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Chlorine in PDB 4fmj: Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide

Protein crystallography data

The structure of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide, PDB code: 4fmj was solved by U.Neu, H.Hengel, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 84.660, 130.150, 165.530, 98.04, 101.02, 105.81
R / Rfree (%) 19.2 / 24.6

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Chlorine atom in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide (pdb code 4fmj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 20 binding sites of Chlorine where determined in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide, PDB code: 4fmj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 20 in 4fmj

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Chlorine binding site 1 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:32.7
occ:1.00
 O2 A:GOL401 2.6 48.3 1.0
OG A:SER246 2.8 25.3 1.0
O A:SER246 3.3 24.6 1.0
C A:SER246 3.4 24.7 1.0
CD2 A:HIS164 3.5 20.7 1.0
C A:ILE247 3.6 23.0 1.0
N A:ILE247 3.7 24.3 1.0
CA A:ILE247 3.7 23.3 1.0
CB A:SER246 3.7 24.7 1.0
C2 A:GOL401 3.8 51.1 1.0
N A:GLN248 3.8 22.0 1.0
O A:ASN162 3.9 22.4 1.0
O A:ILE247 3.9 22.2 1.0
CB A:ASN162 4.1 23.1 1.0
C A:ASN162 4.1 23.2 1.0
CA A:SER246 4.2 24.9 1.0
CB A:GLN248 4.2 21.6 1.0
N A:HIS164 4.2 23.8 1.0
CG A:HIS164 4.4 27.2 1.0
CA A:TYR163 4.4 23.9 1.0
N A:TYR163 4.4 24.9 1.0
NE2 A:HIS164 4.5 27.5 1.0
CB A:HIS164 4.6 25.1 1.0
CA A:GLN248 4.7 22.8 1.0
C A:TYR163 4.7 23.6 1.0
C3 A:GOL401 4.7 52.1 1.0
C1 A:GOL401 4.8 49.3 1.0
CA A:ASN162 4.8 24.5 1.0
N A:SER246 5.0 25.1 1.0
O E:HOH773 5.0 31.3 1.0

Chlorine binding site 2 out of 20 in 4fmj

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Chlorine binding site 2 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:39.8
occ:1.00
 O B:HOH765 3.0 31.5 1.0
O B:HOH760 3.1 28.9 1.0
OG B:SER246 3.1 27.3 1.0
CD2 B:HIS164 3.4 26.0 1.0
O B:SER246 3.7 25.3 1.0
C B:ILE247 3.8 25.6 1.0
C B:SER246 3.8 26.3 1.0
CB B:ASN162 3.9 25.9 1.0
N B:GLN248 3.9 24.4 1.0
O B:ASN162 3.9 27.0 1.0
CA B:ILE247 3.9 25.4 1.0
N B:ILE247 4.0 25.8 1.0
CB B:SER246 4.0 25.5 1.0
CB B:GLN248 4.0 24.6 1.0
C B:ASN162 4.1 27.1 1.0
O B:ILE247 4.2 25.8 1.0
N B:HIS164 4.3 28.6 1.0
CG B:HIS164 4.3 29.7 1.0
NE2 B:HIS164 4.4 27.4 1.0
N B:TYR163 4.4 27.8 1.0
CA B:TYR163 4.5 28.4 1.0
CA B:SER246 4.6 26.5 1.0
CB B:HIS164 4.6 28.8 1.0
CA B:GLN248 4.6 24.9 1.0
CA B:ASN162 4.7 26.8 1.0
C B:TYR163 4.8 29.8 1.0
O B:HOH761 5.0 29.5 1.0
O A:HOH530 5.0 30.2 1.0

