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Zinc in PDB 5d0k: Structure of UBE2D2:RNF165:Ub Complex

Enzymatic activity of Structure of UBE2D2:RNF165:Ub Complex

All present enzymatic activity of Structure of UBE2D2:RNF165:Ub Complex:
6.3.2.19;

Protein crystallography data

The structure of Structure of UBE2D2:RNF165:Ub Complex, PDB code: 5d0k was solved by J.D.Wright, C.L.Day, P.D.Mace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.70 / 2.65
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 113.046, 113.046, 135.667, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of UBE2D2:RNF165:Ub Complex (pdb code 5d0k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of UBE2D2:RNF165:Ub Complex, PDB code: 5d0k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5d0k

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Zinc binding site 1 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:71.1
occ:1.00
 ND1 C:HIS314 2.1 55.7 1.0
SG C:CYS331 2.3 60.2 1.0
SG C:CYS312 2.3 0.9 1.0
SG C:CYS334 2.3 59.5 1.0
CE1 C:HIS314 3.0 59.7 1.0
CB C:CYS312 3.1 52.5 1.0
CG C:HIS314 3.1 54.2 1.0
CB C:CYS331 3.1 52.8 1.0
CB C:HIS314 3.5 52.1 1.0
CB C:CYS334 3.6 49.4 1.0
N C:CYS334 3.6 55.6 1.0
NE2 C:HIS314 4.1 49.6 1.0
CA C:CYS334 4.2 49.2 1.0
CB C:ILE333 4.2 62.4 1.0
CD2 C:HIS314 4.2 50.4 1.0
CA C:CYS312 4.5 66.6 1.0
CA C:CYS331 4.6 64.3 1.0
CG2 E:THR9 4.6 57.6 1.0
C C:ILE333 4.6 61.0 1.0
CA C:ILE333 4.7 65.0 1.0
N C:HIS314 4.7 59.5 1.0
CA C:HIS314 4.8 62.0 1.0
N C:ILE333 4.8 66.9 1.0
N C:ARG335 4.8 56.4 1.0
C C:CYS312 4.8 65.5 1.0
C C:CYS334 4.9 57.5 1.0
CG2 C:ILE333 4.9 48.9 1.0
O C:CYS312 5.0 67.1 1.0

Zinc binding site 2 out of 8 in 5d0k

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Zinc binding site 2 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:60.9
occ:0.73
 ND1 C:HIS317 2.1 75.2 1.0
SG C:CYS320 2.3 62.6 1.0
SG C:CYS297 2.3 85.7 1.0
SG C:CYS294 2.3 74.7 1.0
CB C:CYS294 2.9 63.8 1.0
CG C:HIS317 3.0 78.6 1.0
CE1 C:HIS317 3.1 74.8 1.0
CB C:HIS317 3.2 63.7 1.0
CB C:CYS297 3.3 60.9 1.0
CB C:CYS320 3.3 81.9 1.0
N C:CYS297 3.8 60.8 1.0
CA C:CYS297 4.1 70.5 1.0
CD2 C:HIS317 4.1 75.8 1.0
NE2 C:HIS317 4.1 75.6 1.0
N C:HIS317 4.2 68.1 1.0
CA C:CYS294 4.3 67.1 1.0
CA C:HIS317 4.4 66.5 1.0
CA C:CYS320 4.7 77.2 1.0
O C:CYS294 4.7 68.9 1.0
C C:CYS294 4.7 68.3 1.0
CB C:ILE296 4.8 72.4 1.0
C C:ILE296 4.9 61.5 1.0
N C:LEU298 5.0 79.7 1.0
C C:CYS297 5.0 76.9 1.0

