Atomistry » Zinc » PDB 3nik-3nny » 3nik
Atomistry »
  Zinc »
    PDB 3nik-3nny »
      3nik »

Zinc in PDB 3nik: The Structure of Ubr Box (Reaa)

Protein crystallography data

The structure of The Structure of Ubr Box (Reaa), PDB code: 3nik 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) 38.57 / 1.85
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 44.534, 44.534, 139.636, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 24.3

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the The Structure of Ubr Box (Reaa) (pdb code 3nik). 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 (Reaa), PDB code: 3nik:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 1 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:16.2
occ:1.00
SG A:CYS175 2.3 17.3 1.0
SG A:CYS148 2.3 19.3 1.0
SG A:CYS123 2.4 17.7 1.0
SG A:CYS151 2.5 19.7 1.0
CB A:CYS175 3.0 16.4 1.0
CB A:CYS123 3.1 16.7 1.0
CB A:CYS151 3.3 20.0 1.0
CB A:CYS148 3.5 18.6 1.0
N A:CYS148 3.9 19.6 1.0
CB A:CYS177 4.2 17.4 1.0
CA A:CYS148 4.2 19.7 1.0
ZN A:ZN2 4.4 17.4 1.0
N A:CYS151 4.4 20.1 1.0
CA A:CYS175 4.4 17.5 1.0
CA A:CYS151 4.5 19.6 1.0
CB A:ARG125 4.5 19.8 1.0
CA A:CYS123 4.6 17.4 1.0
C A:CYS148 4.7 19.7 1.0
O D:HOH103 4.7 35.9 1.0
CB A:HIS150 4.8 21.5 1.0
O A:CYS148 4.8 19.5 1.0
C A:CYS175 4.9 17.9 1.0
NE2 A:HIS118 5.0 17.9 1.0

Zinc binding site 2 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 2 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:17.4
occ:1.00
NE2 A:HIS118 2.1 17.9 1.0
SG A:CYS151 2.3 19.7 1.0
SG A:CYS189 2.3 20.0 1.0
SG A:CYS177 2.3 18.2 1.0
CB A:CYS177 3.1 17.4 1.0
CD2 A:HIS118 3.1 18.8 1.0
CE1 A:HIS118 3.1 18.7 1.0
CB A:CYS151 3.1 20.0 1.0
CB A:CYS189 3.2 20.9 1.0
CA A:CYS151 3.9 19.6 1.0
CA A:CYS189 4.1 21.5 1.0
ND1 A:HIS118 4.2 19.6 1.0
CG A:HIS118 4.3 20.8 1.0
O A:HOH35 4.3 20.3 1.0
CB A:CYS123 4.4 16.7 1.0
ZN A:ZN1 4.4 16.2 1.0
O A:HOH228 4.4 27.7 1.0
CA A:CYS177 4.4 17.7 1.0
C A:CYS177 4.7 18.2 1.0
O A:HOH55 4.7 21.4 1.0
O A:CYS177 4.8 17.4 1.0
C A:CYS151 4.8 19.3 1.0
N A:CYS151 4.9 20.1 1.0
O A:CYS151 4.9 19.1 1.0
C A:CYS189 5.0 22.2 1.0

Zinc binding site 3 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 3 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:22.3
occ:1.00
ND1 A:HIS157 2.1 26.4 1.0
ND1 A:HIS160 2.2 27.5 1.0
SG A:CYS136 2.2 26.0 1.0
SG A:CYS139 2.4 26.5 1.0
CE1 A:HIS157 2.9 23.7 1.0
CE1 A:HIS160 3.1 27.7 1.0
CG A:HIS160 3.2 27.8 1.0
CG A:HIS157 3.2 25.2 1.0
CB A:CYS139 3.2 27.1 1.0
CB A:CYS136 3.4 25.2 1.0
CB A:HIS160 3.5 27.5 1.0
CB A:HIS157 3.7 25.3 1.0
N A:CYS139 3.8 27.2 1.0
O A:ASP156 3.9 25.1 1.0
CA A:HIS157 4.0 26.2 1.0
NE2 A:HIS157 4.1 22.2 1.0
CA A:CYS139 4.1 27.5 1.0
NE2 A:HIS160 4.2 27.6 1.0
CD2 A:HIS157 4.2 23.9 1.0
CD2 A:HIS160 4.3 27.5 1.0
CB A:GLU138 4.5 28.1 1.0
C A:ASP156 4.5 25.2 1.0
O A:HOH198 4.6 33.4 1.0
N A:HIS157 4.7 25.2 1.0
C A:GLU138 4.7 27.8 1.0
O A:HOH234 4.7 40.1 1.0
CA A:CYS136 4.8 25.7 1.0
CA A:GLU138 4.9 27.7 1.0

