Atomistry » Calcium » PDB 4ixo-4jml » 4jf7
Atomistry »
  Calcium »
    PDB 4ixo-4jml »
      4jf7 »

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: Sun Jul 14 08:30:18 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy