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Zinc in PDB 3ny2: Structure of the Ubr-Box of UBR2 Ubiquitin Ligase

Protein crystallography data

The structure of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase, PDB code: 3ny2 was solved by E.Matta-Camacho, G.Kozlov, F.Li, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.61
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 29.390, 61.456, 72.806, 65.05, 89.98, 90.01
R / Rfree (%) 23 / 28.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase (pdb code 3ny2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase, PDB code: 3ny2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 3ny2

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Zinc binding site 1 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:18.6
occ:1.00
SG A:CYS99 2.1 35.2 1.0
SG A:CYS127 2.4 22.9 1.0
SG A:CYS124 2.5 27.8 1.0
SG A:CYS149 2.5 31.6 1.0
CB A:CYS149 3.2 31.5 1.0
CB A:CYS99 3.3 35.2 1.0
CB A:CYS124 3.4 27.1 1.0
CB A:CYS127 3.5 24.7 1.0
N A:CYS124 4.2 27.1 1.0
CA A:CYS124 4.3 27.5 1.0
CE1 A:HIS166 4.4 34.5 1.0
CB A:CYS151 4.4 32.5 1.0
ZN A:ZN2 4.6 35.0 1.0
N A:CYS127 4.6 25.7 1.0
CB A:ARG101 4.6 35.9 1.0
CA A:CYS149 4.6 31.5 1.0
CA A:CYS127 4.7 24.8 1.0
CA A:CYS99 4.7 35.0 1.0
C A:CYS124 4.9 27.8 1.0
ND1 A:HIS166 5.0 34.3 1.0
CD A:ARG101 5.0 36.9 1.0

Zinc binding site 2 out of 24 in 3ny2

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Zinc binding site 2 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:35.0
occ:1.00
SG A:CYS163 1.9 29.4 1.0
ND1 A:HIS166 2.0 34.3 1.0
SG A:CYS151 2.2 32.1 1.0
SG A:CYS127 2.6 22.9 1.0
CE1 A:HIS166 2.8 34.5 1.0
CG A:HIS166 3.1 34.7 1.0
CB A:CYS151 3.3 32.5 1.0
CB A:CYS163 3.3 31.4 1.0
CB A:CYS127 3.3 24.7 1.0
CB A:HIS166 3.5 34.8 1.0
CA A:CYS127 4.0 24.8 1.0
NE2 A:HIS166 4.0 34.6 1.0
N A:CYS163 4.1 31.5 1.0
CD2 A:HIS166 4.1 34.8 1.0
CA A:CYS163 4.2 31.6 1.0
N A:HIS166 4.3 34.5 1.0
CB A:CYS99 4.5 35.2 1.0
CA A:HIS166 4.6 34.8 1.0
ZN A:ZN1 4.6 18.6 1.0
CA A:CYS151 4.7 32.4 1.0
C A:CYS163 4.8 31.9 1.0
CB A:LYS165 4.8 34.1 1.0
SG A:CYS99 4.9 35.2 1.0
N A:CYS127 4.9 25.7 1.0
O A:CYS163 4.9 32.0 1.0

Zinc binding site 3 out of 24 in 3ny2

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Zinc binding site 3 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:33.6
occ:1.00
ND1 A:HIS136 2.1 37.5 1.0
ND1 A:HIS133 2.1 28.1 1.0
SG A:CYS112 2.2 32.3 1.0
SG A:CYS115 2.3 32.6 1.0
CE1 A:HIS136 2.8 37.4 1.0
CG A:HIS136 3.0 36.8 1.0
CE1 A:HIS133 3.1 27.1 1.0
CG A:HIS133 3.2 29.2 1.0
CB A:CYS115 3.3 33.3 1.0
CB A:CYS112 3.4 31.8 1.0
CB A:HIS136 3.5 36.0 1.0
CB A:HIS133 3.5 30.1 1.0
NE2 A:HIS136 3.7 37.8 1.0
CA A:HIS133 3.8 30.6 1.0
CD2 A:HIS136 3.8 37.4 1.0
N A:CYS115 4.0 33.4 1.0
NE2 A:HIS133 4.2 27.5 1.0
CB A:ASP114 4.2 33.4 1.0
CD2 A:HIS133 4.3 27.8 1.0
CA A:CYS115 4.3 33.2 1.0
N A:HIS133 4.6 30.1 1.0
CD1 A:ILE132 4.7 29.2 1.0
C A:ASP114 4.8 33.6 1.0
CA A:CYS112 4.8 32.0 1.0
O A:HIS133 4.8 31.7 1.0
OD1 A:ASP114 4.8 33.4 1.0
C A:HIS133 4.8 31.5 1.0
CA A:ASP114 5.0 33.5 1.0