Zinc binding site 4 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 4 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:20.5
occ:1.00
SG B:CYS148 2.3 23.9 1.0
SG B:CYS175 2.3 21.4 1.0
SG B:CYS123 2.4 21.4 1.0
SG B:CYS151 2.4 25.4 1.0
CB B:CYS175 3.1 20.8 1.0
CB B:CYS123 3.1 21.3 1.0
CB B:CYS151 3.3 26.3 1.0
CB B:CYS148 3.5 22.6 1.0
N B:CYS148 3.9 22.6 1.0
CB B:CYS177 4.1 20.8 1.0
CA B:CYS148 4.2 22.7 1.0
N B:CYS151 4.3 26.8 1.0
ZN B:ZN2 4.4 24.6 1.0
CA B:CYS151 4.5 26.8 1.0
CA B:CYS175 4.5 20.9 1.0
CA B:CYS123 4.5 20.9 1.0
CB B:ARG125 4.6 23.4 1.0
O B:CYS148 4.7 21.8 1.0
C B:CYS148 4.8 22.6 1.0
NE2 B:HIS118 4.9 23.4 1.0
O B:HOH214 4.9 31.7 1.0
C B:CYS175 5.0 20.8 1.0

Zinc binding site 5 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 5 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:24.6
occ:1.00
NE2 B:HIS118 2.0 23.4 1.0
SG B:CYS177 2.2 23.0 1.0
SG B:CYS189 2.3 27.3 1.0
SG B:CYS151 2.4 25.4 1.0
CE1 B:HIS118 2.9 23.7 1.0
CB B:CYS151 3.0 26.3 1.0
CB B:CYS177 3.1 20.8 1.0
CD2 B:HIS118 3.2 24.3 1.0
CB B:CYS189 3.2 31.7 1.0
CA B:CYS151 3.8 26.8 1.0
O B:HOH214 4.0 31.7 1.0
ND1 B:HIS118 4.1 24.5 1.0
CA B:CYS189 4.1 32.4 1.0
O B:HOH41 4.2 30.1 1.0
CG B:HIS118 4.2 24.9 1.0
CB B:CYS123 4.3 21.3 1.0
ZN B:ZN1 4.4 20.5 1.0
CA B:CYS177 4.4 20.8 1.0
O B:HOH216 4.6 32.3 1.0
C B:CYS177 4.6 21.2 1.0
C B:CYS151 4.8 27.1 1.0
O B:CYS151 4.8 26.9 1.0
N B:CYS151 4.8 26.8 1.0
O B:CYS177 4.8 21.2 1.0
O B:HOH74 4.9 27.1 1.0

Zinc binding site 6 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 6 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:35.2
occ:1.00
ND1 B:HIS157 2.0 36.9 1.0
SG B:CYS136 2.3 30.6 1.0
ND1 B:HIS160 2.3 38.9 1.0
SG B:CYS139 2.4 35.0 1.0
CE1 B:HIS157 2.9 36.2 1.0
CE1 B:HIS160 3.0 39.5 1.0
CG B:HIS160 3.1 39.7 1.0
CG B:HIS157 3.1 38.1 1.0
CB B:CYS139 3.2 33.1 1.0
CB B:CYS136 3.4 29.3 1.0
CB B:HIS160 3.6 39.2 1.0
CB B:HIS157 3.6 39.3 1.0
O B:ASP156 3.6 39.5 1.0
CA B:HIS157 3.9 39.8 1.0
N B:CYS139 3.9 33.4 1.0
NE2 B:HIS160 4.0 39.4 1.0
CD2 B:HIS160 4.0 39.5 1.0
NE2 B:HIS157 4.1 34.8 1.0
CA B:CYS139 4.1 33.2 1.0
CD2 B:HIS157 4.2 36.1 1.0
C B:ASP156 4.3 39.6 1.0
N B:HIS157 4.5 39.7 1.0
CB B:GLU138 4.5 34.3 1.0
CA B:CYS136 4.8 29.9 1.0
C B:GLU138 4.8 33.8 1.0

Zinc binding site 7 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 7 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:18.5
occ:1.00
SG D:CYS175 2.3 19.5 1.0
SG D:CYS123 2.3 18.1 1.0
SG D:CYS148 2.4 20.4 1.0
SG D:CYS151 2.4 21.5 1.0
CB D:CYS123 3.1 18.1 1.0
CB D:CYS175 3.1 19.5 1.0
CB D:CYS151 3.3 21.6 1.0
CB D:CYS148 3.4 18.6 1.0
N D:CYS148 3.9 19.3 1.0
O D:HOH84 4.0 35.9 1.0
CA D:CYS148 4.2 19.1 1.0
CB D:CYS177 4.2 21.4 1.0
N D:CYS151 4.4 21.6 1.0
ZN D:ZN2 4.4 21.6 1.0
CA D:CYS151 4.4 21.7 1.0
CA D:CYS123 4.5 19.0 1.0
CA D:CYS175 4.6 19.8 1.0
CB D:ARG125 4.6 18.6 1.0
O D:HOH107 4.7 39.8 1.0
C D:CYS148 4.8 19.3 1.0
O D:CYS148 4.8 19.1 1.0

