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Zinc in PDB 3qu6: Crystal Structure of Irf-3 Dbd Free Form

Protein crystallography data

The structure of Crystal Structure of Irf-3 Dbd Free Form, PDB code: 3qu6 was solved by P.E.De Ioannes, C.R.Escalante, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.38 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 64.908, 64.908, 157.621, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 26.3

Other elements in 3qu6:

The structure of Crystal Structure of Irf-3 Dbd Free Form also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Irf-3 Dbd Free Form (pdb code 3qu6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Irf-3 Dbd Free Form, PDB code: 3qu6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3qu6

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Zinc binding site 1 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn114

b:33.5
occ:1.00
OD2 C:ASP17 2.0 32.5 1.0
O C:HOH155 2.1 30.0 1.0
OE1 A:GLU59 2.1 32.2 1.0
CL A:CL123 2.3 34.7 1.0
OE2 A:GLU59 2.6 26.9 1.0
CD A:GLU59 2.6 31.6 1.0
CG C:ASP17 3.0 33.0 1.0
OD1 C:ASP17 3.3 30.5 1.0
CG1 C:VAL13 3.7 26.1 1.0
NE2 A:GLN55 4.0 27.6 1.0
O C:HOH148 4.0 35.9 1.0
O C:HOH152 4.0 29.9 1.0
O A:HOH134 4.1 37.0 1.0
CG A:GLU59 4.2 28.6 1.0
CB C:ASP17 4.3 27.9 1.0
CG A:GLN55 4.4 28.2 1.0
CD A:GLN55 4.4 30.4 1.0
O C:VAL13 4.8 31.0 1.0
CD1 A:PHE51 4.8 35.9 1.0
CB A:GLU59 4.8 28.9 1.0
CA A:ALA56 4.9 24.0 1.0

Zinc binding site 2 out of 9 in 3qu6

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Zinc binding site 2 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn115

b:28.7
occ:1.00
OD2 A:ASP17 2.0 25.4 1.0
O A:HOH164 2.1 24.3 1.0
CL A:CL119 2.3 29.9 1.0
CG A:ASP17 2.9 24.8 1.0
OD1 A:ASP17 3.1 26.6 1.0
CG1 A:VAL13 3.6 27.5 1.0
O A:HOH157 4.1 20.0 1.0
O A:HOH166 4.2 32.6 1.0
O A:HOH158 4.3 27.6 1.0
CB A:ASP17 4.3 26.6 1.0
O A:VAL13 4.8 23.2 1.0
NH2 A:ARG31 4.8 26.4 1.0

Zinc binding site 3 out of 9 in 3qu6

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Zinc binding site 3 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn116

b:40.5
occ:1.00
OD1 A:ASP99 1.9 36.7 1.0
OE1 B:GLU94 2.1 32.4 1.0
CL A:CL120 2.1 52.3 1.0
ND1 A:HIS101 2.1 35.0 1.0
CG A:ASP99 2.7 38.4 1.0
OD2 A:ASP99 2.8 37.3 1.0
CE1 A:HIS101 3.0 32.4 1.0
CG A:HIS101 3.1 37.9 1.0
CD B:GLU94 3.2 36.1 1.0
CB A:HIS101 3.5 28.9 1.0
CG B:GLU94 3.9 37.4 1.0
N A:HIS101 3.9 33.2 1.0
CD A:PRO100 4.1 40.1 1.0
NE2 A:HIS101 4.1 39.2 1.0
CB A:ASP99 4.1 33.1 1.0
OE2 B:GLU94 4.2 29.8 1.0
CD2 A:HIS101 4.2 32.8 1.0
CG A:PRO100 4.2 35.5 1.0
NH2 A:ARG96 4.3 38.3 1.0
CA A:HIS101 4.3 34.3 1.0
CB B:GLU94 4.4 30.8 1.0
N A:PRO100 4.6 37.8 1.0
CL A:CL118 4.6 29.9 1.0
CA A:ASP99 4.8 38.1 1.0
ZN B:ZN114 4.9 26.3 1.0
C A:ASP99 4.9 39.6 1.0
OD1 A:ASP102 5.0 19.3 1.0

