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Calcium in PDB 7bwu: Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa

Protein crystallography data

The structure of Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa, PDB code: 7bwu was solved by F.S.Ma, G.P.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.86 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.88, 142.07, 191.21, 90, 90, 90
R / Rfree (%) 16.7 / 19.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa (pdb code 7bwu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa, PDB code: 7bwu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7bwu

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Calcium binding site 1 out of 4 in the Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1203

b:63.0
occ:1.00
 O B:VAL296 2.3 37.6 1.0
O B:ALA266 2.4 40.6 1.0
O B:ASP261 2.4 40.0 1.0
OG B:SER264 2.5 39.9 1.0
O B:SER264 2.6 40.8 1.0
OD1 B:ASP261 2.7 51.8 1.0
C B:SER264 3.3 42.2 1.0
C B:VAL296 3.4 41.4 1.0
C B:ASP261 3.4 39.6 1.0
CB B:SER264 3.6 42.5 1.0
C B:ALA266 3.6 45.0 1.0
CA B:SER264 3.7 44.1 1.0
CG B:ASP261 3.8 52.8 1.0
CA B:ASP261 3.8 39.7 1.0
O B:HOH1531 3.8 59.0 1.0
N B:SER264 3.9 40.9 1.0
CA B:VAL296 3.9 42.3 1.0
N B:ALA266 4.2 48.4 1.0
CB B:ASP261 4.2 42.0 1.0
C B:VAL265 4.3 47.5 1.0
CB B:VAL296 4.3 38.9 1.0
N B:VAL265 4.3 42.9 1.0
OE2 B:GLU256 4.5 67.4 1.0
O B:VAL265 4.5 47.3 1.0
CA B:ALA266 4.5 46.8 1.0
N B:PRO267 4.5 42.3 1.0
CA B:PRO267 4.5 43.5 1.0
N B:ALA297 4.5 36.3 1.0
N B:TYR262 4.6 39.2 1.0
C B:PRO267 4.7 44.1 1.0
CA B:VAL265 4.8 44.8 1.0
CA B:ALA297 4.8 35.2 1.0
OD2 B:ASP261 4.9 55.0 1.0
N B:THR268 4.9 36.2 1.0
CA B:TYR262 5.0 37.5 1.0

Calcium binding site 2 out of 4 in 7bwu

Go back to Calcium Binding Sites List in 7bwu
Calcium binding site 2 out of 4 in the Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1203

b:67.1
occ:1.00
 O D:VAL296 2.2 62.3 1.0
O D:ALA266 2.3 49.5 1.0
O D:ASP261 2.4 42.5 1.0
O D:SER264 2.6 50.6 1.0
OD1 D:ASP261 2.6 58.1 1.0
OG D:SER264 2.6 49.0 1.0
C D:ASP261 3.4 42.7 1.0
C D:VAL296 3.4 46.9 1.0
C D:SER264 3.4 53.9 1.0
C D:ALA266 3.5 51.6 1.0
CG D:ASP261 3.7 53.5 1.0
CB D:SER264 3.7 51.4 1.0
CA D:ASP261 3.8 43.9 1.0
CA D:SER264 3.9 52.4 1.0
O D:HOH1416 4.0 66.9 1.0
CA D:VAL296 4.0 45.5 1.0
N D:SER264 4.0 51.5 1.0
N D:ALA266 4.1 51.0 1.0
CB D:ASP261 4.3 47.7 1.0
CB D:VAL296 4.4 48.1 1.0
C D:VAL265 4.4 57.1 1.0
CA D:ALA266 4.4 50.5 1.0
N D:VAL265 4.4 60.7 1.0
N D:ALA297 4.4 41.4 1.0
N D:PRO267 4.5 49.9 1.0
N D:TYR262 4.5 38.5 1.0
CA D:PRO267 4.5 42.6 1.0
C D:PRO267 4.6 42.6 1.0
OD2 D:ASP261 4.7 53.8 1.0
CA D:ALA297 4.7 35.3 1.0
O D:VAL265 4.8 57.8 1.0
OE1 D:GLU256 4.8 81.2 1.0
CA D:VAL265 4.9 61.7 1.0
O D:PRO267 4.9 40.5 1.0
CA D:TYR262 5.0 39.9 1.0
CB D:ALA266 5.0 47.9 1.0
N D:THR268 5.0 41.2 1.0
O D:GLU260 5.0 44.8 1.0

