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Chlorine in PDB 6kc6: Hoip-HOIPIN8 Complex

Enzymatic activity of Hoip-HOIPIN8 Complex

All present enzymatic activity of Hoip-HOIPIN8 Complex:
2.3.2.31;

Protein crystallography data

The structure of Hoip-HOIPIN8 Complex, PDB code: 6kc6 was solved by Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.59 / 2.12
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.586, 88.793, 104.438, 90.00, 101.08, 90.00
R / Rfree (%) 21.1 / 26.7

Other elements in 6kc6:

The structure of Hoip-HOIPIN8 Complex also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hoip-HOIPIN8 Complex (pdb code 6kc6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Hoip-HOIPIN8 Complex, PDB code: 6kc6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6kc6

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Chlorine binding site 1 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1106

b:73.6
occ:1.00
 OH A:TYR1021 3.1 42.5 1.0
NH1 A:ARG1032 3.5 57.8 1.0
CZ A:TYR1021 3.8 38.9 1.0
CB A:ALA1029 4.0 48.0 1.0
CE2 A:TYR1021 4.0 44.9 1.0
CE2 A:TYR1033 4.1 44.4 1.0
CB A:ARG928 4.1 40.4 1.0
O A:HOH1205 4.3 37.9 1.0
CA A:ALA1029 4.3 44.9 1.0
OH A:TYR1033 4.7 46.9 1.0
N A:ALA1029 4.7 48.9 1.0
CZ A:ARG1032 4.7 53.0 1.0
CE1 A:TYR1021 4.8 37.6 1.0
CA A:ARG928 4.8 39.4 1.0
CZ A:TYR1033 4.9 46.8 1.0
O A:GLU1025 4.9 45.7 1.0
CD2 A:TYR1033 5.0 45.6 1.0

Chlorine binding site 2 out of 9 in 6kc6

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Chlorine binding site 2 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1107

b:48.6
occ:1.00
 O A:HOH1226 3.1 43.8 1.0
ND2 A:ASN903 3.4 46.5 1.0
N A:GLN1065 3.5 46.2 1.0
CD2 C:LEU1041 3.6 71.9 1.0
CD A:PRO927 3.9 32.5 1.0
CA A:GLY1064 4.0 37.4 1.0
CG A:PRO927 4.0 35.8 1.0
CB A:PRO927 4.1 38.8 1.0
CB A:GLN1065 4.2 45.3 1.0
C A:GLY1064 4.2 47.0 1.0
CG A:ASN903 4.2 47.5 1.0
OD1 A:ASN903 4.2 54.2 1.0
CA A:GLN1065 4.4 46.4 1.0
CD1 C:LEU1041 4.5 69.4 1.0
CG A:GLN1065 4.6 41.1 1.0
CG C:LEU1041 4.6 69.9 1.0
N A:PRO927 4.7 40.5 1.0
N A:SER1066 4.8 49.8 1.0
NE2 A:GLN1065 4.9 48.7 1.0
CA A:PRO927 5.0 35.1 1.0
O A:CYS901 5.0 39.6 1.0
N A:GLY1064 5.0 40.9 1.0

Chlorine binding site 3 out of 9 in 6kc6

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Chlorine binding site 3 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1108

b:90.6
occ:1.00
 NZ A:LYS988 3.6 54.3 1.0
O I:HOH1229 3.9 52.4 1.0
F2 I:D601105 4.0 62.9 1.0
C7 I:D601105 4.0 47.5 1.0
O3 I:D601105 4.2 59.5 1.0
C5 I:D601105 4.3 45.3 1.0
C2 I:D601105 4.3 52.7 1.0
CE A:LYS988 4.4 44.8 1.0
O A:GLY883 4.7 84.7 1.0
C1 I:D601105 4.8 66.6 1.0
C3 I:D601105 4.9 48.0 1.0
C6 I:D601105 4.9 54.4 1.0
C9 I:D601105 5.0 69.6 1.0

Chlorine binding site 4 out of 9 in 6kc6

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Chlorine binding site 4 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1106

b:66.1
occ:1.00
 OH C:TYR1021 3.3 45.9 1.0
NH1 C:ARG1032 3.4 55.5 1.0
CE2 C:TYR1033 3.7 43.7 1.0
CB C:ARG928 3.9 39.1 1.0
CB C:ALA1029 4.0 42.5 1.0
CZ C:TYR1021 4.1 38.7 1.0
CE2 C:TYR1021 4.2 41.8 1.0
CA C:ALA1029 4.3 40.2 1.0
CD C:ARG1032 4.3 55.5 1.0
OH C:TYR1033 4.4 49.1 1.0
CZ C:ARG1032 4.5 54.9 1.0
O C:HOH1209 4.5 36.1 1.0
CZ C:TYR1033 4.6 49.2 1.0
CD2 C:TYR1033 4.6 40.9 1.0
CA C:ARG928 4.7 40.9 1.0
N C:ALA1029 4.7 39.6 1.0
O C:HOH1246 4.8 45.9 1.0
NE C:ARG1032 4.8 55.6 1.0

Chlorine binding site 5 out of 9 in 6kc6

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Chlorine binding site 5 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1106

b:72.6
occ:1.00
 OH E:TYR1021 3.2 50.6 1.0
NH1 E:ARG1032 3.3 65.9 1.0
CB E:ALA1029 3.7 56.1 1.0
CA E:ALA1029 3.9 56.3 1.0
CZ E:TYR1021 3.9 49.4 1.0
CE2 E:TYR1033 4.0 46.7 1.0
CE2 E:TYR1021 4.1 53.1 1.0
N E:ALA1029 4.4 51.9 1.0
CB E:ARG928 4.4 42.5 1.0
CZ E:ARG1032 4.5 66.4 1.0
O E:GLU1025 4.7 60.4 1.0
OH E:TYR1033 4.8 49.3 1.0
CD2 E:TYR1033 4.8 51.4 1.0
CZ E:TYR1033 4.9 46.9 1.0
CE1 E:TYR1021 4.9 54.1 1.0
CD E:ARG1032 4.9 62.7 1.0

