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Chlorine in PDB 4mbz: Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine

Protein crystallography data

The structure of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine, PDB code: 4mbz was solved by Z.M.Khan, U.Neu, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.160, 97.240, 234.220, 90.00, 96.21, 90.00
R / Rfree (%) 16.5 / 19.5

Other elements in 4mbz:

The structure of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine (pdb code 4mbz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine, PDB code: 4mbz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 4mbz

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Chlorine binding site 1 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:25.7
occ:1.00
 O A:HOH816 3.0 36.6 1.0
O A:HOH565 3.2 21.6 1.0
O A:HOH855 3.2 52.1 1.0
N A:LYS181 3.3 19.9 1.0
CA A:ILE180 3.8 17.0 1.0
CA A:ALA194 3.8 18.0 1.0
CG2 A:ILE180 3.8 17.2 1.0
CH2 A:TRP209 4.0 16.5 1.0
C A:ILE180 4.0 19.7 1.0
CB A:LYS181 4.0 27.6 1.0
O A:LYS193 4.1 23.1 1.0
N A:LYS195 4.1 20.3 1.0
CA A:LYS181 4.2 25.7 1.0
CB A:ILE180 4.3 16.0 1.0
O A:LYS195 4.3 21.9 1.0
C A:ALA194 4.3 17.8 1.0
CB A:ALA194 4.4 16.8 1.0
O A:LYS181 4.6 25.4 1.0
O A:HOH575 4.6 20.2 1.0
O A:ALA179 4.7 18.9 1.0
CG1 A:ILE180 4.7 15.9 1.0
N A:ALA194 4.7 19.9 1.0
C A:LYS193 4.8 22.2 1.0
CZ2 A:TRP209 4.8 14.4 1.0
CZ3 A:TRP209 4.8 14.6 1.0
C A:LYS181 4.9 26.2 1.0
N A:ILE180 4.9 17.5 1.0

Chlorine binding site 2 out of 10 in 4mbz

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Chlorine binding site 2 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:27.5
occ:1.00
 N B:LYS181 3.1 19.5 1.0
O B:HOH569 3.1 22.6 1.0
O B:HOH663 3.5 30.1 1.0
CA B:ILE180 3.7 16.4 1.0
CA B:ALA194 3.8 14.5 1.0
CG B:LYS181 3.8 28.6 1.0
CG2 B:ILE180 3.8 15.1 1.0
C B:ILE180 3.9 18.4 1.0
CH2 B:TRP209 4.0 13.9 1.0
CB B:LYS181 4.0 23.7 1.0
O B:LYS193 4.0 18.9 1.0
N B:LYS195 4.1 15.1 1.0
CA B:LYS181 4.1 21.5 1.0
O B:LYS195 4.2 15.8 1.0
CB B:ILE180 4.2 17.0 1.0
C B:ALA194 4.3 14.7 1.0
CB B:ALA194 4.4 15.0 1.0
O B:LYS181 4.5 21.4 1.0
O B:HOH714 4.5 32.8 1.0
O B:ALA179 4.6 16.9 1.0
CG1 B:ILE180 4.7 15.0 1.0
N B:ALA194 4.7 14.9 1.0
C B:LYS193 4.7 18.1 1.0
CZ3 B:TRP209 4.8 12.9 1.0
CZ2 B:TRP209 4.8 13.6 1.0
C B:LYS181 4.8 22.2 1.0
CD B:LYS181 4.9 39.0 1.0
N B:ILE180 4.9 15.5 1.0
C B:LYS195 5.0 15.5 1.0

