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

Protein crystallography data

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

Magnesium Binding Sites:

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 3hw5

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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 3hw5

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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 3hw5

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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 3hw5

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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

Reference:

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
Page generated: Wed Aug 14 15:23:52 2024

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