Chlorine binding site 3 out of 20 in 4fmj

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Chlorine binding site 3 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:38.0
occ:1.00
 O C:HOH550 2.9 35.9 1.0
O2 C:GOL401 2.9 43.9 1.0
OG C:SER246 3.0 24.4 1.0
CD2 C:HIS164 3.5 31.8 1.0
C C:ILE247 3.5 23.6 1.0
O C:SER246 3.6 25.1 1.0
C C:SER246 3.6 24.6 1.0
CA C:ILE247 3.6 23.3 1.0
N C:ILE247 3.7 25.0 1.0
N C:GLN248 3.7 23.1 1.0
CB C:ASN162 3.8 23.4 1.0
O C:ASN162 3.9 25.1 1.0
CB C:SER246 3.9 23.9 1.0
O C:ILE247 4.0 23.3 1.0
C C:ASN162 4.0 25.8 1.0
CB C:GLN248 4.2 24.0 1.0
C2 C:GOL401 4.2 48.2 1.0
N C:HIS164 4.2 25.9 1.0
N C:TYR163 4.4 26.6 1.0
CG C:HIS164 4.4 32.8 1.0
CA C:SER246 4.4 24.8 1.0
NE2 C:HIS164 4.4 33.0 1.0
CA C:TYR163 4.5 27.2 1.0
CA C:GLN248 4.6 24.3 1.0
CA C:ASN162 4.6 25.8 1.0
CB C:HIS164 4.6 27.0 1.0
C1 C:GOL401 4.7 48.8 1.0
C3 C:GOL401 4.7 48.6 1.0
C C:TYR163 4.7 27.5 1.0
O B:HOH731 4.9 43.8 1.0
CG C:ASN162 5.0 25.3 1.0

Chlorine binding site 4 out of 20 in 4fmj

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Chlorine binding site 4 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:27.9
occ:1.00
 O D:HOH783 2.6 20.4 1.0
O D:HOH779 3.0 19.8 1.0
OG D:SER246 3.2 23.2 1.0
CD2 D:HIS164 3.6 24.7 1.0
C D:ILE247 3.7 21.8 1.0
O D:SER246 3.7 21.8 1.0
CA D:ILE247 3.7 21.3 1.0
C D:SER246 3.7 22.1 1.0
N D:ILE247 3.7 22.0 1.0
CB D:ASN162 3.8 16.0 1.0
N D:GLN248 3.9 20.6 1.0
O D:ASN162 4.0 17.0 1.0
CB D:SER246 4.1 22.4 1.0
C D:ASN162 4.1 19.5 1.0
CB D:GLN248 4.1 22.0 1.0
O D:ILE247 4.1 22.9 1.0
N D:HIS164 4.4 19.3 1.0
N D:TYR163 4.4 19.9 1.0
O D:HOH777 4.4 39.7 1.0
CG D:HIS164 4.5 22.9 1.0
CA D:SER246 4.5 21.9 1.0
CA D:TYR163 4.5 20.2 1.0
NE2 D:HIS164 4.6 24.9 1.0
CA D:ASN162 4.6 18.8 1.0
CA D:GLN248 4.6 21.9 1.0
CB D:HIS164 4.7 19.4 1.0
C D:TYR163 4.8 20.1 1.0
CG D:ASN162 4.9 22.0 1.0

Chlorine binding site 5 out of 20 in 4fmj

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Chlorine binding site 5 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl601

b:22.3
occ:1.00
 O E:HOH781 2.8 14.3 1.0
O E:HOH777 2.9 31.6 1.0
OG E:SER246 2.9 22.8 1.0
CD2 E:HIS164 3.3 19.0 1.0
C E:ILE247 3.6 22.5 1.0
O E:SER246 3.7 22.2 1.0
CA E:ILE247 3.7 21.9 1.0
C E:SER246 3.7 22.6 1.0
CB E:ASN162 3.8 23.2 1.0
N E:ILE247 3.8 23.0 1.0
N E:GLN248 3.8 21.4 1.0
O E:ILE247 3.9 23.2 1.0
O E:ASN162 4.0 19.8 1.0
CB E:GLN248 4.0 21.6 1.0
CB E:SER246 4.1 22.9 1.0
C E:ASN162 4.1 22.8 1.0
NE2 E:HIS164 4.2 24.2 1.0
CG E:HIS164 4.3 23.6 1.0
N E:TYR163 4.4 20.9 1.0
N E:HIS164 4.5 22.6 1.0
CA E:TYR163 4.5 21.5 1.0
CA E:SER246 4.5 22.5 1.0
CA E:GLN248 4.5 21.9 1.0
CA E:ASN162 4.6 23.5 1.0
CB E:HIS164 4.8 20.8 1.0
O D:HOH774 4.8 25.2 1.0
C E:TYR163 4.8 22.2 1.0
CG E:ASN162 4.9 26.7 1.0
O E:HOH778 5.0 23.6 1.0