Zinc binding site 3 out of 8 in 5d0k

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Zinc binding site 3 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:46.5
occ:0.65
 ND1 F:HIS314 2.0 56.6 1.0
SG F:CYS334 2.3 54.6 1.0
SG F:CYS312 2.3 54.6 1.0
SG F:CYS331 2.4 55.9 1.0
CE1 F:HIS314 2.9 56.5 1.0
CG F:HIS314 3.1 51.2 1.0
CB F:CYS331 3.1 63.5 1.0
CB F:CYS312 3.3 64.4 1.0
CB F:CYS334 3.4 58.5 1.0
CB F:HIS314 3.5 47.9 1.0
N F:CYS334 3.5 58.3 1.0
CA F:CYS334 4.0 57.5 1.0
NE2 F:HIS314 4.1 54.5 1.0
CD2 F:HIS314 4.1 48.9 1.0
CB F:ILE333 4.2 57.5 1.0
C F:ILE333 4.6 56.9 1.0
CA F:CYS331 4.6 67.9 1.0
CG2 B:THR9 4.6 55.8 1.0
CA F:CYS312 4.6 62.6 1.0
N F:ILE333 4.7 60.8 1.0
CA F:ILE333 4.7 58.6 1.0
N F:ARG335 4.7 58.5 1.0
CA F:HIS314 4.7 57.7 1.0
N F:HIS314 4.8 55.8 1.0
C F:CYS334 4.8 57.7 1.0
C F:CYS312 4.9 63.6 1.0
O F:CYS312 4.9 77.0 1.0

Zinc binding site 4 out of 8 in 5d0k

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Zinc binding site 4 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:92.3
occ:1.00
 ND1 F:HIS317 2.1 79.6 1.0
SG F:CYS294 2.3 77.2 1.0
SG F:CYS297 2.4 88.9 1.0
SG F:CYS320 2.4 66.0 1.0
CB F:CYS294 2.8 59.6 1.0
CG F:HIS317 3.0 72.8 1.0
CE1 F:HIS317 3.1 77.6 1.0
CB F:CYS297 3.2 56.1 1.0
CB F:HIS317 3.3 59.1 1.0
CB F:CYS320 3.4 85.7 1.0
N F:CYS297 3.8 68.0 1.0
CA F:CYS297 4.1 69.9 1.0
NE2 F:HIS317 4.2 72.9 1.0
CD2 F:HIS317 4.2 70.7 1.0
N F:HIS317 4.2 65.8 1.0
CA F:CYS294 4.3 66.2 1.0
CA F:HIS317 4.4 62.1 1.0
O F:CYS294 4.5 60.2 1.0
C F:CYS294 4.6 69.3 1.0
CA F:CYS320 4.8 77.8 1.0
C F:CYS297 4.9 73.3 1.0
N F:LEU298 4.9 78.1 1.0
C F:ILE296 4.9 63.0 1.0
CB F:ILE296 4.9 66.1 1.0

Zinc binding site 5 out of 8 in 5d0k

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Zinc binding site 5 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn401

b:49.5
occ:0.71
 ND1 I:HIS314 2.1 56.4 1.0
SG I:CYS331 2.3 59.8 1.0
SG I:CYS334 2.3 54.1 1.0
SG I:CYS312 2.4 69.5 1.0
CE1 I:HIS314 3.0 56.7 1.0
CG I:HIS314 3.1 55.8 1.0
CB I:CYS331 3.2 58.9 1.0
CB I:CYS312 3.3 64.2 1.0
CB I:CYS334 3.4 51.0 1.0
CB I:HIS314 3.5 50.5 1.0
N I:CYS334 3.6 58.8 1.0
CA I:CYS334 4.1 54.8 1.0
NE2 I:HIS314 4.1 51.7 1.0
CD2 I:HIS314 4.2 52.0 1.0
CB I:ILE333 4.2 56.9 1.0
CG2 K:THR9 4.6 55.1 1.0
CA I:CYS331 4.6 66.8 1.0
C I:ILE333 4.6 56.2 1.0
CA I:CYS312 4.6 61.9 1.0
O I:CYS312 4.7 67.1 1.0
CA I:HIS314 4.7 52.6 1.0
N I:HIS314 4.7 53.5 1.0
N I:ILE333 4.8 63.0 1.0
CA I:ILE333 4.8 58.4 1.0
C I:CYS312 4.8 63.3 1.0
C I:CYS334 4.8 62.3 1.0
N I:ARG335 4.9 61.6 1.0
CG2 I:ILE333 5.0 48.0 1.0

