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Chlorine in PDB 4mj1: Unliganded Bk Polyomavirus VP1 Pentamer

Protein crystallography data

The structure of Unliganded Bk Polyomavirus VP1 Pentamer, PDB code: 4mj1 was solved by U.Neu, L.J.Stroh, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.42 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.900, 152.290, 62.720, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Unliganded Bk Polyomavirus VP1 Pentamer (pdb code 4mj1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Unliganded Bk Polyomavirus VP1 Pentamer, PDB code: 4mj1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4mj1

Go back to Chlorine Binding Sites List in 4mj1
Chlorine binding site 1 out of 5 in the Unliganded Bk Polyomavirus VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Unliganded Bk Polyomavirus VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:28.2
occ:1.00
 CG A:LYS180 3.1 29.7 1.0
N A:LYS180 3.2 19.4 1.0
O A:HOH656 3.3 28.1 1.0
ND1 A:HIS193 3.4 16.8 1.0
CA A:HIS193 3.6 18.8 1.0
CA A:PRO179 3.8 17.4 1.0
C A:PRO179 3.9 19.0 1.0
O A:ASP192 4.0 20.3 1.0
CH2 A:TRP208 4.0 16.8 1.0
CB A:HIS193 4.0 16.9 1.0
CA A:LYS180 4.1 23.3 1.0
CG A:HIS193 4.2 18.3 1.0
CB A:LYS180 4.2 24.8 1.0
C A:HIS193 4.3 18.6 1.0
N A:LYS194 4.4 18.0 1.0
CE1 A:HIS193 4.4 18.7 1.0
N A:HIS193 4.5 18.6 1.0
O A:LYS180 4.5 20.9 1.0
CB A:PRO179 4.5 18.4 1.0
O A:LYS194 4.5 18.8 1.0
C A:ASP192 4.6 21.3 1.0
O A:THR178 4.7 18.3 1.0
CZ3 A:TRP208 4.8 16.4 1.0
C A:LYS180 4.8 21.0 1.0
N A:PRO179 4.9 17.6 1.0
CZ2 A:TRP208 4.9 14.6 1.0

Chlorine binding site 2 out of 5 in 4mj1

Go back to Chlorine Binding Sites List in 4mj1
Chlorine binding site 2 out of 5 in the Unliganded Bk Polyomavirus VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Unliganded Bk Polyomavirus VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:28.9
occ:1.00
 N B:LYS180 3.1 23.7 1.0
ND1 B:HIS193 3.5 21.6 1.0
CA B:HIS193 3.6 19.4 1.0
CA B:PRO179 3.7 20.9 1.0
O B:ASP192 3.9 23.2 1.0
CB B:LYS180 3.9 31.0 1.0
C B:PRO179 3.9 22.1 1.0
CA B:LYS180 4.0 27.8 1.0
CB B:HIS193 4.1 18.7 1.0
CH2 B:TRP208 4.2 18.7 1.0
CG B:HIS193 4.2 19.9 1.0
O B:LYS180 4.3 21.1 1.0
CD B:LYS180 4.3 44.1 1.0
C B:HIS193 4.3 19.2 1.0
N B:LYS194 4.4 20.4 1.0
N B:HIS193 4.4 20.6 1.0
CE1 B:HIS193 4.5 20.5 1.0
C B:ASP192 4.5 22.6 1.0
O B:THR178 4.5 23.1 1.0
CB B:PRO179 4.5 19.5 1.0
CG B:LYS180 4.6 38.6 1.0
O B:LYS194 4.6 20.1 1.0
C B:LYS180 4.7 24.9 1.0
N B:PRO179 4.8 19.8 1.0
CE B:LYS180 5.0 47.2 1.0
CZ2 B:TRP208 5.0 16.7 1.0