Chlorine binding site 6 out of 20 in 4fmj

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Chlorine binding site 6 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl601

b:31.8
occ:1.00
 O F:HOH772 2.8 22.0 1.0
OG F:SER246 2.9 26.1 1.0
CD2 F:HIS164 3.5 28.2 1.0
C F:ILE247 3.6 25.4 1.0
CB F:ASN162 3.8 25.6 1.0
C F:SER246 3.8 25.2 1.0
CA F:ILE247 3.8 24.5 1.0
N F:ILE247 3.8 24.7 1.0
O F:SER246 3.8 26.1 1.0
CB F:SER246 3.9 25.9 1.0
N F:GLN248 3.9 24.4 1.0
O F:ILE247 3.9 25.4 1.0
O F:ASN162 3.9 25.3 1.0
CB F:GLN248 4.0 24.5 1.0
C F:ASN162 4.1 25.9 1.0
N F:TYR163 4.4 25.9 1.0
NE2 F:HIS164 4.4 27.7 1.0
CA F:SER246 4.5 25.4 1.0
CG F:HIS164 4.5 28.8 1.0
N F:HIS164 4.5 27.4 1.0
CA F:TYR163 4.6 27.1 1.0
CA F:GLN248 4.6 24.9 1.0
CA F:ASN162 4.6 25.5 1.0
O F:HOH771 4.8 29.0 1.0
CB F:HIS164 4.8 27.2 1.0
CG F:ASN162 4.9 26.5 1.0
C F:TYR163 4.9 28.1 1.0

Chlorine binding site 7 out of 20 in 4fmj

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Chlorine binding site 7 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl601

b:31.6
occ:1.00
 O G:HOH770 2.8 22.3 1.0
OG G:SER246 2.8 23.1 1.0
O G:HOH773 2.9 35.4 1.0
CD2 G:HIS164 3.4 25.9 1.0
O G:SER246 3.4 23.9 1.0
C G:SER246 3.5 25.0 1.0
C G:ILE247 3.6 23.3 1.0
N G:ILE247 3.7 24.2 1.0
CA G:ILE247 3.7 22.7 1.0
CB G:SER246 3.8 24.3 1.0
O G:ASN162 3.8 21.1 1.0
N G:GLN248 3.9 23.5 1.0
CB G:ASN162 3.9 21.2 1.0
O G:ILE247 4.0 23.1 1.0
C G:ASN162 4.0 21.8 1.0
CB G:GLN248 4.2 22.9 1.0
CG G:HIS164 4.3 26.4 1.0
CA G:SER246 4.3 24.9 1.0
N G:HIS164 4.3 23.0 1.0
N G:TYR163 4.3 21.8 1.0
CA G:TYR163 4.4 22.3 1.0
NE2 G:HIS164 4.4 26.8 1.0
CB G:HIS164 4.5 22.9 1.0
CA G:ASN162 4.6 21.7 1.0
C G:TYR163 4.6 22.9 1.0
CA G:GLN248 4.7 24.4 1.0

Chlorine binding site 8 out of 20 in 4fmj

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Chlorine binding site 8 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl402

b:40.0
occ:1.00
 OG H:SER246 3.0 25.9 1.0
O H:HOH518 3.2 30.8 1.0
O H:HOH564 3.2 32.1 1.0
C H:ILE247 3.6 24.1 1.0
CD2 H:HIS164 3.6 28.6 1.0
O H:SER246 3.6 23.9 1.0
C H:SER246 3.6 24.3 1.0
CA H:ILE247 3.6 23.1 1.0
O H:ASN162 3.6 24.1 1.0
N H:ILE247 3.7 24.0 1.0
N H:GLN248 3.7 24.1 1.0
CB H:ASN162 3.8 25.1 1.0
C H:ASN162 3.9 24.8 1.0
CB H:SER246 3.9 24.2 1.0
O H:ILE247 4.0 24.6 1.0
CB H:GLN248 4.1 24.5 1.0
N H:HIS164 4.3 25.5 1.0
N H:TYR163 4.3 25.0 1.0
CA H:SER246 4.4 24.2 1.0
CA H:TYR163 4.5 24.8 1.0
CG H:HIS164 4.5 28.4 1.0
CA H:ASN162 4.5 25.4 1.0
CA H:GLN248 4.6 24.0 1.0
NE2 H:HIS164 4.6 29.8 1.0
CB H:HIS164 4.6 27.5 1.0
C H:TYR163 4.8 26.9 1.0
CG H:ASN162 5.0 28.6 1.0