Zinc binding site 4 out of 24 in 3ny2

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Zinc binding site 4 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:22.6
occ:1.00
SG B:CYS99 2.2 34.2 1.0
SG B:CYS149 2.3 29.7 1.0
SG B:CYS124 2.4 26.0 1.0
SG B:CYS127 2.5 23.7 1.0
CB B:CYS99 3.1 34.7 1.0
CB B:CYS149 3.1 31.2 1.0
CB B:CYS127 3.4 24.7 1.0
CB B:CYS124 3.6 27.3 1.0
CB B:CYS151 4.1 32.3 1.0
N B:CYS124 4.2 27.2 1.0
CE1 B:HIS166 4.3 30.8 1.0
ZN B:ZN5 4.4 27.1 1.0
CA B:CYS124 4.5 27.4 1.0
CA B:CYS99 4.6 34.9 1.0
N B:CYS127 4.6 25.5 1.0
CA B:CYS127 4.6 24.7 1.0
CA B:CYS149 4.6 31.4 1.0
ND1 B:HIS166 4.8 31.6 1.0
CB B:ARG101 4.9 36.0 1.0
NE B:ARG101 5.0 37.9 1.0

Zinc binding site 5 out of 24 in 3ny2

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Zinc binding site 5 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:27.1
occ:1.00
SG B:CYS151 2.1 31.2 1.0
ND1 B:HIS166 2.2 31.6 1.0
SG B:CYS163 2.2 31.3 1.0
SG B:CYS127 2.3 23.7 1.0
CE1 B:HIS166 3.0 30.8 1.0
CB B:CYS151 3.2 32.3 1.0
CG B:HIS166 3.2 32.9 1.0
CB B:CYS127 3.3 24.7 1.0
CB B:CYS163 3.3 31.6 1.0
CB B:HIS166 3.6 34.1 1.0
N B:CYS163 4.0 31.5 1.0
CA B:CYS127 4.0 24.7 1.0
CA B:CYS163 4.2 31.7 1.0
NE2 B:HIS166 4.2 31.3 1.0
N B:HIS166 4.3 34.3 1.0
CD2 B:HIS166 4.3 31.9 1.0
ZN B:ZN4 4.4 22.6 1.0
CB B:CYS99 4.5 34.7 1.0
CA B:CYS151 4.6 32.4 1.0
CA B:HIS166 4.6 34.6 1.0
C B:CYS163 4.7 32.0 1.0
CB B:LYS165 4.8 33.5 1.0
O B:CYS163 4.9 32.1 1.0
N B:CYS127 4.9 25.5 1.0
SG B:CYS99 5.0 34.2 1.0
C B:CYS151 5.0 32.9 1.0
C B:CYS127 5.0 24.7 1.0

Zinc binding site 6 out of 24 in 3ny2

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Zinc binding site 6 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:30.9
occ:1.00
ND1 B:HIS136 2.1 34.5 1.0
ND1 B:HIS133 2.2 27.7 1.0
SG B:CYS115 2.3 33.5 1.0
SG B:CYS112 2.4 31.5 1.0
CE1 B:HIS136 2.9 34.5 1.0
CG B:HIS136 3.1 34.8 1.0
CG B:HIS133 3.2 29.0 1.0
CE1 B:HIS133 3.2 26.7 1.0
CB B:CYS115 3.3 33.3 1.0
CB B:HIS133 3.4 30.0 1.0
CB B:CYS112 3.4 31.9 1.0
CB B:HIS136 3.5 35.4 1.0
CA B:HIS133 3.7 30.5 1.0
NE2 B:HIS136 4.0 33.9 1.0
N B:CYS115 4.1 33.5 1.0
CD2 B:HIS136 4.1 34.1 1.0
CB B:ASP114 4.2 33.3 1.0
NE2 B:HIS133 4.3 25.2 1.0
CD2 B:HIS133 4.3 26.8 1.0
CA B:CYS115 4.3 33.3 1.0
N B:HIS133 4.5 30.1 1.0
C B:HIS133 4.8 31.4 1.0
C B:ASP114 4.8 33.6 1.0
O B:HIS133 4.8 31.7 1.0
CA B:CYS112 4.9 32.0 1.0
CD1 B:ILE132 4.9 30.6 1.0
OD1 B:ASP114 5.0 32.7 1.0
CA B:ASP114 5.0 33.4 1.0

Zinc binding site 7 out of 24 in 3ny2

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Zinc binding site 7 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn7

b:23.6
occ:1.00
SG C:CYS149 2.1 30.6 1.0
SG C:CYS99 2.2 34.4 1.0
SG C:CYS127 2.4 23.3 1.0
SG C:CYS124 2.5 26.7 1.0
CB C:CYS149 3.1 31.2 1.0
CB C:CYS99 3.1 34.9 1.0
CB C:CYS127 3.5 24.7 1.0
CB C:CYS124 3.6 26.9 1.0
N C:CYS124 4.1 27.1 1.0
CB C:CYS151 4.2 32.3 1.0
CA C:CYS124 4.4 27.4 1.0
CE1 C:HIS166 4.4 33.4 1.0
ZN C:ZN8 4.5 30.9 1.0
CA C:CYS149 4.5 31.5 1.0
CA C:CYS99 4.6 34.9 1.0
CA C:CYS127 4.6 24.8 1.0
N C:CYS127 4.7 25.6 1.0
CB C:ARG101 4.8 35.9 1.0
ND1 C:HIS166 4.9 33.0 1.0
C C:CYS149 5.0 31.4 1.0

