Zinc in PDB 3nil: The Structure of Ubr Box (Rdaa)

The structure of The Structure of Ubr Box (Rdaa), PDB code: 3nil was solved by W.S.Choi, B.-C.Jeong, M.-R.Lee, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.38 / 1.75
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	44.323, 44.323, 139.506, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the The Structure of Ubr Box (Rdaa) (pdb code 3nil). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Structure of Ubr Box (Rdaa), PDB code: 3nil:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:17.2 occ:1.00 SG A:CYS123 2.3 19.6 1.0 SG A:CYS175 2.3 19.3 1.0 SG A:CYS148 2.3 20.8 1.0 SG A:CYS151 2.5 21.4 1.0 CB A:CYS175 3.1 17.3 1.0 CB A:CYS123 3.1 18.6 1.0 CB A:CYS151 3.3 20.2 1.0 CB A:CYS148 3.4 19.3 1.0 N A:CYS148 3.9 18.3 1.0 CA A:CYS148 4.2 18.9 1.0 CB A:CYS177 4.3 18.5 1.0 N A:CYS151 4.3 20.2 1.0 ZN A:ZN2 4.4 17.5 1.0 CA A:CYS151 4.4 20.4 1.0 CA A:CYS175 4.6 17.9 1.0 CB A:ARG125 4.6 20.3 1.0 CA A:CYS123 4.6 18.4 1.0 O D:HOH209 4.6 41.6 1.0 C A:CYS148 4.7 18.8 1.0 O A:CYS148 4.7 17.1 1.0 CB A:HIS150 4.8 22.9 1.0 NE2 A:HIS118 5.0 16.4 1.0 C A:CYS175 5.0 18.3 1.0

Zinc binding site 2 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:17.5 occ:1.00 NE2 A:HIS118 2.1 16.4 1.0 SG A:CYS189 2.3 19.4 1.0 SG A:CYS151 2.3 21.4 1.0 SG A:CYS177 2.3 17.4 1.0 CD2 A:HIS118 3.1 17.7 1.0 CB A:CYS151 3.1 20.2 1.0 CE1 A:HIS118 3.1 20.1 1.0 CB A:CYS189 3.2 20.1 1.0 CB A:CYS177 3.2 18.5 1.0 CA A:CYS151 3.8 20.4 1.0 CA A:CYS189 4.1 20.5 1.0 ND1 A:HIS118 4.2 17.6 1.0 CG A:HIS118 4.2 20.9 1.0 O A:HOH24 4.2 22.4 1.0 CB A:CYS123 4.3 18.6 1.0 O A:HOH34 4.3 30.7 1.0 ZN A:ZN1 4.4 17.2 1.0 CA A:CYS177 4.5 17.9 1.0 O A:HOH23 4.6 21.7 1.0 O A:HOH208 4.7 34.3 1.0 C A:CYS177 4.7 18.5 1.0 C A:CYS151 4.8 19.7 1.0 O A:CYS151 4.8 20.0 1.0 N A:CYS151 4.8 20.2 1.0 O A:CYS177 4.9 17.5 1.0 C A:CYS189 5.0 20.9 1.0

Zinc binding site 3 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:23.7 occ:1.00 ND1 A:HIS157 2.0 26.0 1.0 ND1 A:HIS160 2.1 27.9 1.0 SG A:CYS136 2.2 26.2 1.0 SG A:CYS139 2.3 28.8 1.0 CE1 A:HIS157 2.9 25.4 1.0 CE1 A:HIS160 3.0 28.5 1.0 CG A:HIS160 3.1 29.1 1.0 CG A:HIS157 3.1 26.2 1.0 CB A:CYS139 3.3 29.4 1.0 CB A:CYS136 3.4 27.3 1.0 CB A:HIS160 3.5 29.1 1.0 CB A:HIS157 3.5 27.0 1.0 N A:CYS139 3.8 29.4 1.0 CA A:HIS157 3.9 26.9 1.0 O A:ASP156 3.9 26.1 1.0 NE2 A:HIS157 4.1 24.6 1.0 NE2 A:HIS160 4.1 30.1 1.0 CA A:CYS139 4.1 29.3 1.0 CD2 A:HIS160 4.2 28.3 1.0 CD2 A:HIS157 4.2 25.3 1.0 C A:ASP156 4.5 25.5 1.0 N A:HIS157 4.6 26.4 1.0 CB A:GLU138 4.6 30.3 1.0 O A:HOH231 4.7 41.0 1.0 CA A:CYS136 4.8 27.5 1.0 C A:GLU138 4.8 29.6 1.0 CA A:HIS160 5.0 29.0 1.0