Chlorine binding site 3 out of 10 in 4mbz

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Chlorine binding site 3 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:26.0
occ:1.00
 O C:HOH822 2.6 46.4 1.0
N C:LYS181 3.2 21.5 1.0
O C:HOH564 3.2 22.1 1.0
O C:HOH654 3.6 33.2 1.0
CA C:ILE180 3.8 18.3 1.0
CA C:ALA194 3.8 16.2 1.0
CG C:LYS181 3.8 26.8 0.5
CB C:LYS181 3.9 23.9 0.5
CG2 C:ILE180 3.9 17.0 1.0
O C:LYS193 3.9 18.9 1.0
CB C:LYS181 3.9 24.0 0.5
C C:ILE180 4.0 20.0 1.0
CH2 C:TRP209 4.0 15.5 1.0
N C:LYS195 4.1 17.5 1.0
CA C:LYS181 4.1 23.8 0.5
CA C:LYS181 4.1 23.8 0.5
CG C:LYS181 4.1 27.1 0.5
O C:LYS195 4.2 18.8 1.0
C C:ALA194 4.3 16.3 1.0
CB C:ILE180 4.3 16.4 1.0
CB C:ALA194 4.4 16.3 1.0
O C:LYS181 4.4 23.3 1.0
O C:ALA179 4.6 17.9 1.0
CD C:LYS181 4.7 27.3 0.5
C C:LYS193 4.7 18.0 1.0
N C:ALA194 4.7 17.8 1.0
CG1 C:ILE180 4.7 17.5 1.0
C C:LYS181 4.8 23.5 1.0
O C:HOH758 4.8 37.0 1.0
CZ3 C:TRP209 4.8 14.8 1.0
CZ2 C:TRP209 4.8 14.7 1.0
O C:HOH627 4.9 30.7 1.0
N C:ILE180 4.9 17.5 1.0
C C:LYS195 5.0 18.2 1.0
CD C:LYS181 5.0 26.8 0.5
O C:HOH657 5.0 30.3 1.0

Chlorine binding site 4 out of 10 in 4mbz

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Chlorine binding site 4 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:28.9
occ:1.00
 O D:HOH735 3.0 42.8 1.0
N D:LYS181 3.2 25.5 1.0
O D:HOH608 3.2 23.3 1.0
O D:HOH703 3.3 41.0 1.0
CA D:ILE180 3.8 20.9 1.0
CA D:ALA194 3.8 19.6 1.0
CG2 D:ILE180 3.9 19.5 1.0
CH2 D:TRP209 4.0 18.2 1.0
CB D:LYS181 4.0 30.5 1.0
C D:ILE180 4.0 23.4 1.0
O D:LYS193 4.0 22.6 1.0
CG D:LYS181 4.1 39.0 1.0
CD D:LYS181 4.1 47.8 1.0
N D:LYS195 4.1 21.2 1.0
CA D:LYS181 4.2 28.0 1.0
O D:LYS195 4.2 21.9 1.0
CB D:ILE180 4.3 20.0 1.0
C D:ALA194 4.3 20.1 1.0
CB D:ALA194 4.4 20.7 1.0
O D:LYS181 4.5 28.6 1.0
O D:ALA179 4.6 24.9 1.0
O D:HOH593 4.7 33.6 1.0
CG1 D:ILE180 4.7 19.3 1.0
CZ2 D:TRP209 4.8 18.0 1.0
N D:ALA194 4.8 21.9 1.0
O D:HOH727 4.8 44.3 1.0
C D:LYS193 4.8 22.5 1.0
CZ3 D:TRP209 4.8 16.6 1.0
C D:LYS181 4.9 27.4 1.0
N D:ILE180 4.9 22.1 1.0
C D:LYS195 5.0 21.3 1.0

Chlorine binding site 5 out of 10 in 4mbz

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Chlorine binding site 5 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:28.3
occ:1.00
 O E:HOH839 2.9 41.0 1.0
O E:HOH742 3.0 37.6 1.0
O E:HOH579 3.1 24.9 1.0
N E:LYS181 3.2 24.5 1.0
CA E:ILE180 3.7 19.5 1.0
CG2 E:ILE180 3.8 20.7 1.0
CA E:ALA194 3.8 19.6 1.0
O E:LYS193 3.9 21.8 1.0
CG E:LYS181 3.9 37.0 1.0
C E:ILE180 4.0 22.1 1.0
CH2 E:TRP209 4.0 17.1 1.0
CB E:LYS181 4.1 30.7 1.0
N E:LYS195 4.2 20.7 1.0
CA E:LYS181 4.2 29.1 1.0
O E:LYS195 4.2 19.7 1.0
CB E:ILE180 4.3 19.5 1.0
CB E:ALA194 4.3 19.8 1.0
C E:ALA194 4.3 19.6 1.0
O E:LYS181 4.5 28.3 1.0
O E:ALA179 4.6 20.9 1.0
O E:HOH549 4.6 23.4 1.0
C E:LYS193 4.7 22.7 1.0
N E:ALA194 4.7 20.8 1.0
CZ2 E:TRP209 4.8 16.2 1.0
CD E:LYS181 4.8 44.9 1.0
CG1 E:ILE180 4.8 17.9 1.0
CZ3 E:TRP209 4.8 15.8 1.0
N E:ILE180 4.9 19.7 1.0
C E:LYS181 4.9 27.9 1.0

