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Magnesium in PDB 3hw4: Crystal Structure of Avian Influenza A Virus in Complex with Tmp

Protein crystallography data

The structure of Crystal Structure of Avian Influenza A Virus in Complex with Tmp, PDB code: 3hw4 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) 47.78 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.323, 60.033, 67.114, 96.12, 96.36, 109.51
R / Rfree (%) 21.3 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Avian Influenza A Virus in Complex with Tmp (pdb code 3hw4). 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 A Virus in Complex with Tmp, PDB code: 3hw4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3hw4

Go back to Magnesium Binding Sites List in 3hw4
Magnesium binding site 1 out of 4 in the Crystal Structure of Avian Influenza A Virus in Complex with Tmp


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 A Virus in Complex with Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg999

b:28.1
occ:1.00
OD1 A:ASP108 2.0 24.7 1.0
O3P A:TMP257 2.0 20.0 1.0
O A:HOH1003 2.0 22.4 1.0
OE2 A:GLU80 2.1 27.6 1.0
O A:HOH1002 2.1 28.9 1.0
O A:HOH1001 2.2 29.4 1.0
CG A:ASP108 3.0 23.8 1.0
CD A:GLU80 3.1 29.2 1.0
P A:TMP257 3.4 20.0 1.0
OD2 A:ASP108 3.5 26.6 1.0
O5' A:TMP257 3.8 20.0 1.0
CE1 A:HIS41 3.9 29.5 1.0
O A:PRO107 3.9 25.5 1.0
OE1 A:GLU80 4.0 30.8 1.0
CG A:GLU80 4.0 28.6 1.0
O1P A:TMP257 4.0 20.0 1.0
CB A:GLU80 4.1 27.4 1.0
C A:PRO107 4.2 24.9 1.0
O A:LEU106 4.2 27.7 1.0
CB A:ASP108 4.2 21.4 1.0
CA A:ASP108 4.2 23.0 1.0
OE2 A:GLU119 4.3 28.7 1.0
O A:HOH369 4.3 37.4 1.0
N A:ASP108 4.3 23.2 1.0
NE2 A:HIS41 4.4 26.3 1.0
O A:HOH1041 4.4 41.0 1.0
O2P A:TMP257 4.5 20.0 1.0
C5' A:TMP257 4.7 20.0 1.0
CA A:GLU80 4.8 28.4 1.0
CA A:PRO107 5.0 26.4 1.0

Magnesium binding site 2 out of 4 in 3hw4

Go back to Magnesium Binding Sites List in 3hw4
Magnesium binding site 2 out of 4 in the Crystal Structure of Avian Influenza A Virus in Complex with Tmp


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 A Virus in Complex with Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg999

b:33.6
occ:1.00
O B:HOH1002 2.0 29.2 1.0
OD1 B:ASP108 2.0 25.0 1.0
O B:HOH1004 2.0 31.8 1.0
OE2 B:GLU80 2.2 31.9 1.0
O B:HOH1001 2.2 30.9 1.0
O B:HOH1003 2.3 26.4 1.0
CG B:ASP108 3.1 22.9 1.0
CD B:GLU80 3.3 35.8 1.0
OD2 B:ASP108 3.5 30.4 1.0
CE1 B:HIS41 3.8 25.6 1.0
O B:HOH1042 4.0 41.2 1.0
OE1 B:GLU80 4.1 38.4 1.0
CG B:GLU80 4.2 33.0 1.0
O B:PRO107 4.2 23.2 1.0
O B:HOH1038 4.2 37.9 1.0
OE1 B:GLU119 4.2 39.8 1.0
CB B:ASP108 4.3 22.5 1.0
CA B:ASP108 4.3 23.2 1.0
CB B:GLU80 4.4 28.8 1.0
O B:LEU106 4.4 30.4 1.0
OE2 B:GLU119 4.4 40.7 1.0
C B:PRO107 4.4 23.0 1.0
NE2 B:HIS41 4.4 24.6 1.0
O B:HOH320 4.5 45.5 1.0
N B:ASP108 4.5 22.5 1.0
CD B:GLU119 4.8 42.3 1.0
ND1 B:HIS41 4.8 25.5 1.0
CA B:GLU80 4.9 28.6 1.0