Zinc binding site 4 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:19.0 occ:1.00 SG B:CYS123 2.3 19.5 1.0 SG B:CYS175 2.3 18.9 1.0 SG B:CYS148 2.4 22.9 1.0 SG B:CYS151 2.4 22.9 1.0 CB B:CYS123 3.1 16.3 1.0 CB B:CYS175 3.1 18.4 1.0 CB B:CYS151 3.3 24.7 1.0 CB B:CYS148 3.6 22.0 1.0 N B:CYS148 4.0 21.4 1.0 O B:HOH200 4.2 24.0 1.0 CB B:CYS177 4.2 21.0 1.0 CA B:CYS148 4.3 22.0 1.0 N B:CYS151 4.5 25.5 1.0 ZN B:ZN2 4.5 22.2 1.0 CA B:CYS151 4.5 25.3 1.0 CA B:CYS175 4.5 19.2 1.0 CA B:CYS123 4.6 17.3 1.0 CB B:ARG125 4.6 21.6 1.0 C B:CYS148 4.8 22.2 1.0 O B:CYS148 4.9 20.9 1.0 NE2 B:HIS118 5.0 18.6 1.0 C B:CYS175 5.0 19.1 1.0 CB B:HIS150 5.0 26.2 1.0

Zinc binding site 5 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:22.2 occ:1.00 NE2 B:HIS118 2.1 18.6 1.0 SG B:CYS189 2.3 25.2 1.0 SG B:CYS177 2.4 23.1 1.0 SG B:CYS151 2.4 22.9 1.0 CE1 B:HIS118 3.0 18.7 1.0 CD2 B:HIS118 3.1 18.8 1.0 CB B:CYS189 3.1 28.8 1.0 CB B:CYS151 3.1 24.7 1.0 CB B:CYS177 3.2 21.0 1.0 CA B:CYS151 3.8 25.3 1.0 O B:HOH76 4.1 29.4 1.0 CA B:CYS189 4.1 29.2 1.0 ND1 B:HIS118 4.1 19.5 1.0 O B:HOH46 4.2 24.6 1.0 O B:HOH202 4.2 33.5 1.0 CG B:HIS118 4.2 20.3 1.0 CB B:CYS123 4.4 16.3 1.0 ZN B:ZN1 4.5 19.0 1.0 CA B:CYS177 4.5 21.0 1.0 C B:CYS177 4.6 21.1 1.0 O B:HOH253 4.7 31.2 1.0 O B:CYS151 4.8 25.9 1.0 C B:CYS151 4.8 25.6 1.0 O B:HOH43 4.8 29.4 1.0 O B:CYS177 4.8 21.0 1.0 N B:CYS151 4.8 25.5 1.0 C B:CYS189 5.0 29.3 1.0

Zinc binding site 6 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:38.1 occ:1.00 ND1 B:HIS157 2.0 36.1 1.0 SG B:CYS136 2.2 34.3 1.0 SG B:CYS139 2.3 37.7 1.0 ND1 B:HIS160 2.4 44.4 1.0 CE1 B:HIS157 2.8 36.2 1.0 CG B:HIS157 3.1 37.4 1.0 CE1 B:HIS160 3.1 44.7 1.0 CG B:HIS160 3.1 43.4 1.0 CB B:CYS139 3.3 38.0 1.0 CB B:CYS136 3.3 33.8 1.0 CB B:HIS160 3.6 42.4 1.0 CB B:HIS157 3.6 38.3 1.0 O B:ASP156 3.7 37.6 1.0 CA B:HIS157 3.8 38.7 1.0 N B:CYS139 3.9 38.0 1.0 NE2 B:HIS157 4.0 36.5 1.0 NE2 B:HIS160 4.0 44.8 1.0 CD2 B:HIS160 4.1 44.0 1.0 CD2 B:HIS157 4.1 36.9 1.0 CA B:CYS139 4.2 37.8 1.0 C B:ASP156 4.4 37.7 1.0 N B:HIS157 4.5 38.1 1.0 CB B:GLU138 4.7 38.3 1.0 C B:GLU138 4.7 38.1 1.0 CA B:CYS136 4.7 33.9 1.0

Zinc binding site 7 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:18.9 occ:1.00 SG D:CYS148 2.3 21.0 1.0 SG D:CYS123 2.3 18.8 1.0 SG D:CYS151 2.3 20.9 1.0 SG D:CYS175 2.4 20.7 1.0 CB D:CYS123 3.1 19.6 1.0 CB D:CYS175 3.1 20.9 1.0 CB D:CYS151 3.3 21.6 1.0 CB D:CYS148 3.4 20.7 1.0 O D:HOH373 4.0 43.3 1.0 N D:CYS148 4.0 20.4 1.0 CA D:CYS148 4.2 20.4 1.0 CB D:CYS177 4.2 22.3 1.0 N D:CYS151 4.4 22.1 1.0 ZN D:ZN2 4.4 21.2 1.0 CA D:CYS151 4.4 22.3 1.0 O D:HOH100 4.5 30.9 1.0 CA D:CYS123 4.6 19.9 1.0 CB D:ARG125 4.6 21.4 1.0 CA D:CYS175 4.6 21.4 1.0 C D:CYS148 4.8 20.5 1.0 O D:CYS148 4.8 20.7 1.0

