Zinc in PDB 3a1z: Crystal Structure of Juvenile Hormone Binding Protein From Silkworm

The structure of Crystal Structure of Juvenile Hormone Binding Protein From Silkworm, PDB code: 3a1z was solved by R.Suzuki, Z.Fujimoto, T.Shiotsuki, M.Momma, A.Tase, T.Yamazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.49 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.863, 114.655, 192.850, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 29

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm (pdb code 3a1z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm, PDB code: 3a1z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn226 b:35.6 occ:1.00 OD2 A:ASP36 1.9 31.3 1.0 NE2 A:HIS206 2.0 31.1 1.0 OE2 C:GLU107 2.1 38.9 1.0 O A:HOH258 2.2 42.0 1.0 OE1 C:GLU107 2.7 31.4 1.0 CD C:GLU107 2.7 33.9 1.0 CG A:ASP36 2.7 33.6 1.0 OD1 A:ASP36 2.9 37.6 1.0 CE1 A:HIS206 2.9 29.6 1.0 CD2 A:HIS206 3.0 31.5 1.0 NE1 A:TRP38 3.7 29.0 1.0 O A:HOH264 3.8 49.4 1.0 O A:HOH242 3.9 34.4 1.0 ND1 A:HIS206 4.1 29.8 1.0 CZ2 A:TRP38 4.1 24.2 1.0 CE2 A:TRP38 4.1 25.9 1.0 CG A:HIS206 4.1 30.4 1.0 CG C:GLU107 4.1 35.5 1.0 O A:HOH243 4.2 39.3 1.0 CB A:ASP36 4.2 33.3 1.0 OD1 C:ASP55 4.3 41.7 1.0 O A:ASP36 4.4 34.7 1.0 O C:HOH267 4.6 40.1 1.0 CD1 A:TRP38 4.7 28.1 1.0 N C:GLY57 4.9 37.5 1.0 CA C:GLY57 5.0 37.8 1.0

Zinc binding site 2 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn227 b:37.2 occ:1.00 NE2 A:HIS141 2.0 31.3 1.0 OD1 A:ASP135 2.1 56.8 1.0 OD2 A:ASP135 2.4 55.8 1.0 CE1 A:HIS141 2.5 32.1 1.0 CG A:ASP135 2.6 51.8 1.0 O A:HOH251 2.9 37.4 1.0 CD2 A:HIS141 3.3 31.8 1.0 ND1 A:HIS141 3.8 32.7 1.0 CB A:ASP135 4.0 50.7 1.0 CG A:HIS141 4.2 35.2 1.0 CB A:VAL139 4.6 41.1 1.0 CA A:ASP135 4.7 50.5 1.0 CG1 A:VAL139 4.8 40.3 1.0 O A:LYS213 4.8 38.6 1.0 O A:VAL139 4.9 41.5 1.0

Zinc binding site 3 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


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 Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn228 b:75.3 occ:0.50 ND1 A:HIS96 1.4 47.0 1.0 CE1 A:HIS96 1.6 47.1 1.0 O A:HOH254 2.7 39.0 1.0 CG A:HIS96 2.8 45.5 1.0 O A:HOH253 2.8 37.2 1.0 OD2 A:ASP119 2.9 49.8 1.0 NE2 A:HIS96 2.9 49.5 1.0 CD2 A:HIS96 3.4 49.0 1.0 CB A:HIS96 3.8 40.8 1.0 CG A:ASP119 3.8 46.3 1.0 CB A:ASP119 4.1 41.3 1.0 CA A:HIS96 4.8 40.4 1.0 OD1 A:ASP119 5.0 47.8 1.0

Zinc binding site 4 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


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 Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn229 b:43.6 occ:0.50 OD1 A:ASP94 2.0 52.5 1.0 O A:HOH257 2.2 24.8 1.0 CG A:ASP94 2.6 52.2 1.0 OD2 A:ASP94 2.6 54.3 1.0 OD1 A:ASP119 2.7 47.8 1.0 OD2 A:ASP119 2.8 49.8 1.0 NE2 A:HIS96 2.8 49.5 1.0 CG A:ASP119 3.1 46.3 1.0 CD2 A:HIS96 3.6 49.0 1.0 CE1 A:HIS96 3.7 47.1 1.0 CB A:ASP94 4.1 48.5 1.0 O A:HOH262 4.3 68.3 1.0 CB A:ASP119 4.6 41.3 1.0 O A:HOH254 4.7 39.0 1.0 ND1 A:HIS96 4.7 47.0 1.0 CG A:HIS96 4.7 45.5 1.0 OD1 A:ASN121 4.9 53.0 1.0

Zinc binding site 5 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


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 Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn230 b:77.6 occ:0.30 OE2 A:GLU22 2.5 61.2 1.0 OE1 A:GLU22 2.8 59.8 1.0 CD A:GLU22 3.0 58.9 1.0 CG A:GLN74 3.4 64.2 1.0 CB A:GLN74 3.6 60.8 1.0 CA A:GLN74 4.0 60.9 1.0 N A:ILE75 4.4 62.5 1.0 CG A:GLU22 4.5 58.3 1.0 C A:GLN74 4.7 61.5 1.0 CD A:GLN74 4.9 68.6 1.0