Zinc binding site 6 out of 8 in 5d0k

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Zinc binding site 6 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn402

b:58.7
occ:0.71
 ND1 I:HIS317 2.1 77.8 1.0
SG I:CYS294 2.3 76.7 1.0
SG I:CYS297 2.4 80.3 1.0
SG I:CYS320 2.4 63.6 1.0
CG I:HIS317 2.9 74.2 1.0
CB I:CYS294 3.0 59.0 1.0
CB I:HIS317 3.1 65.3 1.0
CE1 I:HIS317 3.2 80.1 1.0
CB I:CYS320 3.3 80.0 1.0
CB I:CYS297 3.4 63.1 1.0
N I:CYS297 4.0 63.0 1.0
CD2 I:HIS317 4.1 72.3 1.0
N I:HIS317 4.2 70.3 1.0
NE2 I:HIS317 4.2 77.0 1.0
CA I:HIS317 4.2 68.4 1.0
CA I:CYS297 4.3 71.6 1.0
CA I:CYS294 4.4 63.5 1.0
CA I:CYS320 4.7 75.5 1.0
O I:CYS294 4.8 60.6 1.0
C I:CYS294 4.8 66.8 1.0
CB I:ILE296 5.0 67.4 1.0

Zinc binding site 7 out of 8 in 5d0k

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Zinc binding site 7 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn401

b:0.2
occ:1.00
 ND1 L:HIS314 2.1 67.2 1.0
SG L:CYS312 2.3 73.8 1.0
SG L:CYS331 2.3 55.4 1.0
SG L:CYS334 2.4 57.6 1.0
CE1 L:HIS314 3.0 65.5 1.0
CG L:HIS314 3.1 61.3 1.0
CB L:CYS331 3.1 52.2 1.0
CB L:CYS312 3.4 51.3 1.0
CB L:HIS314 3.4 51.3 1.0
CB L:CYS334 4.0 61.4 1.0
N L:CYS334 4.0 55.7 1.0
NE2 L:HIS314 4.1 49.8 1.0
CD2 L:HIS314 4.2 50.4 1.0
CB L:ILE333 4.3 57.4 1.0
N L:HIS314 4.5 51.9 1.0
CA L:HIS314 4.6 55.6 1.0
CA L:CYS312 4.6 61.3 1.0
CG2 H:THR9 4.6 50.0 1.0
CA L:CYS334 4.6 53.4 1.0
CA L:CYS331 4.6 60.9 1.0
C L:CYS312 4.7 58.1 1.0
O L:CYS312 4.7 53.4 1.0
C L:ILE333 4.9 59.6 1.0
CA L:ILE333 4.9 61.7 1.0
N L:ILE333 5.0 64.4 1.0
N L:CYS312 5.0 59.3 1.0

Zinc binding site 8 out of 8 in 5d0k

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Zinc binding site 8 out of 8 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn402

b:59.3
occ:0.72
 ND1 L:HIS317 2.1 77.2 1.0
SG L:CYS320 2.3 63.5 1.0
SG L:CYS294 2.3 72.0 1.0
SG L:CYS297 2.3 76.3 1.0
CG L:HIS317 3.0 74.1 1.0
CE1 L:HIS317 3.1 78.7 1.0
CB L:CYS294 3.1 67.0 1.0
CB L:CYS320 3.3 83.0 1.0
CB L:HIS317 3.3 69.8 1.0
CB L:CYS297 3.7 59.0 1.0
N L:CYS297 4.0 64.4 1.0
NE2 L:HIS317 4.2 78.6 1.0
CD2 L:HIS317 4.2 74.3 1.0
N L:HIS317 4.2 73.5 1.0
CA L:HIS317 4.4 69.6 1.0
CA L:CYS297 4.4 72.1 1.0
CA L:CYS294 4.5 65.9 1.0
CA L:CYS320 4.7 83.4 1.0
O L:CYS294 4.8 66.2 1.0
CB L:ILE296 4.8 64.9 1.0
C L:CYS294 4.9 73.1 1.0
C L:ILE296 5.0 64.8 1.0

Reference:

J.D.Wright, P.D.Mace, C.L.Day. Secondary Ubiquitin-Ring Docking Enhances Arkadia and ARK2C E3 Ligase Activity. Nat.Struct.Mol.Biol. V. 23 45 2016.
ISSN: ESSN 1545-9985
PubMed: 26656854
DOI: 10.1038/NSMB.3142
Page generated: Sun Oct 27 14:31:48 2024

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