Chlorine binding site 6 out of 10 in 4mbz

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Chlorine binding site 6 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl402

b:34.1
occ:1.00
 O F:HOH740 3.1 45.0 1.0
O F:HOH617 3.1 35.6 1.0
O F:HOH562 3.1 31.8 1.0
N F:LYS181 3.2 27.0 1.0
CG2 F:ILE180 3.8 24.9 1.0
CA F:ILE180 3.8 25.6 1.0
CA F:ALA194 4.0 25.9 1.0
C F:ILE180 4.0 26.9 1.0
CB F:LYS181 4.1 30.4 1.0
CH2 F:TRP209 4.2 23.3 1.0
CA F:LYS181 4.2 28.3 1.0
O F:LYS193 4.2 29.9 1.0
CB F:ILE180 4.3 25.2 1.0
CB F:ALA194 4.4 25.0 1.0
N F:LYS195 4.4 25.6 1.0
O F:LYS195 4.5 26.2 1.0
C F:ALA194 4.6 25.1 1.0
O F:LYS181 4.6 29.2 1.0
O F:ALA179 4.6 27.6 1.0
O F:HOH741 4.7 50.2 1.0
CG1 F:ILE180 4.8 23.7 1.0
CZ2 F:TRP209 4.9 23.9 1.0
N F:ALA194 4.9 27.3 1.0
N F:ILE180 4.9 25.8 1.0
C F:LYS181 5.0 29.6 1.0
C F:LYS193 5.0 28.5 1.0

Chlorine binding site 7 out of 10 in 4mbz

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Chlorine binding site 7 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl402

b:38.0
occ:1.00
 O G:HOH650 3.1 36.1 1.0
N G:LYS181 3.2 34.7 1.0
O G:HOH728 3.2 47.4 1.0
CA G:ILE180 3.7 31.0 1.0
CA G:ALA194 3.8 26.3 1.0
C G:ILE180 4.0 32.4 1.0
CH2 G:TRP209 4.0 27.0 1.0
CG2 G:ILE180 4.0 29.8 1.0
CB G:LYS181 4.0 40.9 1.0
O G:LYS193 4.1 30.9 1.0
N G:LYS195 4.1 26.3 1.0
CA G:LYS181 4.2 37.4 1.0
O G:LYS195 4.2 26.9 1.0
CG G:LYS181 4.2 45.8 1.0
O G:HOH723 4.3 36.6 1.0
C G:ALA194 4.3 26.0 1.0
CB G:ILE180 4.4 29.4 1.0
CB G:ALA194 4.4 25.5 1.0
O G:LYS181 4.4 36.3 1.0
O G:ALA179 4.6 29.7 1.0
CD G:LYS181 4.7 53.6 1.0
N G:ALA194 4.7 27.9 1.0
C G:LYS193 4.8 30.9 1.0
CZ2 G:TRP209 4.8 26.5 1.0
CG1 G:ILE180 4.8 27.1 1.0
C G:LYS181 4.8 37.6 1.0
CZ3 G:TRP209 4.8 23.9 1.0
N G:ILE180 4.9 30.8 1.0
C G:LYS195 5.0 26.1 1.0

Chlorine binding site 8 out of 10 in 4mbz

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Chlorine binding site 8 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl402

b:35.2
occ:1.00
 O H:HOH591 3.0 31.0 1.0
N H:LYS181 3.2 34.5 1.0
CA H:ILE180 3.7 31.5 1.0
CA H:ALA194 3.7 28.4 1.0
CG2 H:ILE180 3.7 30.8 1.0
C H:ILE180 4.0 32.9 1.0
O H:LYS193 4.0 29.8 1.0
CH2 H:TRP209 4.0 25.5 1.0
O H:HOH683 4.0 48.0 1.0
CB H:LYS181 4.0 39.4 1.0
N H:LYS195 4.1 27.6 1.0
CG H:LYS181 4.1 47.5 1.0
CA H:LYS181 4.2 39.0 1.0
CB H:ILE180 4.2 30.7 1.0
C H:ALA194 4.3 29.1 1.0
O H:LYS195 4.3 28.2 1.0
CB H:ALA194 4.3 29.1 1.0
O H:LYS181 4.4 34.9 1.0
CD H:LYS181 4.6 50.0 1.0
O H:HOH730 4.6 40.5 1.0
O H:ALA179 4.6 29.4 1.0
N H:ALA194 4.7 29.5 1.0
C H:LYS193 4.7 30.8 1.0
CG1 H:ILE180 4.7 28.2 1.0
CZ2 H:TRP209 4.8 25.4 1.0
C H:LYS181 4.8 38.7 1.0
CZ3 H:TRP209 4.9 24.2 1.0
N H:ILE180 4.9 30.8 1.0