Zinc binding site 4 out of 9 in 3qu6

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Zinc binding site 4 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn117

b:26.9
occ:1.00
OD1 B:ASP102 2.0 25.4 1.0
NE2 A:HIS104 2.0 16.9 1.0
OE1 A:GLU94 2.0 26.2 1.0
CL B:CL116 2.3 34.8 1.0
CG B:ASP102 2.8 26.6 1.0
CD A:GLU94 2.8 28.8 1.0
OE2 A:GLU94 3.0 26.2 1.0
CD2 A:HIS104 3.0 24.5 1.0
CE1 A:HIS104 3.0 25.6 1.0
OD2 B:ASP102 3.0 24.0 1.0
CG1 A:ILE106 3.8 22.8 1.0
CG A:ARG96 3.8 30.9 1.0
ND1 A:HIS104 4.1 21.5 1.0
CG A:HIS104 4.1 20.1 1.0
CB B:ASP102 4.2 22.3 1.0
CG A:GLU94 4.2 31.8 1.0
CE1 B:HIS104 4.3 27.5 1.0
CD1 A:ILE106 4.3 23.4 1.0
OD2 B:ASP99 4.4 38.5 1.0
O B:ASP102 4.5 26.6 1.0
O A:HOH133 4.5 23.4 1.0
N B:ASP102 4.6 28.6 1.0
CB A:ARG96 4.6 30.9 1.0
ZN B:ZN115 4.7 33.0 1.0
CG B:ASP99 4.8 34.5 1.0
ND1 B:HIS104 4.8 26.9 1.0
CA B:ASP102 4.8 27.8 1.0
CD A:ARG96 4.9 32.7 1.0
OD1 B:ASP99 4.9 36.9 1.0
CB A:GLU94 4.9 29.2 1.0
CB B:HIS101 5.0 28.4 1.0
CL A:CL118 5.0 29.9 1.0

Zinc binding site 5 out of 9 in 3qu6

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Zinc binding site 5 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn114

b:26.3
occ:1.00
OD1 A:ASP102 1.9 19.3 1.0
OE2 B:GLU94 2.0 29.8 1.0
NE2 B:HIS104 2.0 26.9 1.0
CL A:CL118 2.3 29.9 1.0
CG A:ASP102 2.7 24.8 1.0
CD B:GLU94 2.9 36.1 1.0
OD2 A:ASP102 2.9 25.4 1.0
CE1 B:HIS104 3.0 27.5 1.0
CD2 B:HIS104 3.1 24.6 1.0
OE1 B:GLU94 3.2 32.4 1.0
CG1 B:ILE106 3.8 26.1 1.0
ND1 B:HIS104 4.1 26.9 1.0
CG B:ARG96 4.1 34.4 1.0
CB A:ASP102 4.2 24.4 1.0
CG B:HIS104 4.2 27.5 1.0
CE1 A:HIS104 4.2 25.6 1.0
CD1 B:ILE106 4.3 22.5 1.0
CG B:GLU94 4.3 37.4 1.0
CD B:ARG96 4.4 37.9 1.0
O A:ASP102 4.4 25.5 1.0
O A:HOH133 4.4 23.4 1.0
OD2 A:ASP99 4.4 37.3 1.0
N A:ASP102 4.5 28.9 1.0
CB B:ARG96 4.6 30.6 1.0
ND1 A:HIS104 4.6 21.5 1.0
CA A:ASP102 4.8 29.1 1.0
CG A:ASP99 4.9 38.4 1.0
CB A:HIS101 4.9 28.9 1.0
ZN A:ZN116 4.9 40.5 1.0
CB B:GLU94 5.0 30.8 1.0
C A:ASP102 5.0 28.4 1.0