Calcium binding site 3 out of 4 in 7bwu

Go back to Calcium Binding Sites List in 7bwu
Calcium binding site 3 out of 4 in the Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1203

b:61.1
occ:1.00
 O A:VAL296 2.4 39.7 1.0
O A:ASP261 2.4 41.1 1.0
OG A:SER264 2.5 48.7 1.0
O A:ALA266 2.5 46.1 1.0
O A:SER264 2.6 46.5 1.0
OD1 A:ASP261 2.9 63.4 1.0
C A:SER264 3.3 48.4 1.0
C A:ASP261 3.4 43.6 1.0
CB A:SER264 3.5 48.5 1.0
C A:VAL296 3.5 40.4 1.0
C A:ALA266 3.7 44.1 1.0
CA A:ASP261 3.7 46.3 1.0
CA A:SER264 3.7 48.8 1.0
O A:HOH1561 3.8 53.2 1.0
CG A:ASP261 3.8 60.3 1.0
N A:SER264 3.9 46.2 1.0
N A:ALA266 4.1 50.6 1.0
CA A:VAL296 4.1 41.3 1.0
CB A:ASP261 4.2 51.8 1.0
OE2 A:GLU256 4.3 72.0 1.0
N A:VAL265 4.3 50.2 1.0
C A:VAL265 4.3 55.1 1.0
CB A:VAL296 4.4 40.4 1.0
CA A:ALA266 4.5 45.0 1.0
N A:TYR262 4.6 41.5 1.0
N A:PRO267 4.6 43.7 1.0
N A:ALA297 4.6 35.6 1.0
CA A:PRO267 4.7 43.4 1.0
O A:HOH1577 4.7 60.5 1.0
O A:VAL265 4.7 57.1 1.0
C A:PRO267 4.8 41.3 1.0
CA A:VAL265 4.8 53.4 1.0
OD2 A:ASP261 4.8 62.9 1.0
O A:GLU260 4.9 39.0 1.0
CA A:ALA297 4.9 33.8 1.0

Calcium binding site 4 out of 4 in 7bwu

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Calcium binding site 4 out of 4 in the Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Restructuring Hemagglutinin-Neuraminidase (Hn) of Newcastle Disease Virus Produced From Oryza Sativa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1203

b:77.2
occ:1.00
 OG C:SER264 2.3 55.0 1.0
O C:ALA266 2.4 48.9 1.0
O C:VAL296 2.4 46.4 1.0
O C:ASP261 2.4 46.4 1.0
O C:SER264 2.9 56.2 1.0
OD1 C:ASP261 2.9 61.4 1.0
C C:SER264 3.4 58.7 1.0
C C:ASP261 3.4 44.9 1.0
CB C:SER264 3.5 55.4 1.0
C C:VAL296 3.6 45.2 1.0
C C:ALA266 3.6 50.2 1.0
CG C:ASP261 3.8 57.0 1.0
CA C:SER264 3.8 59.1 1.0
CA C:ASP261 3.8 44.4 1.0
N C:SER264 4.0 59.4 1.0
N C:ALA266 4.1 58.2 1.0
CA C:VAL296 4.2 46.4 1.0
N C:VAL265 4.3 60.2 1.0
C C:VAL265 4.3 61.9 1.0
CB C:ASP261 4.4 49.6 1.0
CA C:ALA266 4.4 53.7 1.0
CB C:VAL296 4.5 48.6 1.0
N C:PRO267 4.5 45.9 1.0
CA C:PRO267 4.6 42.5 1.0
N C:TYR262 4.6 46.4 1.0
N C:ALA297 4.6 39.4 1.0
C C:PRO267 4.7 42.1 1.0
OE1 C:GLU256 4.7 77.6 1.0
O C:VAL265 4.7 62.7 1.0
OD2 C:ASP261 4.7 58.1 1.0
CA C:VAL265 4.8 61.7 1.0
CA C:ALA297 4.9 34.6 1.0
O C:PRO267 4.9 47.4 1.0
O C:GLU260 5.0 49.3 1.0

Reference:

F.S.Ma, E.Q.Zhang, Q.R.Xu, J.Q.Guo, G.P.Zhang. Restructuring A Dimer Antigen in Transgenic Rice System For High Efficient B Cell Activation: Development of A Super Effective Vaccine Against Newcastle Disease Virus To Be Published.
Page generated: Thu Jul 18 23:23:38 2024

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