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Magnesium in PDB 1efc: Intact Elongation Factor From E.Coli

Protein crystallography data

The structure of Intact Elongation Factor From E.Coli, PDB code: 1efc was solved by H.Song, M.R.Parsons, S.Rowsell, G.Leonard, S.E.V.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 243.120, 61.080, 66.910, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Intact Elongation Factor From E.Coli (pdb code 1efc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Intact Elongation Factor From E.Coli, PDB code: 1efc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1efc

Go back to Magnesium Binding Sites List in 1efc
Magnesium binding site 1 out of 2 in the Intact Elongation Factor From E.Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Intact Elongation Factor From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:13.7
occ:1.00
OG1 A:THR25 1.9 13.3 1.0
O2B A:GDP513 2.0 11.6 1.0
O A:HOH518 2.0 13.6 1.0
O A:HOH514 2.3 15.2 1.0
O A:HOH525 2.3 14.2 1.0
O A:HOH523 2.3 14.4 1.0
CB A:THR25 3.0 13.3 1.0
PB A:GDP513 3.2 14.1 1.0
O3B A:GDP513 3.6 12.7 1.0
N A:THR25 3.6 9.9 1.0
CA A:THR25 3.9 11.1 1.0
OD1 A:ASP80 4.0 15.3 1.0
O2A A:GDP513 4.0 16.5 1.0
O A:CYS81 4.1 16.2 1.0
CG2 A:THR25 4.1 14.0 1.0
O A:HOH519 4.2 15.5 1.0
OD2 A:ASP50 4.2 25.1 1.0
O1B A:GDP513 4.3 11.4 1.0
O3A A:GDP513 4.3 13.8 1.0
OD2 A:ASP80 4.4 17.7 1.0
PA A:GDP513 4.4 16.8 1.0
O1A A:GDP513 4.5 15.9 1.0
O A:PRO82 4.5 21.2 1.0
O A:HOH613 4.6 21.6 1.0
CA A:PRO82 4.6 19.4 1.0
C A:LYS24 4.6 11.7 1.0
CB A:LYS24 4.6 11.4 1.0
CG A:ASP80 4.6 17.4 1.0
CE A:LYS24 4.8 9.9 1.0
C A:CYS81 4.8 18.8 1.0
NZ A:LYS24 4.9 9.1 1.0

Magnesium binding site 2 out of 2 in 1efc

Go back to Magnesium Binding Sites List in 1efc
Magnesium binding site 2 out of 2 in the Intact Elongation Factor From E.Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Intact Elongation Factor From E.Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:16.5
occ:1.00
O2B B:GDP514 2.0 14.6 1.0
OG1 B:THR25 2.0 11.4 1.0
O B:HOH521 2.1 16.6 1.0
O B:HOH523 2.1 15.6 1.0
O B:HOH520 2.1 15.8 1.0
O B:HOH522 2.2 11.9 1.0
CB B:THR25 3.1 13.8 1.0
PB B:GDP514 3.2 18.3 1.0
O3B B:GDP514 3.5 17.2 1.0
N B:THR25 3.8 15.1 1.0
O2A B:GDP514 4.0 17.9 1.0
OD1 B:ASP80 4.0 19.0 1.0
CA B:THR25 4.0 15.1 1.0
CG2 B:THR25 4.2 14.0 1.0
O B:CYS81 4.2 17.4 1.0
OD2 B:ASP50 4.2 25.4 1.0
O1B B:GDP514 4.3 15.4 1.0
O B:HOH519 4.3 16.4 1.0
O3A B:GDP514 4.3 14.8 1.0
O B:HOH599 4.3 27.8 1.0
CA B:PRO82 4.4 17.7 1.0
OD2 B:ASP80 4.5 18.4 1.0
PA B:GDP514 4.5 16.7 1.0
O B:HOH515 4.5 24.6 1.0
O B:PRO82 4.5 17.3 1.0
O1A B:GDP514 4.5 17.5 1.0
CG B:ASP80 4.6 18.3 1.0
CB B:LYS24 4.7 14.6 1.0
C B:CYS81 4.8 18.2 1.0
C B:LYS24 4.8 15.2 1.0
N B:PRO82 4.9 18.3 1.0
NZ B:LYS24 5.0 14.0 1.0
C B:PRO82 5.0 16.3 1.0

Reference:

H.Song, M.R.Parsons, S.Rowsell, G.Leonard, S.E.Phillips. Crystal Structure of Intact Elongation Factor Ef-Tu From Escherichia Coli in Gdp Conformation at 2.05 A Resolution. J.Mol.Biol. V. 285 1245 1999.
ISSN: ISSN 0022-2836
PubMed: 9918724
DOI: 10.1006/JMBI.1998.2387
Page generated: Mon Dec 14 05:51:58 2020

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