Zinc binding site 8 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 8 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:21.6
occ:1.00
NE2 D:HIS118 2.1 21.8 1.0
SG D:CYS189 2.3 25.2 1.0
SG D:CYS151 2.3 21.5 1.0
SG D:CYS177 2.4 23.3 1.0
CD2 D:HIS118 3.0 25.1 1.0
CB D:CYS151 3.1 21.6 1.0
CB D:CYS177 3.1 21.4 1.0
CE1 D:HIS118 3.2 23.9 1.0
CB D:CYS189 3.2 29.7 1.0
CA D:CYS151 3.8 21.7 1.0
O D:HOH430 4.0 32.0 1.0
CG D:HIS118 4.2 25.6 1.0
CA D:CYS189 4.2 29.7 1.0
ND1 D:HIS118 4.2 23.6 1.0
CB D:CYS123 4.3 18.1 1.0
O D:HOH324 4.3 26.4 1.0
ZN D:ZN1 4.4 18.5 1.0
CA D:CYS177 4.5 22.1 1.0
O D:HOH91 4.7 19.3 1.0
C D:CYS177 4.7 22.7 1.0
C D:CYS151 4.7 21.9 1.0
O D:CYS151 4.7 21.4 1.0
N D:CYS151 4.8 21.6 1.0
O D:CYS177 4.9 23.2 1.0
O D:HOH376 5.0 43.1 1.0

Zinc binding site 9 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 9 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn3

b:26.1
occ:1.00
ND1 D:HIS157 2.1 27.0 1.0
SG D:CYS136 2.2 25.5 1.0
ND1 D:HIS160 2.2 30.3 1.0
SG D:CYS139 2.3 29.5 1.0
CE1 D:HIS157 2.9 27.3 1.0
CE1 D:HIS160 3.1 31.7 1.0
CG D:HIS157 3.2 28.8 1.0
CG D:HIS160 3.2 30.2 1.0
CB D:CYS139 3.2 29.0 1.0
CB D:CYS136 3.3 25.3 1.0
CB D:HIS160 3.5 30.2 1.0
CB D:HIS157 3.6 30.4 1.0
N D:CYS139 3.9 28.7 1.0
O D:ASP156 4.0 31.1 1.0
CA D:HIS157 4.0 31.1 1.0
NE2 D:HIS157 4.1 25.8 1.0
CA D:CYS139 4.2 29.1 1.0
NE2 D:HIS160 4.2 30.1 1.0
CD2 D:HIS157 4.2 27.3 1.0
CD2 D:HIS160 4.3 29.8 1.0
C D:ASP156 4.6 31.0 1.0
CB D:GLU138 4.6 29.2 1.0
N D:HIS157 4.7 30.9 1.0
CA D:CYS136 4.8 25.2 1.0
C D:GLU138 4.8 28.9 1.0

Zinc binding site 10 out of 12 in 3nik

Go back to Zinc Binding Sites List in 3nik
Zinc binding site 10 out of 12 in the The Structure of Ubr Box (Reaa)


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 (Reaa) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1

b:19.1
occ:1.00
SG F:CYS175 2.2 22.9 1.0
SG F:CYS123 2.3 20.3 1.0
SG F:CYS151 2.3 21.0 1.0
SG F:CYS148 2.4 20.4 1.0
CB F:CYS175 3.1 24.1 1.0
CB F:CYS123 3.1 21.1 1.0
CB F:CYS151 3.3 20.4 1.0
CB F:CYS148 3.4 20.1 1.0
N F:CYS148 4.0 20.6 1.0
O F:HOH242 4.0 39.2 1.0
CB F:CYS177 4.2 24.0 1.0
CA F:CYS148 4.2 20.1 1.0
N F:CYS151 4.4 20.4 1.0
ZN F:ZN2 4.4 20.0 1.0
CA F:CYS151 4.5 20.2 1.0
CA F:CYS175 4.5 24.5 1.0
CA F:CYS123 4.6 21.5 1.0
CB F:ARG125 4.7 23.1 1.0
O F:CYS148 4.8 19.1 1.0
O F:HOH214 4.8 0.3 1.0
C F:CYS148 4.8 19.9 1.0

Reference:

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
Page generated: Sat Oct 26 10:19:26 2024

Last articles

Ba in 5FK1
Ba in 4Y1I
Ba in 5EBI
Ba in 5E1J
Ba in 5EW7
Ba in 5ET9
Ba in 5ET2
Ba in 4ZWU
Ba in 5CQC
Ba in 4ZWP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy