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Chlorine in PDB 5n8d: Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native

Protein crystallography data

The structure of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native, PDB code: 5n8d was solved by A.K.Singh, M.J.Van Raaij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.880, 100.600, 95.470, 90.00, 116.28, 90.00
R / Rfree (%) 16.8 / 20.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native (pdb code 5n8d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native, PDB code: 5n8d:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5n8d

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Chlorine binding site 1 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:34.8
occ:1.00
 NE2 A:GLN618 3.1 20.6 1.0
O3 B:GOL802 3.2 58.1 1.0
NH1 A:ARG615 3.2 47.9 1.0
CB A:PRO617 3.8 26.1 1.0
CG A:PRO617 3.8 26.7 1.0
CG A:GLN618 3.9 19.6 1.0
CD A:GLN618 4.0 19.1 1.0
CZ B:PHE633 4.0 22.6 1.0
CD A:PRO617 4.1 25.1 1.0
CB A:ARG615 4.2 26.7 1.0
CZ A:ARG615 4.3 48.6 1.0
CD A:ARG615 4.4 35.4 1.0
C3 B:GOL802 4.5 58.2 1.0
CG A:ARG615 4.5 30.2 1.0
CE2 B:PHE633 4.7 23.8 1.0
CG2 B:VAL713 4.7 34.2 1.0
O A:HOH1093 4.8 58.3 1.0
NE A:ARG615 4.8 39.4 1.0
CA A:PRO617 4.9 24.5 1.0
N A:PRO617 4.9 24.0 1.0
CE1 B:PHE633 5.0 24.0 1.0

Chlorine binding site 2 out of 8 in 5n8d

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Chlorine binding site 2 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:37.8
occ:1.00
 O C:HOH1110 2.6 37.5 1.0
O C:HOH988 3.0 49.1 1.0
N A:ASP712 3.1 21.0 1.0
O A:HOH1090 3.6 54.7 1.0
CG C:PRO617 3.6 18.7 1.0
OG C:SER616 3.6 17.1 0.3
CA A:LEU711 3.7 19.3 1.0
CB A:ASP712 3.9 22.6 1.0
C A:LEU711 3.9 19.6 1.0
CD C:PRO617 4.0 18.3 1.0
CA A:ASP712 4.0 21.2 1.0
N C:PRO617 4.0 16.6 1.0
CB A:LEU711 4.1 18.9 1.0
CB C:SER616 4.2 17.0 0.3
CD2 A:LEU711 4.2 18.9 1.0
O A:HOH1010 4.2 35.3 1.0
CA C:PRO617 4.3 16.8 1.0
O C:HOH1118 4.3 41.0 1.0
C C:SER616 4.3 16.4 1.0
CB C:SER616 4.3 17.3 0.3
CB C:PRO617 4.4 18.0 1.0
CB C:SER616 4.4 17.1 0.3
OG C:SER616 4.4 17.3 0.3
O A:HOH958 4.5 14.9 0.5
O A:HOH1087 4.5 25.0 0.5
O C:SER616 4.6 17.1 1.0
O A:GLU710 4.7 20.2 1.0
C A:ASP712 4.7 19.9 1.0
O A:ASP712 4.7 19.3 1.0
CG A:LEU711 4.8 18.5 1.0
O A:HOH910 4.8 30.3 0.5
CA C:SER616 4.9 16.8 0.3
CA C:SER616 4.9 16.9 0.3
CA C:SER616 4.9 16.9 0.3
N A:LEU711 5.0 18.7 1.0

Chlorine binding site 3 out of 8 in 5n8d

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Chlorine binding site 3 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl803

b:33.8
occ:1.00
 NH1 B:ARG615 3.0 48.5 1.0
NE2 B:GLN618 3.1 18.1 1.0
O B:HOH1145 3.4 45.0 1.0
CG B:PRO617 3.6 23.3 1.0
CB B:PRO617 3.7 22.9 1.0
O C:HOH1136 3.8 46.9 1.0
CG B:GLN618 3.8 16.5 1.0
CD B:ARG615 3.9 43.2 1.0
CZ C:PHE633 3.9 17.5 1.0
CD B:GLN618 3.9 16.8 1.0
CZ B:ARG615 3.9 51.3 1.0
CD B:PRO617 4.0 22.2 1.0
NE B:ARG615 4.3 48.5 1.0
CB B:ARG615 4.4 28.9 1.0
CG B:ARG615 4.5 36.6 1.0
CE2 C:PHE633 4.6 17.9 1.0
CG2 C:VAL713 4.8 26.5 1.0
CA B:PRO617 4.8 22.8 1.0
CE1 C:PHE633 4.8 18.5 1.0
N B:PRO617 4.9 21.2 1.0
C B:PRO617 5.0 22.7 1.0
NH2 B:ARG615 5.0 54.3 1.0