Chlorine binding site 9 out of 10 in 4mbz

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Chlorine binding site 9 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl402

b:33.2
occ:1.00
 O I:HOH715 3.0 49.5 1.0
O I:HOH636 3.1 35.4 1.0
O I:HOH700 3.2 46.2 1.0
N I:LYS181 3.3 37.0 1.0
CA I:ALA194 3.7 29.7 1.0
CE I:LYS181 3.7 68.6 1.0
CA I:ILE180 3.8 31.1 1.0
CG2 I:ILE180 3.9 29.5 1.0
CH2 I:TRP209 4.0 25.1 1.0
N I:LYS195 4.0 30.5 1.0
O I:LYS193 4.0 31.5 1.0
CB I:LYS181 4.0 46.0 1.0
C I:ILE180 4.0 34.4 1.0
O I:LYS195 4.1 28.9 1.0
CA I:LYS181 4.2 43.2 1.0
C I:ALA194 4.2 30.2 1.0
CB I:ALA194 4.3 28.4 1.0
CB I:ILE180 4.3 29.0 1.0
CG I:LYS181 4.4 53.7 1.0
O I:LYS181 4.5 38.1 1.0
O I:HOH618 4.5 43.8 1.0
O I:ALA179 4.7 32.0 1.0
N I:ALA194 4.7 30.7 1.0
CD I:LYS181 4.7 60.0 1.0
C I:LYS193 4.7 32.2 1.0
CG1 I:ILE180 4.7 28.5 1.0
NZ I:LYS181 4.8 77.9 1.0
CZ3 I:TRP209 4.8 25.3 1.0
CZ2 I:TRP209 4.8 25.7 1.0
C I:LYS195 4.9 29.3 1.0
C I:LYS181 4.9 40.9 1.0
N I:ILE180 4.9 30.5 1.0

Chlorine binding site 10 out of 10 in 4mbz

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Chlorine binding site 10 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl402

b:31.1
occ:1.00
 O J:HOH589 3.1 31.2 1.0
O J:HOH742 3.2 41.8 1.0
O J:HOH760 3.2 48.8 1.0
N J:LYS181 3.3 29.2 1.0
CA J:ILE180 3.8 25.3 1.0
CA J:ALA194 3.8 24.6 1.0
CG2 J:ILE180 3.8 23.4 1.0
CG J:LYS181 3.8 44.0 1.0
C J:ILE180 4.0 26.9 1.0
O J:LYS193 4.1 25.2 1.0
CH2 J:TRP209 4.1 23.7 1.0
CB J:LYS181 4.1 36.2 1.0
N J:LYS195 4.2 24.2 1.0
CA J:LYS181 4.3 31.2 1.0
CB J:ILE180 4.3 23.7 1.0
O J:LYS195 4.3 24.5 1.0
CB J:ALA194 4.4 23.3 1.0
CE J:LYS181 4.4 65.6 1.0
C J:ALA194 4.4 23.9 1.0
O J:LYS181 4.6 30.1 1.0
CG1 J:ILE180 4.7 22.2 1.0
CD J:LYS181 4.7 57.4 1.0
O J:ALA179 4.7 26.0 1.0
O J:HOH617 4.7 40.9 1.0
N J:ALA194 4.7 24.1 1.0
NZ J:LYS181 4.8 75.0 1.0
C J:LYS193 4.8 25.8 1.0
CZ3 J:TRP209 4.9 22.4 1.0
CZ2 J:TRP209 5.0 23.5 1.0
N J:ILE180 5.0 24.5 1.0
C J:LYS181 5.0 31.1 1.0

Reference:

U.Neu, Z.M.Khan, B.Schuch, A.S.Palma, Y.Liu, M.Pawlita, T.Feizi, T.Stehle. Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. Plos Pathog. V. 9 03714 2013.
ISSN: ISSN 1553-7366
PubMed: 24204265
DOI: 10.1371/JOURNAL.PPAT.1003714
Page generated: Sun Jul 21 19:40:56 2024

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