Zinc in PDB 6y3j: Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose

Enzymatic activity of Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose

All present enzymatic activity of Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose:
2.3.2.27;

Protein crystallography data

The structure of Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose, PDB code: 6y3j was solved by M.Gabrielssen, L.Buetow, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.44 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.933, 104.933, 74.544, 90.00, 90.00, 120.00
R / Rfree (%) 23.8 / 28.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose (pdb code 6y3j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose, PDB code: 6y3j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6y3j

Go back to Zinc Binding Sites List in 6y3j
Zinc binding site 1 out of 2 in the Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:57.9
occ:1.00
ND1 A:HIS447 1.9 59.2 1.0
SG A:CYS469 2.4 55.1 1.0
SG A:CYS445 2.4 69.5 1.0
SG A:CYS472 2.6 63.8 1.0
CE1 A:HIS447 2.8 59.8 1.0
CB A:CYS445 2.9 60.4 1.0
OG A:SER471 3.0 57.8 1.0
CG A:HIS447 3.0 71.0 1.0
CB A:CYS469 3.4 53.5 1.0
CB A:HIS447 3.4 59.8 1.0
CB A:CYS472 3.6 63.4 1.0
N A:CYS472 3.9 64.3 1.0
NE2 A:HIS447 3.9 61.1 1.0
CD2 A:HIS447 4.0 71.8 1.0
O A:CYS445 4.1 61.4 1.0
CA A:CYS445 4.1 58.5 1.0
C A:CYS445 4.2 65.7 1.0
CA A:CYS472 4.3 58.1 1.0
CB A:SER471 4.3 57.9 1.0
N A:HIS447 4.4 64.8 1.0
OG1 A:THR474 4.5 53.8 1.0
CD1 A:LEU442 4.5 55.4 1.0
CA A:HIS447 4.5 61.0 1.0
CA A:CYS469 4.8 52.4 1.0
C A:SER471 4.9 63.3 1.0
N A:SER471 5.0 55.3 1.0
CA A:SER471 5.0 64.6 1.0
N A:SER446 5.0 74.3 1.0
C A:CYS472 5.0 57.3 1.0

Zinc binding site 2 out of 2 in 6y3j

Go back to Zinc Binding Sites List in 6y3j
Zinc binding site 2 out of 2 in the Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ring-Dtc Domains of Deltex 2, Bound to Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:64.1
occ:1.00
SG A:CYS453 2.1 58.9 1.0
ND1 A:HIS450 2.2 64.2 1.0
SG A:CYS415 2.3 62.5 1.0
SG A:CYS412 2.3 73.6 1.0
CB A:CYS415 3.0 60.9 1.0
CG A:HIS450 3.0 62.9 1.0
CB A:HIS450 3.1 61.4 1.0
CB A:CYS453 3.2 57.5 1.0
CE1 A:HIS450 3.3 68.5 1.0
CB A:CYS412 3.4 84.4 1.0
N A:CYS415 3.6 76.2 1.0
CA A:CYS415 3.9 82.4 1.0
N A:HIS450 4.1 73.5 1.0
CD2 A:HIS450 4.2 66.1 1.0
CA A:HIS450 4.2 61.2 1.0
NE2 A:HIS450 4.3 69.2 1.0
CB A:SER423 4.3 62.1 1.0
CA A:SER423 4.3 63.5 1.0
OG A:SER423 4.3 60.9 1.0
CA A:CYS453 4.5 56.4 1.0
N A:GLY424 4.6 63.2 1.0
C A:ILE414 4.6 74.9 1.0
CB A:ILE414 4.6 62.3 1.0
O A:HIS450 4.6 58.5 1.0
C A:CYS415 4.8 86.6 1.0
N A:CYS453 4.8 71.2 1.0
CA A:CYS412 4.8 90.0 1.0
N A:ILE414 4.9 72.2 1.0
CA A:ILE414 4.9 69.1 1.0
O A:CYS412 5.0 90.6 1.0
C A:HIS450 5.0 59.6 1.0

Reference:

S.F.Ahmed, L.Buetow, M.Gabrielsen, S.Lilla, C.Chatrin, G.J.Sibbet, S.Zanivan, D.T.Huang. DELTEX2 C-Terminal Domain Recognizes and Recruits Adp-Ribosylated Proteins For Ubiquitination. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 32937373
DOI: 10.1126/SCIADV.ABC0629
Page generated: Wed Dec 16 13:13:58 2020

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