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

Go back to Calcium Binding Sites List in 7bwu
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

Go back to Calcium Binding Sites List in 7bwu
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: Sat Jul 10 11:14:53 2021

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy