Calcium in PDB 4jf7: Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain

Enzymatic activity of Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain

All present enzymatic activity of Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain:
3.2.1.18;

Protein crystallography data

The structure of Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain, PDB code: 4jf7 was solved by B.D.Welch, P.Yuan, S.Bose, C.A.Kors, R.A.Lamb, T.S.Jardetzky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.36 / 2.50
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 194.390, 194.390, 185.979, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain (pdb code 4jf7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain, PDB code: 4jf7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4jf7

Go back to Calcium Binding Sites List in 4jf7
Calcium binding site 1 out of 4 in the Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:80.0
occ:1.00
 O D:ALA255 2.7 39.1 1.0
O D:ASP250 2.7 37.3 1.0
OG D:SER253 2.8 46.8 1.0
O D:HOH821 2.8 54.1 1.0
O D:ALA285 2.8 40.9 1.0
O D:SER253 2.9 48.6 1.0
C D:SER253 3.4 37.3 1.0
CB D:SER253 3.4 43.2 1.0
C D:ASP250 3.5 30.2 1.0
C D:ALA255 3.6 33.8 1.0
CA D:SER253 3.7 39.1 1.0
CA D:ASP250 3.7 28.1 1.0
C D:ALA285 3.9 38.6 1.0
N D:SER253 3.9 36.8 1.0
O D:HOH891 4.1 49.6 1.0
O D:ASP249 4.1 39.0 1.0
N D:ALA255 4.1 38.3 1.0
CA D:PRO256 4.2 29.6 1.0
N D:PRO256 4.3 32.6 1.0
NE2 D:GLN245 4.3 39.7 1.0
N D:ALA254 4.4 40.4 1.0
CA D:ALA255 4.5 40.4 1.0
CA D:ALA285 4.6 37.9 1.0
CB D:ASP250 4.6 35.6 1.0
OD1 D:ASP250 4.6 47.0 1.0
N D:TYR251 4.7 38.2 1.0
OD2 A:ASP282 4.7 67.3 1.0
CB D:THR286 4.7 33.1 1.0
C D:ALA254 4.7 39.1 1.0
C D:PRO256 4.8 30.6 1.0
CB D:ALA285 4.8 40.2 1.0
N D:ASP250 4.8 30.8 1.0
N D:THR286 4.8 35.7 1.0
CD D:PRO257 4.9 34.9 1.0
C D:ASP249 4.9 38.2 1.0
CA D:THR286 4.9 33.3 1.0
CA D:ALA254 4.9 42.5 1.0
C D:PHE252 5.0 44.2 1.0
N D:PRO257 5.0 31.7 1.0

Calcium binding site 2 out of 4 in 4jf7

Go back to Calcium Binding Sites List in 4jf7
Calcium binding site 2 out of 4 in the Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:74.2
occ:1.00
 O A:ALA285 2.7 35.3 1.0
O A:ALA255 2.7 45.2 1.0
O A:ASP250 2.8 42.0 1.0
OG A:SER253 2.8 33.6 1.0
O A:SER253 2.8 42.0 1.0
O A:HOH723 2.8 53.0 1.0
C A:SER253 3.4 40.4 1.0
C A:ASP250 3.6 35.7 1.0
C A:ALA255 3.6 47.2 1.0
CA A:ASP250 3.7 31.8 1.0
C A:ALA285 3.8 38.5 1.0
CB A:SER253 3.8 42.3 1.0
CA A:SER253 3.9 43.6 1.0
N A:SER253 4.1 41.4 1.0
O D:HOH829 4.1 38.1 1.0
N A:ALA255 4.1 40.9 1.0
CA A:PRO256 4.2 41.3 1.0
OD2 D:ASP282 4.2 44.8 1.0
NE2 A:GLN245 4.2 37.9 1.0
N A:PRO256 4.3 47.5 1.0
O A:ASP249 4.3 37.2 1.0
N A:ALA254 4.3 40.7 1.0
CB A:ASP250 4.4 38.4 1.0
CA A:ALA255 4.5 44.9 1.0
CA A:ALA285 4.5 36.0 1.0
CB A:THR286 4.6 39.0 1.0
C A:PRO256 4.6 37.3 1.0
OD1 A:ASP250 4.6 51.2 1.0
CD A:PRO257 4.6 40.7 1.0
N A:THR286 4.7 38.5 1.0
C A:ALA254 4.7 44.1 1.0
OD1 D:ASP282 4.8 48.7 1.0
CB A:ALA285 4.8 25.3 1.0
N A:PRO257 4.8 38.1 1.0
N A:TYR251 4.8 40.3 1.0
CA A:THR286 4.8 36.5 1.0
N A:ASP250 4.8 30.8 1.0
CG D:ASP282 4.9 44.6 1.0
CA A:ALA254 4.9 38.8 1.0
CG A:ASP250 5.0 47.3 1.0

