Magnesium in PDB 3ebj: Crystal Structure of An Avian Influenza Virus Protein

The structure of Crystal Structure of An Avian Influenza Virus Protein, PDB code: 3ebj was solved by P.Yuan, M.Bartlam, Z.Lou, S.Chen, Z.Rao, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.049, 59.825, 67.165, 96.55, 96.82, 109.51
R / Rfree (%)	23.1 / 25.2

The binding sites of Magnesium atom in the Crystal Structure of An Avian Influenza Virus Protein (pdb code 3ebj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of An Avian Influenza Virus Protein, PDB code: 3ebj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of An Avian Influenza Virus Protein


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 An Avian Influenza Virus Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg999 b:45.4 occ:1.00 O A:HOH1003 2.3 31.4 1.0 O A:HOH1001 2.4 35.7 1.0 OE2 A:GLU80 2.5 50.0 1.0 OD1 A:ASP108 2.5 44.8 1.0 O A:HOH1002 2.6 53.2 1.0 CD A:GLU80 3.1 48.3 1.0 OE1 A:GLU80 3.5 45.2 1.0 CG A:ASP108 3.7 42.6 1.0 CG A:GLU80 4.2 48.8 1.0 CE1 A:HIS41 4.2 25.3 1.0 OD2 A:ASP108 4.3 45.0 1.0 O A:LEU106 4.3 37.5 1.0 CB A:GLU80 4.4 48.1 1.0 O A:PRO107 4.5 34.2 1.0 OE2 A:GLU119 4.7 40.0 1.0 CA A:ASP108 4.8 40.8 1.0 CB A:ASP108 4.8 40.2 1.0 C A:PRO107 4.8 36.9 1.0 CA A:GLU80 4.9 47.6 1.0 N A:ASP108 4.9 39.7 1.0 O A:HOH1020 4.9 48.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of An Avian Influenza Virus Protein


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 An Avian Influenza Virus Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg999 b:31.8 occ:1.00 O B:HOH1003 2.2 30.2 1.0 O B:HOH1021 2.3 37.5 1.0 OD1 B:ASP108 2.4 36.7 1.0 O B:HOH1001 2.4 58.3 1.0 OE1 B:GLU80 2.7 41.5 1.0 CG B:ASP108 3.4 39.6 1.0 O B:LEU106 3.5 43.6 1.0 CD B:GLU80 3.5 42.5 1.0 OD2 B:ASP108 3.9 44.7 1.0 OE2 B:GLU80 3.9 40.5 1.0 OE2 B:GLU119 4.1 51.6 1.0 O B:PRO107 4.1 34.6 1.0 C B:PRO107 4.2 36.5 1.0 N B:ASP108 4.4 37.6 1.0 CE1 B:HIS41 4.4 30.8 1.0 C B:LEU106 4.5 45.4 1.0 CA B:ASP108 4.6 41.4 1.0 CB B:ASP108 4.6 39.4 1.0 CA B:PRO107 4.7 38.9 1.0 CG B:GLU80 4.7 42.9 1.0 CB B:GLU80 4.8 42.3 1.0 NE2 B:HIS41 5.0 35.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of An Avian Influenza Virus Protein


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 An Avian Influenza Virus Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg999 b:46.8 occ:1.00 O C:HOH1001 2.2 29.8 1.0 OE1 C:GLU80 2.3 56.5 1.0 O C:HOH1003 2.3 43.3 1.0 OD1 C:ASP108 2.3 40.6 1.0 O C:HOH1002 2.4 27.6 1.0 CG C:ASP108 3.4 44.9 1.0 CD C:GLU80 3.5 52.6 1.0 OD2 C:ASP108 3.9 42.2 1.0 O C:LEU106 4.0 50.0 1.0 O C:PRO107 4.1 47.4 1.0 CE1 C:HIS41 4.1 42.6 1.0 OE2 C:GLU80 4.2 58.8 1.0 C C:PRO107 4.3 48.4 1.0 OE2 C:GLU119 4.4 51.5 1.0 CG C:GLU80 4.5 50.6 1.0 CB C:GLU80 4.5 50.7 1.0 N C:ASP108 4.5 45.8 1.0 CB C:ASP108 4.5 44.0 1.0 CA C:ASP108 4.6 44.2 1.0 ND1 C:HIS41 4.9 41.1 1.0 OE1 C:GLU119 4.9 49.0 1.0 C C:LEU106 4.9 48.6 1.0 CA C:PRO107 4.9 49.6 1.0 NE2 C:HIS41 5.0 41.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of An Avian Influenza Virus Protein


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 An Avian Influenza Virus Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg999 b:67.2 occ:1.00 O D:HOH1003 1.7 39.5 1.0 O D:HOH1002 2.4 50.8 1.0 O D:HOH1001 2.4 41.0 1.0 OD1 D:ASP108 2.7 51.4 1.0 CG D:ASP108 3.3 44.8 1.0 OE1 D:GLU119 3.3 64.3 1.0 OE1 D:GLU80 3.5 59.4 1.0 OD2 D:ASP108 3.5 42.0 1.0 O D:LEU106 3.8 43.1 1.0 O D:PRO107 3.9 43.2 1.0 CD D:GLU80 4.0 60.0 1.0 C D:PRO107 4.1 41.2 1.0 CE1 D:HIS41 4.2 41.0 1.0 CD D:GLU119 4.3 61.7 1.0 N D:ASP108 4.3 39.4 1.0 CA D:ASP108 4.3 39.6 1.0 OE2 D:GLU80 4.4 59.4 1.0 CB D:ASP108 4.4 41.6 1.0 OE2 D:GLU119 4.5 59.1 1.0 CB D:GLU80 4.6 54.3 1.0 CG D:GLU80 4.7 58.7 1.0 C D:LEU106 4.8 42.2 1.0 CA D:PRO107 4.9 40.1 1.0

P.Yuan, M.Bartlam, Z.Lou, S.Chen, J.Zhou, X.He, Z.Lv, R.Ge, X.Li, T.Deng, E.Fodor, Z.Rao, Y.Liu. Crystal Structure of An Avian Influenza Polymerase Pa(N) Reveals An Endonuclease Active Site Nature V. 458 909 2009.
ISSN: ISSN 0028-0836
PubMed: 19194458
DOI: 10.1038/NATURE07720