Chlorine binding site 9 out of 20 in 4fmj

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Chlorine binding site 9 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl601

b:43.2
occ:1.00
 O I:HOH743 2.8 32.6 1.0
O I:HOH740 2.9 35.1 1.0
OG I:SER246 3.0 27.5 1.0
C I:ILE247 3.4 25.6 1.0
O I:SER246 3.6 26.9 1.0
CD2 I:HIS164 3.6 39.0 1.0
N I:GLN248 3.6 26.0 1.0
CA I:ILE247 3.7 24.7 1.0
C I:SER246 3.7 26.6 1.0
CB I:ASN162 3.7 31.3 1.0
N I:ILE247 3.8 26.8 1.0
O I:ILE247 3.8 25.4 1.0
O I:ASN162 3.8 33.5 1.0
CB I:GLN248 3.8 26.2 1.0
CB I:SER246 3.9 26.3 1.0
C I:ASN162 4.0 32.9 1.0
CA I:GLN248 4.4 26.3 1.0
N I:TYR163 4.5 32.4 1.0
CA I:SER246 4.5 27.0 1.0
N I:HIS164 4.5 31.9 1.0
CG I:HIS164 4.5 38.7 1.0
NE2 I:HIS164 4.6 40.6 1.0
CA I:ASN162 4.6 32.6 1.0
CA I:TYR163 4.6 32.6 1.0
CB I:HIS164 4.8 32.4 1.0
O H:HOH519 4.8 33.5 1.0
CG I:ASN162 4.8 28.6 1.0
C I:TYR163 4.9 32.5 1.0
OD1 I:ASN162 5.0 31.9 1.0

Chlorine binding site 10 out of 20 in 4fmj

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Chlorine binding site 10 out of 20 in the Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Merkel Cell Polyomavirus VP1 in Complex with GD1A Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl601

b:33.9
occ:1.00
 O J:HOH749 2.7 34.0 1.0
O J:HOH751 2.9 26.6 1.0
OG J:SER246 3.1 25.9 1.0
C J:ILE247 3.5 25.8 1.0
C J:SER246 3.6 26.5 1.0
O J:SER246 3.6 27.0 1.0
N J:ILE247 3.6 25.9 1.0
CA J:ILE247 3.6 25.6 1.0
CD2 J:HIS164 3.7 34.3 1.0
O J:ILE247 3.8 26.8 1.0
CB J:SER246 3.8 26.2 1.0
N J:GLN248 3.9 24.9 1.0
CB J:ASN162 3.9 23.8 1.0
O J:ASN162 3.9 26.3 1.0
CB J:GLN248 4.0 25.9 1.0
C J:ASN162 4.1 25.7 1.0
CA J:SER246 4.3 26.3 1.0
N J:HIS164 4.4 28.4 1.0
N J:TYR163 4.4 26.6 1.0
CA J:TYR163 4.5 27.4 1.0
CG J:HIS164 4.6 32.0 1.0
NE2 J:HIS164 4.6 32.3 1.0
CA J:GLN248 4.6 26.1 1.0
CA J:ASN162 4.7 25.2 1.0
O I:HOH729 4.7 32.3 1.0
CB J:HIS164 4.8 30.1 1.0
C J:TYR163 4.9 28.6 1.0

Reference:

U.Neu, H.Hengel, B.S.Blaum, R.M.Schowalter, D.Macejak, M.Gilbert, W.W.Wakarchuk, A.Imamura, H.Ando, M.Kiso, N.Arnberg, R.L.Garcea, T.Peters, C.B.Buck, T.Stehle. Structures of Merkel Cell Polyomavirus VP1 Complexes Define A Sialic Acid Binding Site Required For Infection. Plos Pathog. V. 8 02738 2012.
ISSN: ISSN 1553-7366
PubMed: 22910713
DOI: 10.1371/JOURNAL.PPAT.1002738
Page generated: Sun Jul 21 13:52:53 2024

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