Magnesium binding site 3 out of 4 in 3hw4

Go back to Magnesium Binding Sites List in 3hw4
Magnesium binding site 3 out of 4 in the Crystal Structure of Avian Influenza A Virus in Complex with Tmp


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 A Virus in Complex with Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg999

b:32.7
occ:1.00
OD1 C:ASP108 2.0 25.7 1.0
OE2 C:GLU80 2.0 31.8 1.0
O C:HOH1003 2.1 28.4 1.0
O C:HOH1002 2.1 29.3 1.0
O C:HOH330 2.1 28.8 1.0
O C:HOH1001 2.2 29.2 1.0
CG C:ASP108 3.1 26.7 1.0
CD C:GLU80 3.1 34.5 1.0
OD2 C:ASP108 3.6 32.7 1.0
O C:HOH388 3.6 49.6 1.0
OE1 C:GLU80 3.9 39.0 1.0
CE1 C:HIS41 4.0 27.1 1.0
O C:HOH1046 4.0 36.5 1.0
CG C:GLU80 4.0 35.3 1.0
O C:PRO107 4.2 26.4 1.0
CB C:GLU80 4.2 34.0 1.0
CB C:ASP108 4.2 24.8 1.0
O C:LEU106 4.2 29.5 1.0
C C:PRO107 4.3 28.7 1.0
CA C:ASP108 4.3 27.1 1.0
N C:ASP108 4.4 26.5 1.0
OE2 C:GLU119 4.4 33.6 1.0
O C:HOH1018 4.4 43.1 1.0
O C:HOH398 4.6 52.6 1.0
NE2 C:HIS41 4.6 29.9 1.0
CA C:GLU80 4.8 33.5 1.0
ND1 C:HIS41 4.9 26.4 1.0
O C:HOH392 5.0 51.9 1.0

Magnesium binding site 4 out of 4 in 3hw4

Go back to Magnesium Binding Sites List in 3hw4
Magnesium binding site 4 out of 4 in the Crystal Structure of Avian Influenza A Virus in Complex with Tmp


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 A Virus in Complex with Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg999

b:36.2
occ:1.00
OD1 D:ASP108 1.8 26.8 1.0
O D:HOH1002 2.0 27.4 1.0
O D:HOH1001 2.2 28.3 1.0
O2P D:TMP257 2.2 47.0 1.0
OE2 D:GLU80 2.4 38.1 1.0
O D:HOH1003 2.6 40.5 1.0
CG D:ASP108 2.9 26.1 1.0
OD2 D:ASP108 3.4 27.9 1.0
CD D:GLU80 3.5 39.8 1.0
P D:TMP257 3.6 50.2 1.0
O D:PRO107 4.0 27.7 1.0
OE1 D:GLU119 4.0 38.1 1.0
CE1 D:HIS41 4.1 29.0 1.0
O D:LEU106 4.1 28.9 1.0
CB D:ASP108 4.1 22.8 1.0
C D:PRO107 4.2 27.4 1.0
OE2 D:GLU119 4.2 40.7 1.0
CA D:ASP108 4.2 23.4 1.0
O D:HOH1050 4.2 49.0 1.0
O5' D:TMP257 4.2 49.3 1.0
O3P D:TMP257 4.2 33.5 1.0
N D:ASP108 4.3 23.8 1.0
CG D:GLU80 4.3 35.5 1.0
OE1 D:GLU80 4.4 45.4 1.0
O D:HOH279 4.4 35.7 1.0
CB D:GLU80 4.4 33.2 1.0
CD D:GLU119 4.6 39.5 1.0
NE2 D:HIS41 4.6 31.1 1.0
O1P D:TMP257 4.7 45.4 1.0
C5' D:TMP257 4.8 58.5 1.0
CA D:PRO107 4.9 27.2 1.0
C D:LEU106 4.9 29.5 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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