Chlorine binding site 4 out of 8 in 5n8d

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Chlorine binding site 4 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl802

b:27.5
occ:1.00
 O C:HOH1148 3.0 33.7 1.0
NE2 C:GLN618 3.2 19.0 1.0
NH1 C:ARG615 3.2 23.1 0.5
O A:HOH902 3.7 42.1 1.0
CG C:PRO617 3.7 18.7 1.0
CD C:ARG615 3.8 20.1 0.5
CB C:PRO617 3.8 18.0 1.0
CD C:PRO617 3.9 18.3 1.0
CB C:ARG615 4.0 19.4 0.5
CB C:ARG615 4.0 18.8 0.5
CG C:GLN618 4.0 15.4 1.0
CZ A:PHE633 4.0 18.3 1.0
CD C:GLN618 4.1 16.4 1.0
CG C:ARG615 4.1 19.3 0.5
CZ C:ARG615 4.3 21.8 0.5
CG C:ARG615 4.4 20.4 0.5
NE C:ARG615 4.5 22.1 0.5
CG2 A:VAL713 4.7 22.6 1.0
CD C:ARG615 4.7 22.2 0.5
CE2 A:PHE633 4.8 19.9 1.0
N C:PRO617 4.8 16.6 1.0
CE1 A:PHE633 4.8 19.3 1.0
CA C:PRO617 4.9 16.8 1.0

Chlorine binding site 5 out of 8 in 5n8d

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Chlorine binding site 5 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl802

b:34.7
occ:1.00
 NE D:ARG615 3.0 45.4 1.0
O D:HOH1070 3.0 51.9 1.0
NE2 D:GLN618 3.1 20.2 1.0
O D:HOH1139 3.4 46.9 1.0
NH2 D:ARG615 3.5 45.6 1.0
CG D:PRO617 3.6 23.0 1.0
CB D:PRO617 3.7 23.1 1.0
CZ D:ARG615 3.7 45.8 1.0
CG D:GLN618 3.8 18.2 1.0
CZ E:PHE633 3.9 19.8 1.0
CD D:GLN618 3.9 18.5 1.0
CD D:ARG615 4.0 40.1 1.0
CD D:PRO617 4.0 22.6 1.0
CB D:ARG615 4.4 28.3 1.0
CE2 E:PHE633 4.6 20.0 1.0
CG D:ARG615 4.6 35.1 1.0
CG2 E:VAL713 4.7 27.0 1.0
CA D:PRO617 4.7 23.1 1.0
CE1 E:PHE633 4.8 20.1 1.0
N D:PRO617 4.8 21.3 1.0
C D:PRO617 4.9 22.0 1.0
N D:GLN618 4.9 19.8 1.0

Chlorine binding site 6 out of 8 in 5n8d

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Chlorine binding site 6 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl802

b:26.6
occ:1.00
 O E:HOH1151 2.9 30.6 1.0
NH1 E:ARG615 3.2 22.0 0.5
NE2 E:GLN618 3.3 18.0 1.0
CG E:PRO617 3.8 20.5 1.0
CD E:ARG615 3.8 20.0 0.5
CB E:PRO617 3.9 20.9 1.0
CB E:ARG615 4.0 18.7 0.5
CB E:ARG615 4.0 18.4 0.5
CG E:GLN618 4.0 16.0 1.0
CD E:PRO617 4.0 19.7 1.0
CZ F:PHE633 4.1 18.9 1.0
CD E:GLN618 4.1 17.9 1.0
CG E:ARG615 4.1 19.3 0.5
CZ E:ARG615 4.3 21.6 0.5
CG E:ARG615 4.4 19.6 0.5
NE E:ARG615 4.5 21.8 0.5
CG2 F:VAL713 4.7 22.2 1.0
CD E:ARG615 4.8 21.1 0.5
CE2 F:PHE633 4.8 21.8 1.0
N E:PRO617 4.9 18.5 1.0
CA E:PRO617 4.9 18.4 1.0
CE1 F:PHE633 4.9 20.1 1.0

