Magnesium in PDB 4j0q: Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu)

The structure of Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu), PDB code: 4j0q was solved by J.S.Scotti, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 2.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	212.505, 155.624, 99.298, 90.00, 114.76, 90.00
R / Rfree (%)	17.4 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu) (pdb code 4j0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu), PDB code: 4j0q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu)


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 Pseudomonas Putida Elongation Factor Tu (Ef-Tu) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:39.6 occ:1.00 O1B A:GDP402 2.0 33.6 1.0 O A:HOH542 2.0 33.5 1.0 O A:HOH543 2.0 42.4 1.0 O A:HOH541 2.1 45.0 1.0 O A:HOH513 2.1 39.6 1.0 OG1 A:THR26 2.1 44.7 1.0 CB A:THR26 3.1 49.8 1.0 PB A:GDP402 3.2 37.4 1.0 O3B A:GDP402 3.4 35.4 1.0 N A:THR26 3.8 39.7 1.0 O2A A:GDP402 4.0 30.4 1.0 CA A:THR26 4.0 44.4 1.0 OD1 A:ASP81 4.1 51.9 1.0 O A:CYS82 4.2 46.1 1.0 CG2 A:THR26 4.2 34.8 1.0 O A:PRO83 4.3 62.3 1.0 O2B A:GDP402 4.3 37.9 1.0 O3A A:GDP402 4.4 36.5 1.0 OD2 A:ASP81 4.4 54.7 1.0 CA A:PRO83 4.6 54.4 1.0 O A:HOH556 4.6 55.9 1.0 PA A:GDP402 4.6 38.4 1.0 NZ A:LYS25 4.7 47.0 1.0 CG A:ASP81 4.7 47.5 1.0 CB A:LYS25 4.7 33.9 1.0 C A:LYS25 4.8 39.0 1.0 O A:HOH516 4.9 42.1 1.0 C A:PRO83 4.9 65.7 1.0 O1A A:GDP402 4.9 39.5 1.0 C A:CYS82 5.0 48.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu)


