Magnesium in PDB 3hw5: Crystal Structure of Avian Influenza Virus PA_N in Complex with Amp

The structure of Crystal Structure of Avian Influenza Virus PA_N in Complex with Amp, PDB code: 3hw5 was solved by C.Zhao, Z.Lou, Y.Guo, M.Ma, Y.Chen, S.Liang, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.81
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.617, 60.029, 67.177, 96.02, 96.22, 109.35
R / Rfree (%)	20.6 / 26.3

The binding sites of Magnesium atom in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Amp (pdb code 3hw5). 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 Avian Influenza Virus PA_N in Complex with Amp, PDB code: 3hw5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Amp


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 Avian Influenza Virus PA_N in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg999 b:18.5 occ:1.00 OD1 A:ASP108 2.0 21.2 1.0 O A:HOH1003 2.0 13.6 1.0 OE2 A:GLU80 2.1 16.9 1.0 O1P A:AMP257 2.1 20.3 1.0 O A:HOH1002 2.1 19.5 1.0 O A:HOH1001 2.3 22.6 1.0 CD A:GLU80 3.1 21.0 1.0 CG A:ASP108 3.1 20.0 1.0 P A:AMP257 3.5 36.4 1.0 OD2 A:ASP108 3.6 18.5 1.0 O A:HOH1004 3.8 21.9 1.0 OE1 A:GLU80 3.8 23.0 1.0 CG A:GLU80 3.9 19.3 1.0 CE1 A:HIS41 4.0 22.3 1.0 O5' A:AMP257 4.0 37.6 1.0 O A:PRO107 4.0 18.7 1.0 O A:HOH595 4.1 31.3 1.0 O2P A:AMP257 4.1 32.8 1.0 CB A:GLU80 4.1 17.5 1.0 C A:PRO107 4.3 16.8 1.0 O A:HOH1074 4.3 27.3 1.0 CB A:ASP108 4.3 15.8 1.0 C5' A:AMP257 4.3 44.4 1.0 OE2 A:GLU119 4.3 24.2 1.0 CA A:ASP108 4.3 16.0 1.0 O A:LEU106 4.4 15.9 1.0 NE2 A:HIS41 4.4 16.1 1.0 N A:ASP108 4.4 15.6 1.0 O A:HOH294 4.5 28.0 1.0 O3P A:AMP257 4.7 29.0 1.0 CA A:GLU80 4.8 18.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Amp


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 Avian Influenza Virus PA_N in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg999 b:28.9 occ:1.00 OD1 B:ASP108 2.0 20.9 1.0 O B:HOH1004 2.1 23.1 1.0 O B:HOH1003 2.2 20.1 1.0 O B:HOH1001 2.2 24.3 1.0 O B:HOH1002 2.2 24.5 1.0 OE2 B:GLU80 2.2 22.5 1.0 CG B:ASP108 3.1 19.9 1.0 CD B:GLU80 3.3 24.4 1.0 OD2 B:ASP108 3.6 19.9 1.0 O B:HOH339 4.0 39.9 1.0 CE1 B:HIS41 4.0 22.6 1.0 O B:HOH348 4.0 34.1 1.0 OE1 B:GLU119 4.0 32.3 1.0 O B:PRO107 4.1 18.1 1.0 OE1 B:GLU80 4.1 22.1 1.0 O B:HOH1043 4.1 27.2 1.0 CG B:GLU80 4.1 22.4 1.0 O B:HOH1005 4.1 32.1 1.0 O B:HOH505 4.2 42.7 1.0 O B:LEU106 4.3 20.5 1.0 C B:PRO107 4.3 17.5 1.0 O B:HOH412 4.3 42.9 1.0 CB B:ASP108 4.3 16.5 1.0 CA B:ASP108 4.4 17.6 1.0 CB B:GLU80 4.4 20.6 1.0 N B:ASP108 4.5 15.8 1.0 NE2 B:HIS41 4.5 21.1 1.0 CA B:GLU80 4.9 20.6 1.0 O B:HOH271 5.0 32.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Amp


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 Avian Influenza Virus PA_N in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg999 b:25.8 occ:1.00 OD1 C:ASP108 2.0 19.2 1.0 OE2 C:GLU80 2.1 22.2 1.0 O C:HOH1002 2.1 21.8 1.0 O C:HOH1003 2.1 21.4 1.0 O C:HOH1001 2.1 21.0 1.0 O C:HOH1004 2.3 26.9 1.0 CG C:ASP108 3.1 18.6 1.0 CD C:GLU80 3.1 23.6 1.0 OD2 C:ASP108 3.6 18.8 1.0 O C:HOH1042 3.9 36.9 1.0 OE1 C:GLU80 3.9 30.3 1.0 CG C:GLU80 4.0 23.1 1.0 CE1 C:HIS41 4.0 19.0 1.0 O C:LEU106 4.1 19.9 1.0 O C:PRO107 4.1 16.9 1.0 CB C:GLU80 4.1 25.1 1.0 C C:PRO107 4.2 18.1 1.0 CB C:ASP108 4.3 15.1 1.0 O C:HOH627 4.3 49.3 1.0 CA C:ASP108 4.3 16.8 1.0 OE2 C:GLU119 4.3 31.6 1.0 N C:ASP108 4.4 15.9 1.0 O C:HOH1005 4.4 34.0 1.0 NE2 C:HIS41 4.7 21.0 1.0 CA C:GLU80 4.7 24.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Amp


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 Avian Influenza Virus PA_N in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg999 b:27.9 occ:1.00 OD1 D:ASP108 1.9 20.4 1.0 O D:HOH1002 2.1 24.3 1.0 O D:HOH1004 2.2 27.1 1.0 O D:HOH1001 2.2 22.0 1.0 O D:HOH1003 2.4 29.4 1.0 OE2 D:GLU80 2.4 27.5 1.0 CG D:ASP108 3.0 20.1 1.0 CD D:GLU80 3.5 24.0 1.0 OD2 D:ASP108 3.5 20.0 1.0 O D:PRO107 4.0 19.2 1.0 O D:HOH528 4.1 44.7 1.0 CE1 D:HIS41 4.1 19.8 1.0 C D:PRO107 4.2 18.7 1.0 CB D:ASP108 4.2 17.1 1.0 O D:LEU106 4.2 19.4 1.0 CG D:GLU80 4.2 26.6 1.0 CA D:ASP108 4.2 17.0 1.0 OE1 D:GLU119 4.3 31.6 1.0 N D:ASP108 4.3 15.7 1.0 O D:HOH1046 4.4 29.7 1.0 OE2 D:GLU119 4.4 36.2 1.0 OE1 D:GLU80 4.4 31.7 1.0 CB D:GLU80 4.5 23.9 1.0 NE2 D:HIS41 4.7 18.3 1.0 CD D:GLU119 4.8 33.6 1.0 CA D:PRO107 4.9 19.6 1.0 C D:LEU106 5.0 21.8 1.0

C.Zhao, Z.Lou, Y.Guo, M.Ma, Y.Chen, S.Liang, L.Zhang, S.Chen, X.Li, Y.Liu, M.Bartlam, Z.Rao. Nucleoside Monophosphate Complex Structures of the Endonuclease Domain From the Influenza Virus Polymerase Pa Subunit Reveal the Substrate Binding Site Inside the Catalytic Center J.Virol. V. 83 9024 2009.
ISSN: ISSN 0022-538X
PubMed: 19587036
DOI: 10.1128/JVI.00911-09