Chlorine binding site 7 out of 8 in 5n8d

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Chlorine binding site 7 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl802

b:33.7
occ:1.00
 O F:HOH1119 2.8 47.2 1.0
NE2 F:GLN618 3.1 18.8 1.0
NH1 F:ARG615 3.2 27.8 0.5
O D:HOH1171 3.7 27.6 0.5
CD F:ARG615 3.7 27.8 0.5
CB F:PRO617 3.8 24.4 1.0
CG F:PRO617 3.8 25.9 1.0
CG F:GLN618 3.9 19.2 1.0
CZ D:PHE633 4.0 22.9 1.0
CD F:GLN618 4.0 17.9 1.0
CD F:PRO617 4.1 25.0 1.0
CZ F:ARG615 4.1 28.5 0.5
CB F:ARG615 4.2 25.1 0.5
CB F:ARG615 4.2 25.3 0.5
CG F:ARG615 4.3 26.9 0.5
NE F:ARG615 4.3 28.6 0.5
CG F:ARG615 4.6 26.7 0.5
O F:HOH1080 4.6 54.5 1.0
CE2 D:PHE633 4.6 25.2 1.0
CG2 D:VAL713 4.9 35.6 1.0
CA F:PRO617 4.9 23.9 1.0
CD F:ARG615 4.9 27.6 0.5
N F:PRO617 4.9 23.1 1.0
CE1 D:PHE633 5.0 23.7 1.0

Chlorine binding site 8 out of 8 in 5n8d

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Chlorine binding site 8 out of 8 in the Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the Distal Domain of Mouse Adenovirus 2 Fibre, P21 Native within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl803

b:37.6
occ:1.00
 O E:HOH1147 2.6 38.5 1.0
O E:HOH1054 2.8 27.7 0.5
N F:ASP712 3.1 19.7 1.0
O F:HOH1090 3.2 49.1 1.0
CG E:PRO617 3.6 20.5 1.0
OG E:SER616 3.6 29.3 1.0
CA F:LEU711 3.8 18.8 1.0
CB F:ASP712 3.9 21.9 1.0
C F:LEU711 4.0 20.2 1.0
CD E:PRO617 4.0 19.7 1.0
CA F:ASP712 4.0 21.0 1.0
N E:PRO617 4.1 18.5 1.0
CB F:LEU711 4.2 18.8 1.0
CD2 F:LEU711 4.3 19.3 1.0
O F:HOH1021 4.3 37.5 1.0
CA E:PRO617 4.3 18.4 1.0
C E:SER616 4.3 17.4 1.0
CB E:PRO617 4.4 20.9 1.0
O E:HOH1150 4.4 41.4 1.0
O F:HOH1098 4.5 23.8 0.5
CB E:SER616 4.5 21.6 1.0
O F:HOH1008 4.5 33.5 1.0
O E:SER616 4.6 18.3 1.0
C F:ASP712 4.7 19.9 1.0
O F:GLU710 4.7 20.6 1.0
O F:HOH929 4.7 25.9 0.5
O F:ASP712 4.8 21.6 1.0
CG F:LEU711 4.9 18.0 1.0
CA E:SER616 5.0 18.3 1.0
N F:LEU711 5.0 19.0 1.0

Reference:

A.K.Singh, T.H.Nguyen, M.Z.Vidovszky, B.Harrach, M.Benko, A.Kirwan, L.Joshi, M.Kilcoyne, M.A.Berbis, F.J.Canada, J.Jimenez-Barbero, M.Menendez, S.S.Wilson, B.A.Bromme, J.G.Smith, M.J.Van Raaij. Structure and N-Acetylglucosamine Binding of the Distal Domain of Mouse Adenovirus 2 Fibre. J. Gen. Virol. V. 99 1494 2018.
ISSN: ESSN 1465-2099
PubMed: 30277856
DOI: 10.1099/JGV.0.001145
Page generated: Fri Jul 26 13:17:49 2024

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