Calcium binding site 3 out of 4 in 4jf7

Go back to Calcium Binding Sites List in 4jf7
Calcium binding site 3 out of 4 in the Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:92.4
occ:1.00
 O B:ALA255 2.7 47.8 1.0
O B:ASP250 2.8 51.1 1.0
OG B:SER253 3.0 66.2 1.0
O B:ALA285 3.0 51.4 1.0
CA B:ASP250 3.5 47.8 1.0
C B:ASP250 3.5 50.7 1.0
CB B:SER253 3.6 64.8 1.0
O B:SER253 3.6 66.8 1.0
C B:ALA255 3.8 50.7 1.0
C B:SER253 4.0 64.8 1.0
OD1 B:ASP250 4.0 65.4 1.0
NE2 B:GLN245 4.1 46.6 1.0
CA B:PRO256 4.2 42.8 1.0
CA B:SER253 4.2 67.0 1.0
O B:ASP249 4.2 51.7 1.0
CB B:ASP250 4.2 54.1 1.0
C B:ALA285 4.2 54.2 1.0
CD B:PRO257 4.4 39.8 1.0
N B:SER253 4.4 65.2 1.0
C B:PRO256 4.4 43.6 1.0
N B:PRO256 4.5 44.3 1.0
N B:PRO257 4.5 47.4 1.0
N B:ASP250 4.6 53.1 1.0
CG B:ASP250 4.6 63.4 1.0
N B:ALA255 4.7 46.2 1.0
N B:TYR251 4.8 50.5 1.0
CB B:THR286 4.8 52.1 1.0
C B:ASP249 4.8 52.4 1.0
N B:ALA254 4.8 58.8 1.0
CA B:ALA255 4.9 52.0 1.0
CG B:PRO257 4.9 36.0 1.0

Calcium binding site 4 out of 4 in 4jf7

Go back to Calcium Binding Sites List in 4jf7
Calcium binding site 4 out of 4 in the Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin- Neuraminidase (Hn) Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:81.2
occ:1.00
 O C:ASP250 2.7 53.5 1.0
O C:ALA255 2.7 41.5 1.0
O C:ALA285 2.8 56.2 1.0
OG C:SER253 2.8 54.2 1.0
O C:SER253 2.9 61.4 1.0
O C:HOH751 3.0 51.2 1.0
C C:SER253 3.3 54.2 1.0
CB C:SER253 3.5 56.2 1.0
C C:ASP250 3.5 52.6 1.0
C C:ALA285 3.6 47.1 1.0
C C:ALA255 3.7 46.6 1.0
CA C:SER253 3.7 53.3 1.0
CA C:ASP250 3.8 44.4 1.0
N C:SER253 3.8 51.4 1.0
CA C:PRO256 4.2 48.4 1.0
N C:ALA255 4.2 50.6 1.0
N C:ALA254 4.2 58.6 1.0
CA C:ALA285 4.3 42.8 1.0
N C:PRO256 4.4 48.5 1.0
N C:THR286 4.4 48.6 1.0
CB C:ALA285 4.4 44.6 1.0
C C:ALA254 4.5 52.3 1.0
CB C:THR286 4.5 35.6 1.0
O C:ASP249 4.5 43.5 1.0
CB C:ASP250 4.5 40.9 1.0
O C:HOH827 4.5 49.8 1.0
CA C:THR286 4.6 46.4 1.0
CA C:ALA255 4.6 44.4 1.0
CD C:PRO257 4.7 42.9 1.0
N C:TYR251 4.7 51.5 1.0
C C:PRO256 4.8 46.0 1.0
CA C:ALA254 4.8 58.2 1.0
O C:ALA254 4.9 48.5 1.0
NE2 C:GLN245 4.9 48.8 1.0
N C:PRO257 4.9 45.1 1.0
C C:TYR251 5.0 49.9 1.0
C C:PHE252 5.0 52.6 1.0
OD1 C:ASP250 5.0 52.5 1.0

Reference:

B.D.Welch, P.Yuan, S.Bose, C.A.Kors, R.A.Lamb, T.S.Jardetzky. Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin-Neuraminidase (Hn) Ectodomain. Plos Pathog. V. 9 03534 2013.
ISSN: ISSN 1553-7366
PubMed: 23950713
DOI: 10.1371/JOURNAL.PPAT.1003534
Page generated: Sat Dec 12 04:53:13 2020

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