Chlorine binding site 6 out of 9 in 6kc6

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Chlorine binding site 6 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1106

b:78.2
occ:1.00
 OH G:TYR1021 3.4 52.6 1.0
NH1 G:ARG1032 3.5 73.0 1.0
CB G:ALA1029 3.8 56.6 1.0
CE2 G:TYR1033 3.8 46.0 1.0
CA G:ALA1029 4.0 58.7 1.0
CZ G:TYR1021 4.1 46.3 1.0
CB G:ARG928 4.2 44.2 1.0
CE2 G:TYR1021 4.3 48.5 1.0
CD G:ARG1032 4.5 70.2 1.0
N G:ALA1029 4.6 61.1 1.0
O G:HOH1209 4.6 44.1 1.0
CD2 G:TYR1033 4.6 50.4 1.0
OH G:TYR1033 4.7 48.5 1.0
CZ G:ARG1032 4.7 70.0 1.0
CZ G:TYR1033 4.7 54.7 1.0
CG2 G:THR1028 4.8 59.6 1.0
O G:GLU1025 4.8 57.5 1.0
CA G:ARG928 4.9 43.8 1.0
O G:HOH1230 4.9 52.5 1.0

Chlorine binding site 7 out of 9 in 6kc6

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Chlorine binding site 7 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1106

b:74.5
occ:1.00
 OH I:TYR1021 3.2 52.5 1.0
NH1 I:ARG1032 3.4 54.8 1.0
CE2 I:TYR1033 3.7 46.5 1.0
CZ I:TYR1021 4.0 45.1 1.0
CB I:ARG928 4.1 49.0 1.0
CB I:ALA1029 4.2 54.2 1.0
CE2 I:TYR1021 4.2 46.2 1.0
CA I:ALA1029 4.3 53.3 1.0
OH I:TYR1033 4.3 49.2 1.0
O I:HOH1207 4.5 42.8 1.0
CZ I:TYR1033 4.5 48.0 1.0
CZ I:ARG1032 4.6 58.5 1.0
CD2 I:TYR1033 4.6 46.7 1.0
N I:ALA1029 4.7 53.9 1.0
CD I:ARG1032 4.7 54.0 1.0
CA I:ARG928 4.7 46.0 1.0
CE1 I:TYR1021 5.0 44.1 1.0

Chlorine binding site 8 out of 9 in 6kc6

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Chlorine binding site 8 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1107

b:86.5
occ:1.00
 NZ I:LYS988 3.4 50.2 1.0
O A:HOH1210 3.9 43.7 1.0
C7 A:D601105 4.1 43.8 1.0
F2 A:D601105 4.2 55.2 1.0
CE I:LYS988 4.2 45.3 1.0
C5 A:D601105 4.3 44.8 1.0
O3 A:D601105 4.4 64.2 1.0
O A:HOH1258 4.5 44.8 1.0
C2 A:D601105 4.5 52.4 1.0
CD2 A:LEU922 4.6 61.5 1.0
O A:LEU922 4.8 42.9 1.0
C3 A:D601105 4.9 46.1 1.0
C1 A:D601105 5.0 65.5 1.0

Chlorine binding site 9 out of 9 in 6kc6

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Chlorine binding site 9 out of 9 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Hoip-HOIPIN8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl1106

b:81.1
occ:1.00
 NH1 K:ARG1032 3.0 72.1 1.0
OH K:TYR1021 3.4 55.6 1.0
CB K:ARG928 4.0 49.9 1.0
CE2 K:TYR1033 4.1 53.7 1.0
OH K:TYR1033 4.1 54.5 1.0
CZ K:ARG1032 4.3 75.2 1.0
CZ K:TYR1021 4.3 53.9 1.0
O K:HOH1212 4.3 49.7 1.0
CB K:ALA1029 4.4 60.4 1.0
CA K:ARG928 4.4 46.7 1.0
CZ K:TYR1033 4.6 53.3 1.0
CD2 K:TYR933 4.6 43.0 1.0
CE2 K:TYR1021 4.7 52.8 1.0
O K:HOH1221 4.7 53.6 1.0
CE2 K:TYR933 4.7 45.6 1.0
CD K:ARG1032 4.7 66.6 1.0
CA K:ALA1029 4.7 61.9 1.0
CG K:TYR933 4.8 48.4 1.0
CZ K:TYR933 4.8 50.2 1.0
CD1 K:TYR933 4.9 49.1 1.0
CE1 K:TYR933 4.9 46.6 1.0
NE K:ARG1032 5.0 74.9 1.0

Reference:

D.Oikawa, Y.Sato, F.Ohtake, K.Komakura, K.Hanada, K.Sugawara, S.Terawaki, Y.Mizukami, H.T.Phuong, K.Iio, S.Obika, M.Fukushi, T.Irie, D.Tsuruta, S.Sakamoto, K.Tanaka, Y.Saeki, S.Fukai, F.Tokunaga. Molecular Bases For Hoipins-Mediated Inhibition of Lubac and Innate Immune Responses. Commun Biol V. 3 163 2020.
ISSN: ESSN 2399-3642
PubMed: 32246052
DOI: 10.1038/S42003-020-0882-8
Page generated: Sun Jul 28 02:26:01 2024

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