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Chlorine in PDB 4mj0: Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide

Protein crystallography data

The structure of Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide, PDB code: 4mj0 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) 48.00 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.680, 152.640, 63.190, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide (pdb code 4mj0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide, PDB code: 4mj0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4mj0

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Chlorine binding site 1 out of 5 in the Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:26.0
occ:1.00
 O A:HOH795 2.6 36.9 1.0
N A:LYS180 3.2 19.3 1.0
O A:HOH731 3.4 33.4 1.0
ND1 A:HIS193 3.5 15.7 1.0
CA A:HIS193 3.6 14.5 1.0
CA A:PRO179 3.8 16.2 1.0
CB A:LYS180 3.9 25.0 1.0
C A:PRO179 4.0 18.6 1.0
O A:ASP192 4.0 18.3 1.0
CB A:HIS193 4.0 14.7 1.0
CA A:LYS180 4.1 22.4 1.0
CH2 A:TRP208 4.1 15.9 1.0
CG A:LYS180 4.1 33.2 1.0
CG A:HIS193 4.2 15.0 1.0
C A:HIS193 4.2 14.9 1.0
N A:LYS194 4.3 15.3 1.0
O A:LYS194 4.4 17.1 1.0
O A:LYS180 4.5 20.0 1.0
N A:HIS193 4.5 15.8 1.0
CE1 A:HIS193 4.5 16.9 1.0
NZ A:LYS180 4.5 47.2 1.0
CB A:PRO179 4.6 16.3 1.0
C A:ASP192 4.6 19.1 1.0
O A:THR178 4.6 17.4 1.0
C A:LYS180 4.8 21.5 1.0
N A:PRO179 4.8 14.9 1.0
O A:HOH796 4.9 44.0 1.0
CZ3 A:TRP208 4.9 12.9 1.0
CZ2 A:TRP208 4.9 12.3 1.0
CE A:LYS180 5.0 45.3 1.0

Chlorine binding site 2 out of 5 in 4mj0

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Chlorine binding site 2 out of 5 in the Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:28.4
occ:1.00
 N B:LYS180 3.1 20.3 1.0
O B:HOH711 3.3 47.5 1.0
ND1 B:HIS193 3.4 17.4 1.0
O B:HOH683 3.5 33.1 1.0
CA B:HIS193 3.6 16.4 1.0
CA B:PRO179 3.8 18.0 1.0
CB B:LYS180 3.8 23.4 1.0
O B:ASP192 3.9 20.4 1.0
C B:PRO179 4.0 19.5 1.0
CA B:LYS180 4.0 22.6 1.0
CB B:HIS193 4.0 16.4 1.0
CG B:HIS193 4.1 15.9 1.0
O B:LYS180 4.2 22.1 1.0
CH2 B:TRP208 4.2 17.7 1.0
C B:HIS193 4.3 16.8 1.0
N B:LYS194 4.4 18.4 1.0
N B:HIS193 4.4 18.5 1.0
CE1 B:HIS193 4.5 20.3 1.0
C B:ASP192 4.5 19.5 1.0
CB B:PRO179 4.5 17.1 1.0
O B:LYS194 4.6 20.0 1.0
C B:LYS180 4.6 22.5 1.0
O B:THR178 4.6 19.3 1.0
N B:PRO179 4.9 17.0 1.0

Chlorine binding site 3 out of 5 in 4mj0

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Chlorine binding site 3 out of 5 in the Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl405