Chlorine binding site 3 out of 5 in 4mj1

Go back to Chlorine Binding Sites List in 4mj1
Chlorine binding site 3 out of 5 in the Unliganded Bk Polyomavirus VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Unliganded Bk Polyomavirus VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:39.8
occ:1.00
 N C:LYS180 3.1 23.6 1.0
ND1 C:HIS193 3.3 18.7 1.0
CA C:HIS193 3.5 21.2 1.0
CA C:PRO179 3.7 21.4 1.0
O C:ASP192 3.9 24.6 1.0
C C:PRO179 3.9 22.3 1.0
CB C:HIS193 4.0 21.4 1.0
CG C:LYS180 4.0 35.3 1.0
CB C:LYS180 4.0 30.0 1.0
CG C:HIS193 4.0 20.6 1.0
CA C:LYS180 4.1 26.9 1.0
CH2 C:TRP208 4.2 19.1 1.0
C C:HIS193 4.3 21.0 1.0
O C:LYS180 4.3 23.7 1.0
N C:LYS194 4.3 21.9 1.0
CE1 C:HIS193 4.3 22.3 1.0
N C:HIS193 4.4 22.0 1.0
CB C:PRO179 4.4 20.5 1.0
C C:ASP192 4.4 23.7 1.0
O C:LYS194 4.6 22.6 1.0
C C:LYS180 4.7 26.3 1.0
O C:THR178 4.7 23.0 1.0
N C:PRO179 4.8 20.4 1.0
CZ3 C:TRP208 5.0 19.2 1.0

Chlorine binding site 4 out of 5 in 4mj1

Go back to Chlorine Binding Sites List in 4mj1
Chlorine binding site 4 out of 5 in the Unliganded Bk Polyomavirus VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Unliganded Bk Polyomavirus VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:35.3
occ:1.00
 N D:LYS180 3.1 25.4 1.0
ND1 D:HIS193 3.4 19.3 1.0
CA D:PRO179 3.7 21.2 1.0
CA D:HIS193 3.7 20.1 1.0
C D:PRO179 3.9 23.0 1.0
CB D:LYS180 3.9 31.1 1.0
O D:ASP192 3.9 20.5 1.0
CA D:LYS180 4.0 28.2 1.0
CG D:LYS180 4.1 35.3 1.0
CB D:HIS193 4.1 20.7 1.0
CG D:HIS193 4.2 21.1 1.0
CH2 D:TRP208 4.2 18.0 1.0
O D:LYS180 4.3 27.8 1.0
CE1 D:HIS193 4.4 21.4 1.0
C D:HIS193 4.4 20.1 1.0
N D:LYS194 4.5 20.4 1.0
N D:HIS193 4.5 20.1 1.0
CB D:PRO179 4.5 22.2 1.0
C D:ASP192 4.5 23.5 1.0
O D:LYS194 4.6 20.7 1.0
O D:THR178 4.6 19.7 1.0
C D:LYS180 4.7 28.7 1.0
N D:PRO179 4.7 20.3 1.0
CZ2 D:TRP208 5.0 17.5 1.0

Chlorine binding site 5 out of 5 in 4mj1

Go back to Chlorine Binding Sites List in 4mj1
Chlorine binding site 5 out of 5 in the Unliganded Bk Polyomavirus VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Unliganded Bk Polyomavirus VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:28.4
occ:1.00
 N E:LYS180 3.2 23.0 1.0
ND1 E:HIS193 3.4 17.5 1.0
CA E:HIS193 3.5 18.7 1.0
CA E:PRO179 3.7 19.1 1.0
O E:ASP192 3.9 21.4 1.0
C E:PRO179 4.0 21.2 1.0
CB E:HIS193 4.0 18.5 1.0
CB E:LYS180 4.0 28.1 1.0
CG E:HIS193 4.1 17.0 1.0
CH2 E:TRP208 4.1 15.9 1.0
CA E:LYS180 4.2 24.8 1.0
N E:LYS194 4.2 17.8 1.0
C E:HIS193 4.2 17.7 1.0
CG E:LYS180 4.2 30.9 1.0
N E:HIS193 4.4 18.5 1.0
O E:LYS194 4.4 16.7 1.0
CE1 E:HIS193 4.4 19.5 1.0
O E:LYS180 4.5 24.0 1.0
CB E:PRO179 4.5 19.0 1.0
C E:ASP192 4.5 20.9 1.0
CD E:LYS180 4.7 36.6 1.0
O E:THR178 4.7 18.5 1.0
N E:PRO179 4.8 16.8 1.0
C E:LYS180 4.8 25.1 1.0
CZ3 E:TRP208 4.9 14.2 1.0
CZ2 E:TRP208 5.0 14.8 1.0

Reference:

U.Neu, S.A.Allen, B.S.Blaum, Y.Liu, M.Frank, A.S.Palma, L.J.Stroh, T.Feizi, T.Peters, W.J.Atwood, T.Stehle. A Structure-Guided Mutation in the Major Capsid Protein Retargets Bk Polyomavirus. Plos Pathog. V. 9 03688 2013.
ISSN: ISSN 1553-7366
PubMed: 24130487
DOI: 10.1371/JOURNAL.PPAT.1003688
Page generated: Sun Jul 21 19:54:49 2024

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