Zinc binding site 6 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


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 Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn226 b:47.3 occ:1.00 OD2 B:ASP36 1.6 42.5 1.0 NE2 B:HIS206 2.0 31.7 1.0 OE2 D:GLU107 2.2 42.9 1.0 CG B:ASP36 2.6 47.1 1.0 OD1 B:ASP36 2.8 49.2 1.0 CD D:GLU107 2.9 42.7 1.0 OE1 D:GLU107 2.9 40.2 1.0 CD2 B:HIS206 3.0 28.2 1.0 CE1 B:HIS206 3.0 28.1 1.0 NE1 B:TRP38 3.7 35.1 1.0 OD1 D:ASP55 3.7 54.6 1.0 CB B:ASP36 4.0 48.6 1.0 ND1 B:HIS206 4.1 30.3 1.0 CG B:HIS206 4.1 32.0 1.0 CG D:GLU107 4.3 41.9 1.0 CE2 B:TRP38 4.3 32.4 1.0 O B:ASP36 4.4 49.2 1.0 CZ2 B:TRP38 4.4 31.2 1.0 N D:GLY57 4.6 45.4 1.0 CA D:GLY57 4.6 44.3 1.0 CD1 B:TRP38 4.7 36.9 1.0 CG D:ASP55 4.7 52.0 1.0

Zinc binding site 7 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


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 Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn227 b:81.8 occ:1.00 NE2 B:HIS141 2.1 55.2 1.0 OD1 B:ASP135 2.4 71.1 1.0 O B:HOH251 2.5 53.3 1.0 CD2 B:HIS141 3.0 56.0 1.0 OD2 B:ASP135 3.0 74.4 1.0 CG B:ASP135 3.1 71.4 1.0 CE1 B:HIS141 3.1 54.1 1.0 CG1 B:VAL139 3.7 64.9 1.0 CG B:HIS141 4.2 56.5 1.0 ND1 B:HIS141 4.2 56.1 1.0 CB B:VAL139 4.4 64.3 1.0 CB B:ASP135 4.5 70.0 1.0

Zinc binding site 8 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


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 Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn228 b:49.4 occ:0.50 CD2 B:HIS96 1.8 56.5 1.0 OD1 B:ASP119 2.3 53.9 1.0 CG B:HIS96 2.4 55.5 1.0 NE2 B:HIS96 2.8 58.5 1.0 O B:HOH252 2.8 38.0 1.0 OD2 B:ASP119 2.8 53.2 1.0 CG B:ASP119 2.9 50.1 1.0 CB B:HIS96 3.0 51.6 1.0 ND1 B:HIS96 3.4 57.0 1.0 CE1 B:HIS96 3.6 58.7 1.0 CA B:HIS96 4.0 50.8 1.0 CB B:ASP119 4.5 46.9 1.0 ZN B:ZN229 5.0 84.2 0.5 N B:HIS96 5.0 51.2 1.0

Zinc binding site 9 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


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 Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn229 b:84.2 occ:0.50 NE2 B:HIS96 2.4 58.5 1.0 OD2 B:ASP94 2.8 64.5 1.0 CE1 B:HIS96 3.0 58.7 1.0 O B:HOH236 3.0 34.4 1.0 OD1 B:ASP94 3.2 64.4 1.0 CG B:ASP94 3.3 61.9 1.0 CD2 B:HIS96 3.6 56.5 1.0 ND1 B:HIS96 4.2 57.0 1.0 OD1 B:ASP119 4.4 53.9 1.0 CG B:HIS96 4.5 55.5 1.0 CB B:ASP94 4.6 58.3 1.0 CG B:ASP119 4.7 50.1 1.0 ZN B:ZN228 5.0 49.4 0.5

Zinc binding site 10 out of 20 in the Crystal Structure of Juvenile Hormone Binding Protein From Silkworm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Juvenile Hormone Binding Protein From Silkworm within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn226 b:34.3 occ:1.00 OD2 C:ASP36 1.9 27.9 1.0 NE2 C:HIS206 2.1 25.9 1.0 OE2 A:GLU107 2.3 33.5 1.0 CG C:ASP36 2.6 29.8 1.0 OD1 C:ASP36 2.6 31.4 1.0 OE1 A:GLU107 2.8 30.6 1.0 CD A:GLU107 2.8 33.3 1.0 CE1 C:HIS206 3.1 25.2 1.0 CD2 C:HIS206 3.1 24.8 1.0 OD1 A:ASP55 3.6 49.5 1.0 O C:HOH259 3.8 37.2 1.0 NE1 C:TRP38 3.9 25.8 1.0 CB C:ASP36 4.0 30.9 1.0 O C:HOH265 4.1 47.2 1.0 CZ2 C:TRP38 4.2 24.9 1.0 ND1 C:HIS206 4.2 26.8 1.0 CE2 C:TRP38 4.3 23.8 1.0 CG C:HIS206 4.3 27.6 1.0 CG A:GLU107 4.3 30.6 1.0 O C:ASP36 4.6 32.9 1.0 CG A:ASP55 4.7 47.3 1.0 N A:GLY57 4.7 38.7 1.0 CD1 C:TRP38 4.8 25.0 1.0 CA A:GLY57 4.9 37.8 1.0

Z.Fujimoto, R.Suzuki, T.Shiotsuki, W.Tsuchiya, A.Tase, M.Momma, T.Yamazaki. Crystal Structure of Silkworm Bombyx Mori Jhbp in Complex with 2-Methyl-2,4-Pentanediol: Plasticity of Jh-Binding Pocket and Ligand-Induced Conformational Change of the Second Cavity in Jhbp Plos One V. 8 56261 2013.
ISSN: ESSN 1932-6203
PubMed: 23437107
DOI: 10.1371/JOURNAL.PONE.0056261