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Nickel in PDB 5tr8: Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6.

Protein crystallography data

The structure of Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6., PDB code: 5tr8 was solved by M.G.Joyce, M.Kanekiyo, J.R.Mascola, B.S.Graham, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.61 / 2.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.463, 83.332, 83.160, 90.00, 105.69, 90.00
R / Rfree (%) 17.4 / 19.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6. (pdb code 5tr8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6., PDB code: 5tr8:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5tr8

Go back to Nickel Binding Sites List in 5tr8
Nickel binding site 1 out of 2 in the Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni301

b:46.4
occ:1.00
OD1 L:ASP1 1.9 61.3 1.0
N L:ASP1 2.1 48.6 1.0
O L:ASP1 2.2 48.2 1.0
NZ L:LYS3 2.3 62.8 1.0
CA L:ASP1 2.8 45.6 1.0
C L:ASP1 2.8 44.2 1.0
CG L:ASP1 2.9 62.5 1.0
CE L:LYS3 3.1 63.1 1.0
CB L:ASP1 3.3 48.3 1.0
CD L:LYS3 3.8 60.4 1.0
OD2 L:ASP1 3.9 71.3 1.0
N L:ILE2 4.1 42.3 1.0
O L:HOH491 4.5 54.3 1.0
CA L:ILE2 4.9 41.1 1.0
CG L:LYS3 5.0 54.7 1.0
C L:ILE2 5.0 40.4 1.0

Nickel binding site 2 out of 2 in 5tr8

Go back to Nickel Binding Sites List in 5tr8
Nickel binding site 2 out of 2 in the Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Vaccine-Elicited Pan- Influenza H1N1 Neutralizing Murine Antibody 441D6. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni302

b:74.5
occ:1.00
O L:HOH404 1.7 66.7 1.0
O L:HOH435 2.2 63.4 1.0
O H:HOH494 2.2 63.1 1.0
OD2 L:ASP167 2.2 63.2 1.0
NE2 H:HIS164 2.4 51.2 1.0
O L:HOH403 2.8 63.3 1.0
CG L:ASP167 3.2 59.7 1.0
CD2 H:HIS164 3.2 35.8 1.0
CE1 H:HIS164 3.4 54.2 1.0
OD1 L:ASP167 3.5 64.0 1.0
OD1 L:ASN138 3.9 46.3 1.0
OD2 L:ASP170 4.1 59.6 1.0
O L:HOH504 4.2 67.4 1.0
CG H:HIS164 4.3 40.3 1.0
O L:HOH459 4.4 38.0 1.0
ND1 H:HIS164 4.4 52.8 1.0
CB L:ASP167 4.4 46.8 1.0
O H:VAL163 4.5 42.3 1.0
OD1 L:ASP170 4.6 56.1 1.0
CG L:ASP170 4.7 55.8 1.0
O L:HOH499 4.8 60.1 1.0
CG L:ASN138 5.0 42.4 1.0

Reference:

M.Kanekiyo, M.G.Joyce, R.A.Gillespie, J.R.Gallagher, S.F.Andrews, H.M.Yassine, A.K.Wheatley, B.E.Fisher, D.R.Ambrozak, A.Creanga, K.Leung, E.S.Yang, S.Boyoglu-Barnum, I.S.Georgiev, Y.Tsybovsky, M.S.Prabhakaran, H.Andersen, W.P.Kong, U.Baxa, K.L.Zephir, J.E.Ledgerwood, R.A.Koup, P.D.Kwong, A.K.Harris, A.B.Mcdermott, J.R.Mascola, B.S.Graham. Mosaic Nanoparticle Display of Diverse Influenza Virus Hemagglutinins Elicits Broad B Cell Responses. Nat.Immunol. V. 20 362 2019.
ISSN: ESSN 1529-2916
PubMed: 30742080
DOI: 10.1038/S41590-018-0305-X
Page generated: Wed Dec 16 01:49:10 2020

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