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 Pseudomonas Putida Elongation Factor Tu (Ef-Tu) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:49.9 occ:1.00 OG1 B:THR26 2.0 51.2 1.0 O B:HOH537 2.0 48.9 1.0 O B:HOH538 2.1 36.4 1.0 O B:HOH511 2.1 43.2 1.0 O1B B:GDP402 2.1 41.3 1.0 O B:HOH539 2.2 59.4 1.0 CB B:THR26 3.2 49.9 1.0 PB B:GDP402 3.5 42.8 1.0 O3B B:GDP402 3.6 36.1 1.0 N B:THR26 4.0 42.0 1.0 O2A B:GDP402 4.1 38.5 1.0 OD2 B:ASP81 4.1 51.6 1.0 O B:CYS82 4.1 50.9 1.0 CA B:THR26 4.1 43.5 1.0 CG2 B:THR26 4.2 46.0 1.0 OD1 B:ASP81 4.4 51.9 1.0 CA B:PRO83 4.4 65.2 1.0 O B:PRO83 4.4 69.2 1.0 O2B B:GDP402 4.5 39.9 1.0 O3A B:GDP402 4.5 51.1 1.0 CG B:ASP81 4.7 54.3 1.0 PA B:GDP402 4.8 39.0 1.0 NZ B:LYS25 4.9 53.6 1.0 C B:CYS82 4.9 59.8 1.0 CB B:LYS25 4.9 38.1 1.0 C B:PRO83 4.9 71.3 1.0 O1A B:GDP402 5.0 32.8 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:39.7 occ:1.00 O C:HOH549 2.0 31.4 1.0 O C:HOH508 2.1 43.6 1.0 OG1 C:THR26 2.1 43.5 1.0 O C:HOH502 2.1 38.3 1.0 O C:HOH541 2.1 43.2 1.0 O1B C:GDP402 2.2 39.7 1.0 CB C:THR26 3.3 39.0 1.0 PB C:GDP402 3.4 38.1 1.0 O3B C:GDP402 3.6 31.9 1.0 N C:THR26 4.0 29.2 1.0 O2A C:GDP402 4.1 38.0 1.0 OD1 C:ASP81 4.1 48.0 1.0 O C:CYS82 4.2 46.2 1.0 CA C:THR26 4.2 36.4 1.0 CG2 C:THR26 4.3 34.0 1.0 O2B C:GDP402 4.4 32.1 1.0 O C:PRO83 4.4 55.4 1.0 O3A C:GDP402 4.4 40.5 1.0 CA C:PRO83 4.5 54.2 1.0 OD2 C:ASP81 4.5 45.4 1.0 PA C:GDP402 4.7 36.8 1.0 NZ C:LYS25 4.7 37.1 1.0 CG C:ASP81 4.7 50.1 1.0 O C:HOH566 4.8 44.5 1.0 C C:CYS82 5.0 46.2 1.0 CB C:LYS25 5.0 36.2 1.0 C C:PRO83 5.0 61.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:42.1 occ:1.00 O D:HOH525 2.0 42.0 1.0 O1B D:GDP402 2.1 33.2 1.0 O D:HOH501 2.1 35.0 1.0 O D:HOH524 2.1 34.0 1.0 OG1 D:THR26 2.2 44.2 1.0 O D:HOH502 2.2 45.0 1.0 CB D:THR26 3.3 43.9 1.0 PB D:GDP402 3.4 41.0 1.0 O3B D:GDP402 3.6 39.4 1.0 O2A D:GDP402 4.1 32.8 1.0 N D:THR26 4.1 36.8 1.0 OD1 D:ASP81 4.2 56.3 1.0 CA D:THR26 4.2 41.9 1.0 O2B D:GDP402 4.3 39.6 1.0 CG2 D:THR26 4.3 39.2 1.0 O D:CYS82 4.3 52.6 1.0 CA D:PRO83 4.4 72.0 1.0 O D:PRO83 4.5 84.3 1.0 OD2 D:ASP81 4.5 55.8 1.0 O3A D:GDP402 4.5 33.9 1.0 PA D:GDP402 4.7 38.6 1.0 NZ D:LYS25 4.8 45.9 1.0 CG D:ASP81 4.8 59.9 1.0 O1A D:GDP402 4.9 35.5 1.0 O D:HOH534 4.9 43.3 1.0 C D:PRO83 5.0 79.2 1.0 CB D:LYS25 5.0 47.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pseudomonas Putida Elongation Factor Tu (Ef-Tu) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:77.5 occ:1.00 O E:HOH501 2.0 63.4 1.0 O E:HOH510 2.0 68.7 1.0 O E:HOH509 2.1 70.8 1.0 O E:HOH511 2.1 63.9 1.0 OG1 E:THR26 2.2 74.9 1.0 O1B E:GDP402 2.3 86.0 1.0 CB E:THR26 3.3 72.8 1.0 O3B E:GDP402 3.4 85.0 1.0 PB E:GDP402 3.5 83.0 1.0 O2A E:GDP402 3.9 67.6 1.0 OD1 E:ASP81 4.1 88.3 1.0 N E:THR26 4.2 79.5 1.0 O E:PRO83 4.2 96.6 1.0 CG2 E:THR26 4.3 70.8 1.0 CA E:THR26 4.3 75.2 1.0 CA E:PRO83 4.4 89.3 1.0 O E:CYS82 4.4 75.7 1.0 O2B E:GDP402 4.5 68.1 1.0 O3A E:GDP402 4.6 54.6 1.0 NZ E:LYS25 4.6 87.7 1.0 PA E:GDP402 4.7 76.0 1.0 C E:PRO83 4.8 92.3 1.0 OD2 E:ASP81 4.9 90.3 1.0 CG E:ASP81 4.9 90.7 1.0 O1A E:GDP402 5.0 82.6 1.0

J.S.Scotti, I.K.H.Leung, W.Ge, M.A.Bentley, J.Paps, H.B.Kramer, J.Lee, W.Aik, H.Choi, S.M.Paulsen, L.A.H.Bowman, N.D.Loik, S.Horita, C.H.Ho, N.J.Kershaw, C.M.Tang, T.D.W.Claridge, G.M.Preston, M.A.Mcdonough, C.J.Schofield. Human Oxygen Sensing May Have Origins in Prokaryotic Elongation Factor Tu Prolyl-Hydroxylation Proc.Natl.Acad.Sci.Usa V. 111 13331 2014.
ISSN: ISSN 0027-8424
PubMed: 25197067
DOI: 10.1073/PNAS.1409916111