7 42.5 0.8 O L:CYS81 3.9 8.6 1.0 O L:PRO82 4.0 24.0 1.0 CA L:PRO82 4.1 16.6 1.0 O3B L:GDP6999 4.1 18.2 1.0 OD2 L:ASP80 4.2 15.2 1.0 N K:THR25 4.2 25.6 1.0 O10 L:TAC6888 4.3 36.2 0.8 C1C L:TAC6888 4.4 51.8 0.8 O1 L:TAC6888 4.4 61.0 0.8 CA K:THR25 4.5 23.7 1.0 CG2 K:THR25 4.5 18.9 1.0 O2A L:GDP6999 4.5 31.2 1.0 O1C L:TAC6888 4.5 55.1 0.8 C1A L:TAC6888 4.5 36.8 0.8 C L:PRO82 4.6 17.5 1.0 O3A L:GDP6999 4.6 27.8 1.0 OD1 L:ASP80 4.6 20.0 1.0 C L:CYS81 4.6 13.7 1.0 CG L:ASP80 4.8 15.6 1.0 NZ K:LYS24 4.8 19.4 1.0 CE K:LYS24 4.8 15.2 1.0 N L:PRO82 4.8 16.9 1.0 CB K:LYS24 4.8 13.4 1.0 PA L:GDP6999 4.9 36.4 1.0 O L:HOH6006 4.9 49.0 1.0 C1 L:TAC6888 4.9 56.4 0.8 C10 L:TAC6888 5.0 37.4 0.8

S.E.Heffron, S.Mui, A.Aorora, K.Abel, E.Bergmann, F.Jurnak. Molecular Complementarity Between Tetracycline and the Gtpase Active Site of Elongation Factor Tu. Acta Crystallogr.,Sect.D V. 62 1392 2006.
ISSN: ISSN 0907-4449
PubMed: 17057344
DOI: 10.1107/S0907444906035426