b:35.2
occ:1.00
 N C:LYS180 3.2 20.6 1.0
ND1 C:HIS193 3.3 18.0 1.0
O C:HOH631 3.5 38.8 1.0
CA C:HIS193 3.5 18.8 1.0
CA C:PRO179 3.7 20.9 1.0
O C:ASP192 3.9 22.6 1.0
C C:PRO179 3.9 21.3 1.0
CB C:LYS180 4.0 26.7 1.0
CB C:HIS193 4.0 18.9 1.0
CG C:HIS193 4.1 18.6 1.0
CA C:LYS180 4.1 23.2 1.0
CG C:LYS180 4.2 31.9 1.0
O C:LYS180 4.3 23.1 1.0
CE1 C:HIS193 4.3 21.1 1.0
C C:HIS193 4.3 18.4 1.0
N C:HIS193 4.3 19.4 1.0
CH2 C:TRP208 4.3 18.0 1.0
N C:LYS194 4.4 19.8 1.0
C C:ASP192 4.4 21.9 1.0
CB C:PRO179 4.4 19.5 1.0
O C:LYS194 4.6 23.2 1.0
O C:THR178 4.7 21.7 1.0
C C:LYS180 4.7 22.9 1.0
N C:PRO179 4.8 19.8 1.0

Chlorine binding site 4 out of 5 in 4mj0

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Chlorine binding site 4 out of 5 in the Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:27.8
occ:1.00
 O D:HOH705 3.2 33.7 1.0
N D:LYS180 3.3 22.6 1.0
ND1 D:HIS193 3.6 15.6 1.0
CA D:HIS193 3.6 17.2 1.0
O D:HOH699 3.6 32.9 1.0
CG D:LYS180 3.6 33.8 1.0
CA D:PRO179 3.8 18.1 1.0
O D:ASP192 3.9 18.3 1.0
O D:HOH760 4.0 53.5 1.0
CB D:HIS193 4.0 16.6 1.0
C D:PRO179 4.1 20.1 1.0
CH2 D:TRP208 4.1 16.7 1.0
CG D:HIS193 4.2 17.0 1.0
C D:HIS193 4.3 17.0 1.0
N D:LYS194 4.3 16.4 1.0
CA D:LYS180 4.3 24.4 1.0
CB D:LYS180 4.3 29.1 1.0
O D:LYS194 4.4 17.6 1.0
N D:HIS193 4.5 16.6 1.0
O D:LYS180 4.5 23.0 1.0
C D:ASP192 4.5 19.6 1.0
CE1 D:HIS193 4.6 19.9 1.0
CB D:PRO179 4.6 19.0 1.0
O D:THR178 4.7 18.3 1.0
N D:PRO179 4.8 18.3 1.0
CD D:LYS180 4.8 37.9 1.0
CZ3 D:TRP208 4.9 13.5 1.0
C D:LYS180 4.9 23.5 1.0
CZ2 D:TRP208 4.9 14.0 1.0

Chlorine binding site 5 out of 5 in 4mj0

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Chlorine binding site 5 out of 5 in the Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bk Polyomavirus VP1 Pentamer in Complex with GD3 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl403

b:28.4
occ:1.00
 N E:LYS180 3.2 19.6 1.0
O E:HOH748 3.3 49.6 1.0
O E:HOH718 3.4 31.9 1.0
ND1 E:HIS193 3.5 14.9 1.0
CA E:HIS193 3.6 15.0 1.0
CA E:PRO179 3.8 16.4 1.0
CB E:LYS180 3.9 21.3 1.0
O E:ASP192 4.0 19.1 1.0
C E:PRO179 4.0 17.8 1.0
CG E:LYS180 4.0 26.9 1.0
CB E:HIS193 4.1 15.1 1.0
CA E:LYS180 4.1 20.2 1.0
CG E:HIS193 4.2 13.9 1.0
CH2 E:TRP208 4.3 14.7 1.0
C E:HIS193 4.3 15.0 1.0
N E:LYS194 4.3 16.4 1.0
O E:LYS180 4.4 22.6 1.0
CE1 E:HIS193 4.5 18.3 1.0
N E:HIS193 4.5 16.6 1.0
CB E:PRO179 4.5 16.9 1.0
O E:LYS194 4.5 18.2 1.0
C E:ASP192 4.5 19.3 1.0
CD E:LYS180 4.6 33.3 1.0
O E:THR178 4.7 16.6 1.0
C E:LYS180 4.8 21.3 1.0
N E:PRO179 4.9 15.3 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 19:54:33 2024

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