Zinc binding site 8 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2 b:21.2 occ:1.00 NE2 D:HIS118 2.2 23.0 1.0 SG D:CYS177 2.3 23.1 1.0 SG D:CYS189 2.3 23.8 1.0 SG D:CYS151 2.4 20.9 1.0 CB D:CYS151 3.0 21.6 1.0 CD2 D:HIS118 3.1 24.7 1.0 CB D:CYS177 3.1 22.3 1.0 CE1 D:HIS118 3.2 24.6 1.0 CB D:CYS189 3.3 28.1 1.0 CA D:CYS151 3.8 22.3 1.0 O D:HOH90 4.2 21.9 1.0 CG D:HIS118 4.2 25.7 1.0 CA D:CYS189 4.2 28.6 1.0 ND1 D:HIS118 4.3 26.2 1.0 CB D:CYS123 4.3 19.6 1.0 ZN D:ZN1 4.4 18.9 1.0 CA D:CYS177 4.5 22.6 1.0 O D:HOH406 4.6 44.7 1.0 O D:HOH99 4.6 23.5 1.0 C D:CYS177 4.7 23.7 1.0 C D:CYS151 4.8 23.1 1.0 O D:CYS151 4.8 23.1 1.0 N D:CYS151 4.8 22.1 1.0 O D:CYS177 4.9 23.0 1.0

Zinc binding site 9 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3 b:27.1 occ:1.00 ND1 D:HIS157 2.1 35.6 1.0 ND1 D:HIS160 2.1 33.5 1.0 SG D:CYS139 2.2 30.8 1.0 SG D:CYS136 2.2 28.5 1.0 CE1 D:HIS160 3.0 34.6 1.0 CE1 D:HIS157 3.1 35.9 1.0 CG D:HIS157 3.1 36.9 1.0 CG D:HIS160 3.1 33.7 1.0 CB D:CYS139 3.2 30.0 1.0 CB D:CYS136 3.3 26.4 1.0 CB D:HIS157 3.4 38.2 1.0 CB D:HIS160 3.5 34.0 1.0 CA D:HIS157 3.8 38.9 1.0 N D:CYS139 3.9 29.2 1.0 O D:ASP156 4.1 38.5 1.0 CA D:CYS139 4.1 30.4 1.0 NE2 D:HIS160 4.2 34.9 1.0 NE2 D:HIS157 4.2 34.6 1.0 CD2 D:HIS157 4.2 35.7 1.0 CD2 D:HIS160 4.2 33.8 1.0 CB D:GLU138 4.5 28.3 1.0 N D:HIS157 4.6 38.5 1.0 O D:HOH274 4.6 34.9 1.0 C D:ASP156 4.6 38.4 1.0 CA D:CYS136 4.7 26.7 1.0 C D:GLU138 4.8 28.6 1.0 C D:HIS157 5.0 39.2 1.0

Zinc binding site 10 out of 12 in the The Structure of Ubr Box (Rdaa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure of Ubr Box (Rdaa) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1 b:18.0 occ:1.00 SG F:CYS175 2.3 22.0 1.0 SG F:CYS123 2.3 17.9 1.0 SG F:CYS151 2.4 19.1 1.0 SG F:CYS148 2.4 18.8 1.0 CB F:CYS123 3.1 18.4 1.0 CB F:CYS175 3.2 23.1 1.0 CB F:CYS151 3.3 20.7 1.0 CB F:CYS148 3.4 19.7 1.0 N F:CYS148 3.9 20.5 1.0 O F:HOH79 4.0 26.1 1.0 CA F:CYS148 4.2 19.8 1.0 CB F:CYS177 4.3 25.8 1.0 N F:CYS151 4.4 19.7 1.0 ZN F:ZN2 4.4 22.5 1.0 CA F:CYS151 4.4 20.8 1.0 CA F:CYS123 4.5 18.6 1.0 CB F:ARG125 4.6 18.0 1.0 CA F:CYS175 4.7 23.9 1.0 O F:CYS148 4.8 19.9 1.0 C F:CYS148 4.8 19.6 1.0 NE2 F:HIS118 5.0 21.7 1.0

W.S.Choi, B.-C.Jeong, Y.J.Joo, M.-R.Lee, J.Kim, M.J.Eck, H.K.Song. Structural Basis For the Recognition of N-End Rule Substrates By the Ubr Box of Ubiquitin Ligases Nat.Struct.Mol.Biol. V. 17 1175 2010.
ISSN: ISSN 1545-9993
PubMed: 20835240
DOI: 10.1038/NSMB.1907