Zinc binding site 6 out of 9 in 3qu6

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Zinc binding site 6 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn115

b:33.0
occ:1.00
OD1 B:ASP99 1.9 36.9 1.0
OE2 A:GLU94 2.0 26.2 1.0
ND1 B:HIS101 2.1 34.8 1.0
CG B:ASP99 2.7 34.5 1.0
OD2 B:ASP99 2.9 38.5 1.0
CE1 B:HIS101 2.9 36.9 1.0
CD A:GLU94 3.1 28.8 1.0
CG B:HIS101 3.1 38.0 1.0
CB B:HIS101 3.5 28.4 1.0
CG A:GLU94 3.6 31.8 1.0
NE2 B:HIS101 4.1 38.4 1.0
N B:HIS101 4.1 30.6 1.0
CB B:ASP99 4.1 33.7 1.0
CD2 B:HIS101 4.2 39.6 1.0
OE1 A:GLU94 4.2 26.2 1.0
CD B:PRO100 4.2 34.7 1.0
CB A:GLU94 4.2 29.2 1.0
CA B:HIS101 4.4 33.0 1.0
CL B:CL116 4.5 34.8 1.0
NH1 B:ARG96 4.5 37.5 1.0
CG B:PRO100 4.6 34.0 1.0
ZN A:ZN117 4.7 26.9 1.0
N B:PRO100 4.7 38.8 1.0
CA B:ASP99 4.9 30.7 1.0
OD1 B:ASP102 4.9 25.4 1.0
C B:ASP99 5.0 37.6 1.0

Zinc binding site 7 out of 9 in 3qu6

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Zinc binding site 7 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn114

b:35.1
occ:1.00
CL C:CL118 2.1 34.0 1.0
OE1 C:GLU59 2.3 38.1 1.0
O C:HOH165 2.3 34.9 1.0
OE2 C:GLU59 2.5 33.6 1.0
CD C:GLU59 2.7 41.4 1.0
NE2 C:GLN55 3.8 33.0 1.0
CG C:GLU59 4.3 33.1 1.0
O C:HOH159 4.3 38.5 1.0
CD C:GLN55 4.3 34.6 1.0
CG C:GLN55 4.4 28.3 1.0
CD1 C:PHE51 4.8 39.6 1.0
CA C:ALA56 4.9 32.2 1.0
O C:GLN55 5.0 29.6 1.0
CB C:GLU59 5.0 31.5 1.0

Zinc binding site 8 out of 9 in 3qu6

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Zinc binding site 8 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn115

b:41.9
occ:1.00
NE2 C:HIS104 2.0 35.0 1.0
OE1 C:GLU94 2.1 44.6 1.0
CL C:CL119 2.5 47.2 1.0
CD2 C:HIS104 3.0 41.7 1.0
CE1 C:HIS104 3.0 39.6 1.0
CD C:GLU94 3.0 45.0 1.0
OE2 C:GLU94 3.3 46.2 1.0
CG1 C:ILE106 3.6 38.1 1.0
CG C:ARG96 4.0 43.2 1.0
ND1 C:HIS104 4.1 39.5 1.0
CG C:HIS104 4.1 37.7 1.0
CD1 C:ILE106 4.2 36.1 1.0
CG C:GLU94 4.4 48.9 1.0
O C:HOH140 4.4 36.8 0.5
CB C:ARG96 4.7 44.5 1.0
CB C:GLU94 4.8 46.5 1.0
CB C:ILE106 4.9 38.9 1.0
ZN C:ZN116 4.9 57.9 1.0

Zinc binding site 9 out of 9 in 3qu6

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Zinc binding site 9 out of 9 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn116

b:57.9
occ:1.00
OE2 C:GLU94 2.0 46.2 1.0
O C:HOH142 2.4 42.6 1.0
CD C:GLU94 3.0 45.0 1.0
CG C:GLU94 3.5 48.9 1.0
OE1 C:GLU94 4.0 44.6 1.0
CL C:CL119 4.6 47.2 1.0
CB C:GLU94 4.7 46.5 1.0
ZN C:ZN115 4.9 41.9 1.0

Reference:

P.De Ioannes, C.R.Escalante, A.K.Aggarwal. Structures of Apo Irf-3 and Irf-7 Dna Binding Domains: Effect of Loop L1 on Dna Binding. Nucleic Acids Res. V. 39 7300 2011.
ISSN: ISSN 0305-1048
PubMed: 21596780
DOI: 10.1093/NAR/GKR325
Page generated: Wed Dec 16 04:46:04 2020

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