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Magnesium in PDB 3hw3: The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump

Protein crystallography data

The structure of The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump, PDB code: 3hw3 was solved by C.Zhao, Z.Lou, Y.Guo, M.Ma, Y.Chen, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.132, 59.695, 66.850, 96.28, 96.65, 109.44
R / Rfree (%) 21.8 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump (pdb code 3hw3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump, PDB code: 3hw3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3hw3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg999

b:25.0
occ:1.00
OD1 A:ASP108 1.9 22.4 1.0
O3P A:U5P257 2.0 27.0 1.0
O A:HOH1003 2.0 18.8 1.0
O A:HOH1002 2.1 23.3 1.0
OE2 A:GLU80 2.2 20.1 1.0
O A:HOH1001 2.2 24.6 1.0
CG A:ASP108 3.0 19.5 1.0
CD A:GLU80 3.1 21.0 1.0
P A:U5P257 3.4 38.0 1.0
OD2 A:ASP108 3.6 19.1 1.0
O5' A:U5P257 3.8 39.2 1.0
O A:PRO107 3.9 18.0 1.0
OE1 A:GLU80 3.9 21.1 1.0
CG A:GLU80 4.0 20.2 1.0
CE1 A:HIS41 4.0 20.9 1.0
O1P A:U5P257 4.0 33.1 1.0
C A:PRO107 4.2 19.0 1.0
O A:LEU106 4.2 18.5 1.0
CB A:ASP108 4.2 17.3 1.0
CB A:GLU80 4.2 20.7 1.0
CA A:ASP108 4.3 17.6 1.0
N A:ASP108 4.3 17.7 1.0
OE2 A:GLU119 4.3 21.4 1.0
O A:HOH1071 4.4 31.1 1.0
O A:HOH1004 4.4 33.5 1.0
NE2 A:HIS41 4.5 16.2 1.0
O2P A:U5P257 4.5 35.7 1.0
CA A:GLU80 4.8 20.6 1.0
CA A:PRO107 5.0 18.9 1.0

Magnesium binding site 2 out of 4 in 3hw3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg999

b:23.8
occ:1.00
O B:HOH1004 1.9 17.1 1.0
OD1 B:ASP108 2.1 15.3 1.0
O B:HOH1001 2.1 21.7 1.0
O B:HOH1002 2.1 20.7 1.0
OE2 B:GLU80 2.1 20.4 1.0
O B:HOH1003 2.2 20.4 1.0
CG B:ASP108 3.1 15.7 1.0
CD B:GLU80 3.3 21.2 1.0
OD2 B:ASP108 3.6 19.2 1.0
CE1 B:HIS41 3.9 16.2 1.0
O B:HOH443 3.9 38.5 1.0
OE1 B:GLU119 4.1 25.3 1.0
OE1 B:GLU80 4.1 21.7 1.0
O B:HOH294 4.2 34.4 1.0
O B:HOH1049 4.2 24.7 1.0
O B:PRO107 4.2 17.6 1.0
CG B:GLU80 4.3 20.4 1.0
O B:LEU106 4.3 23.0 1.0
OE2 B:GLU119 4.3 25.2 1.0
CB B:ASP108 4.4 16.6 1.0
C B:PRO107 4.4 18.6 1.0
NE2 B:HIS41 4.4 17.4 1.0
CA B:ASP108 4.5 16.4 1.0
CB B:GLU80 4.5 19.6 1.0
N B:ASP108 4.6 17.5 1.0
CD B:GLU119 4.6 27.9 1.0
ND1 B:HIS41 4.9 16.4 1.0

Magnesium binding site 3 out of 4 in 3hw3

Go back to Magnesium Binding Sites List in 3hw3
Magnesium binding site 3 out of 4 in the The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg999

b:23.9
occ:1.00
OD1 C:ASP108 2.0 19.4 1.0
O C:HOH1003 2.1 24.3 1.0
O C:HOH1001 2.1 23.2 1.0
O C:HOH1004 2.1 26.0 1.0
OE2 C:GLU80 2.1 23.0 1.0
O C:HOH1002 2.2 24.6 1.0
CG C:ASP108 3.1 21.4 1.0
CD C:GLU80 3.2 25.8 1.0
OD2 C:ASP108 3.6 22.6 1.0
O C:HOH297 3.9 27.7 1.0
OE1 C:GLU80 3.9 29.7 1.0
CE1 C:HIS41 3.9 20.4 1.0
O C:LEU106 4.0 23.9 1.0
CG C:GLU80 4.1 28.5 1.0
O C:PRO107 4.1 19.7 1.0
CB C:GLU80 4.2 29.7 1.0
O C:HOH1022 4.2 32.5 1.0
C C:PRO107 4.3 21.0 1.0
CB C:ASP108 4.3 18.9 1.0
CA C:ASP108 4.4 19.6 1.0
OE2 C:GLU119 4.4 27.9 1.0
N C:ASP108 4.4 19.6 1.0
NE2 C:HIS41 4.5 19.2 1.0
CA C:GLU80 4.8 29.6 1.0
ND1 C:HIS41 4.9 20.9 1.0

Magnesium binding site 4 out of 4 in 3hw3

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Avian Influenza Virus PA_N in Complex with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg999

b:35.4
occ:1.00
OD1 D:ASP108 1.9 21.2 1.0
O D:HOH1003 1.9 29.6 1.0
O D:HOH1001 2.2 25.0 1.0
O D:HOH1002 2.2 22.9 1.0
O D:HOH1004 2.8 32.9 1.0
OE2 D:GLU80 2.8 33.7 1.0
CG D:ASP108 2.9 18.3 1.0
OD2 D:ASP108 3.4 19.8 1.0
OE1 D:GLU119 3.7 34.0 1.0
CD D:GLU80 3.7 30.7 1.0
O D:PRO107 3.8 18.7 1.0
C D:PRO107 3.9 18.4 1.0
O D:LEU106 4.0 20.3 1.0
CB D:ASP108 4.1 15.6 1.0
CA D:ASP108 4.1 16.3 1.0
N D:ASP108 4.1 16.0 1.0
CE1 D:HIS41 4.2 24.1 1.0
CG D:GLU80 4.4 29.2 1.0
CB D:GLU80 4.5 26.2 1.0
CD D:GLU119 4.5 33.0 1.0
OE1 D:GLU80 4.6 33.8 1.0
OE2 D:GLU119 4.6 39.1 1.0
CA D:PRO107 4.6 19.8 1.0
NE2 D:HIS41 4.7 21.9 1.0
C D:LEU106 4.8 21.4 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: Mon Dec 14 08:14:51 2020

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