Manganese in PDB 5vqn: E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7

Protein crystallography data

The structure of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vqn was solved by G.Kumar, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.47 / 2.00
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.848, 89.848, 133.261, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.2

Other elements in 5vqn:

The structure of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 (pdb code 5vqn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vqn:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5vqn

Go back to Manganese Binding Sites List in 5vqn
Manganese binding site 1 out of 2 in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:49.4
occ:1.00
O17 A:R07205 1.9 51.6 1.0
OD2 A:ASP108 2.1 41.7 1.0
O A:ILE120 2.1 51.5 1.0
NE2 A:HIS41 2.2 51.5 1.0
O15 A:R07205 2.5 54.8 1.0
C01 A:R07205 2.7 59.6 1.0
OD1 A:ASP119 2.7 70.3 1.0
C08 A:R07205 2.9 45.0 1.0
CG A:ASP108 3.0 54.3 1.0
CE1 A:HIS41 3.1 49.5 1.0
H20 A:R07205 3.1 66.0 1.0
HE1 A:HIS41 3.2 59.6 1.0
H A:ILE120 3.2 59.4 1.0
C A:ILE120 3.3 53.3 1.0
OD1 A:ASP108 3.3 53.6 1.0
CD2 A:HIS41 3.3 43.9 1.0
HD2 A:HIS41 3.5 52.9 1.0
N A:ILE120 3.6 49.3 1.0
MN A:MN202 3.7 53.5 1.0
HB A:ILE120 3.8 59.5 1.0
HZ2 A:LYS134 3.9 95.0 1.0
CA A:ILE120 3.9 43.3 1.0
O A:HOH301 3.9 59.8 1.0
HA2 A:GLY121 4.0 55.1 1.0
CG A:ASP119 4.0 70.3 1.0
HZ1 A:LYS134 4.0 95.0 1.0
C02 A:R07205 4.0 47.8 1.0
HA A:ASP119 4.2 67.8 1.0
ND1 A:HIS41 4.2 52.1 1.0
CB A:ILE120 4.3 49.4 1.0
N A:GLY121 4.3 55.2 1.0
CG A:HIS41 4.3 53.5 1.0
NZ A:LYS134 4.4 79.0 1.0
C A:ASP119 4.4 49.5 1.0
H1 A:R07205 4.4 57.5 1.0
CB A:ASP108 4.4 50.2 1.0
HE3 A:LYS134 4.4 0.9 1.0
HG22 A:ILE120 4.4 57.7 1.0
C07 A:R07205 4.5 53.1 1.0
HB2 A:ASP108 4.5 60.4 1.0
CA A:GLY121 4.6 45.8 1.0
CA A:ASP119 4.7 56.4 1.0
O A:HOH314 4.7 60.6 1.0
OD2 A:ASP119 4.7 80.5 1.0
HB3 A:ASP108 4.8 60.4 1.0
HA A:ILE120 4.8 52.1 1.0
HG A:CYS45 4.9 57.9 1.0
O18 A:R07205 4.9 58.7 1.0
HD1 A:HIS41 4.9 62.7 1.0
CG2 A:ILE120 5.0 47.9 1.0
CB A:ASP119 5.0 58.7 1.0
CE A:LYS134 5.0 85.6 1.0
OE1 A:GLU80 5.0 48.9 1.0

Manganese binding site 2 out of 2 in 5vqn

Go back to Manganese Binding Sites List in 5vqn
Manganese binding site 2 out of 2 in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:53.5
occ:1.00
H20 A:R07205 1.8 66.0 1.0
O15 A:R07205 1.9 54.8 1.0
O18 A:R07205 2.1 58.7 1.0
OD1 A:ASP108 2.1 53.6 1.0
O A:HOH310 2.1 48.5 1.0
OE1 A:GLU80 2.2 48.9 1.0
O A:HOH301 2.4 59.8 1.0
C08 A:R07205 3.1 45.0 1.0
C14 A:R07205 3.1 55.3 1.0
HE1 A:HIS41 3.1 59.6 1.0
CG A:ASP108 3.2 54.3 1.0
CD A:GLU80 3.4 61.2 1.0
C07 A:R07205 3.6 53.1 1.0
MN A:MN201 3.7 49.4 1.0
OD2 A:ASP108 3.7 41.7 1.0
HB2 A:GLU80 3.8 66.4 1.0
CE1 A:HIS41 3.8 49.5 1.0
HA A:ASP108 3.9 54.2 1.0
H6 A:R07205 4.0 68.3 1.0
O A:PRO107 4.0 56.8 1.0
HG2 A:GLU80 4.2 77.6 1.0
N13 A:R07205 4.2 62.5 1.0
CG A:GLU80 4.2 64.6 1.0
OE2 A:GLU80 4.2 64.2 1.0
C01 A:R07205 4.3 59.6 1.0
F28 A:R07205 4.4 62.3 1.0
NE2 A:HIS41 4.4 51.5 1.0
CB A:ASP108 4.4 50.2 1.0
CB A:GLU80 4.4 55.2 1.0
C A:PRO107 4.4 57.9 1.0
O A:LEU106 4.5 64.7 1.0
CA A:ASP108 4.5 45.0 1.0
HA A:GLU80 4.5 61.8 1.0
C20 A:R07205 4.6 56.8 1.0
O17 A:R07205 4.6 51.6 1.0
N A:ASP108 4.6 47.6 1.0
H16 A:R07205 4.7 66.0 1.0
OD1 A:ASP119 4.7 70.3 1.0
HB3 A:LEU106 4.8 63.5 1.0
HB3 A:ASP108 4.8 60.4 1.0
ND1 A:HIS41 4.9 52.1 1.0
N06 A:R07205 5.0 58.2 1.0

Reference:

J.C.Jones, G.Kumar, S.Barman, I.Najera, S.W.White, R.J.Webby, E.A.Govorkova. Identification of the I38T Pa Substitution As A Resistance Marker For Next-Generation Influenza Virus Endonuclease Inhibitors. Mbio V. 9 2018.
ISSN: ESSN 2150-7511
PubMed: 29691337
DOI: 10.1128/MBIO.00430-18
Page generated: Tue Dec 15 04:47:54 2020

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