Zinc binding site 8 out of 24 in 3ny2

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Zinc binding site 8 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn8

b:30.9
occ:1.00
ND1 C:HIS166 2.1 33.0 1.0
SG C:CYS151 2.1 31.0 1.0
SG C:CYS163 2.3 29.5 1.0
SG C:CYS127 2.5 23.3 1.0
CE1 C:HIS166 3.0 33.4 1.0
CG C:HIS166 3.2 33.7 1.0
CB C:CYS151 3.2 32.3 1.0
CB C:CYS163 3.3 31.2 1.0
CB C:CYS127 3.3 24.7 1.0
CB C:HIS166 3.6 34.3 1.0
N C:CYS163 4.0 31.4 1.0
CA C:CYS127 4.0 24.8 1.0
NE2 C:HIS166 4.1 33.8 1.0
CA C:CYS163 4.2 31.5 1.0
CD2 C:HIS166 4.2 33.6 1.0
N C:HIS166 4.3 34.4 1.0
CB C:CYS99 4.5 34.9 1.0
ZN C:ZN7 4.5 23.6 1.0
CA C:CYS151 4.6 32.3 1.0
CA C:HIS166 4.6 34.7 1.0
C C:CYS163 4.8 31.9 1.0
O C:CYS163 4.9 32.0 1.0
C C:CYS151 5.0 32.9 1.0
SG C:CYS99 5.0 34.4 1.0

Zinc binding site 9 out of 24 in 3ny2

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Zinc binding site 9 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn9

b:32.1
occ:1.00
ND1 C:HIS136 2.0 36.3 1.0
ND1 C:HIS133 2.1 25.6 1.0
SG C:CYS112 2.3 31.8 1.0
SG C:CYS115 2.5 34.5 1.0
CE1 C:HIS136 2.7 35.9 1.0
CE1 C:HIS133 2.9 25.0 1.0
CB C:CYS115 3.1 33.6 1.0
CG C:HIS136 3.2 36.2 1.0
CG C:HIS133 3.2 27.9 1.0
CB C:CYS112 3.5 32.1 1.0
CB C:HIS133 3.7 29.9 1.0
CB C:HIS136 3.7 35.8 1.0
CA C:HIS133 3.9 30.5 1.0
N C:CYS115 3.9 33.5 1.0
NE2 C:HIS136 3.9 36.2 1.0
NE2 C:HIS133 4.1 25.7 1.0
CA C:CYS115 4.1 33.4 1.0
CD2 C:HIS136 4.2 36.3 1.0
CD2 C:HIS133 4.3 25.6 1.0
CB C:ASP114 4.4 33.5 1.0
OD1 C:ASP114 4.6 35.4 1.0
CD1 C:ILE132 4.6 27.1 1.0
N C:HIS133 4.7 30.0 1.0
C C:ASP114 4.7 33.7 1.0
CA C:CYS112 4.9 32.0 1.0
CG1 C:ILE132 5.0 27.7 1.0
CA C:ASP114 5.0 33.5 1.0

Zinc binding site 10 out of 24 in 3ny2

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Zinc binding site 10 out of 24 in the Structure of the Ubr-Box of UBR2 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Ubr-Box of UBR2 Ubiquitin Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn10

b:28.0
occ:1.00
SG D:CYS124 2.2 26.1 1.0
SG D:CYS99 2.3 34.0 1.0
SG D:CYS149 2.4 30.3 1.0
SG D:CYS127 2.4 23.3 1.0
CB D:CYS149 3.2 31.4 1.0
CB D:CYS99 3.3 34.9 1.0
CB D:CYS127 3.3 24.6 1.0
CB D:CYS124 3.6 27.1 1.0
N D:CYS124 4.1 27.1 1.0
CB D:CYS151 4.1 32.3 1.0
ZN D:ZN11 4.4 27.1 1.0
CA D:CYS124 4.4 27.4 1.0
N D:CYS127 4.4 25.6 1.0
CA D:CYS127 4.4 24.8 1.0
CE1 D:HIS166 4.5 32.8 1.0
CA D:CYS149 4.7 31.4 1.0
CA D:CYS99 4.7 34.9 1.0
O D:CYS124 4.8 27.9 1.0
C D:CYS124 4.9 27.7 1.0
CB D:ARG101 4.9 36.0 1.0
ND1 D:HIS166 4.9 33.4 1.0

Reference:

E.Matta-Camacho, G.Kozlov, F.F.Li, K.Gehring. Structural Basis of Substrate Recognition and Specificity in the N-End Rule Pathway. Nat.Struct.Mol.Biol. V. 17 1182 2010.
ISSN: ISSN 1545-9993
PubMed: 20835242
DOI: 10.1038/NSMB.1894
Page generated: Wed Dec 16 04:39:27 2020

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