Zinc in PDB 6y5p: Ring-Dtc Domain of DELTEX1 Bound to Nad

Enzymatic activity of Ring-Dtc Domain of DELTEX1 Bound to Nad

All present enzymatic activity of Ring-Dtc Domain of DELTEX1 Bound to Nad:
2.3.2.27;

Protein crystallography data

The structure of Ring-Dtc Domain of DELTEX1 Bound to Nad, PDB code: 6y5p was solved by M.Gabrielsen, L.Buetow, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.48 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.850, 85.254, 130.949, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Ring-Dtc Domain of DELTEX1 Bound to Nad (pdb code 6y5p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ring-Dtc Domain of DELTEX1 Bound to Nad, PDB code: 6y5p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6y5p

Go back to Zinc Binding Sites List in 6y5p
Zinc binding site 1 out of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn708

b:23.9
occ:1.00
ND1 A:HIS449 2.0 23.5 1.0
SG A:CYS452 2.3 24.1 1.0
SG A:CYS411 2.3 28.8 1.0
SG A:CYS414 2.3 23.5 1.0
HB3 A:CYS411 2.8 32.7 1.0
HB2 A:HIS449 2.9 27.8 1.0
CE1 A:HIS449 2.9 25.8 1.0
HB3 A:CYS414 3.0 28.5 1.0
H A:CYS414 3.0 29.4 1.0
CB A:CYS411 3.0 27.2 1.0
HE1 A:HIS449 3.1 31.0 1.0
CG A:HIS449 3.1 25.4 1.0
CB A:CYS414 3.2 23.7 1.0
HB2 A:CYS411 3.2 32.7 1.0
H A:HIS449 3.3 30.1 1.0
HB2 A:CYS452 3.3 29.3 1.0
CB A:CYS452 3.4 24.4 1.0
CB A:HIS449 3.5 23.1 1.0
HA A:SER422 3.5 30.4 1.0
HB3 A:CYS452 3.6 29.3 1.0
HG A:SER422 3.7 34.0 1.0
N A:CYS414 3.7 24.4 1.0
HB A:ILE413 3.8 25.6 1.0
H A:GLY423 3.8 35.1 1.0
HB2 A:CYS414 4.0 28.5 1.0
N A:HIS449 4.0 25.0 1.0
CA A:CYS414 4.1 24.5 1.0
NE2 A:HIS449 4.1 28.9 1.0
CD2 A:HIS449 4.2 27.1 1.0
HB2 A:SER422 4.2 29.6 1.0
HB3 A:HIS449 4.2 27.8 1.0
CA A:HIS449 4.3 22.2 1.0
CA A:SER422 4.4 25.3 1.0
H A:ILE413 4.4 29.6 1.0
OG A:SER422 4.4 28.2 1.0
H A:GLU416 4.5 32.4 1.0
CA A:CYS411 4.5 24.5 1.0
H A:CYS452 4.5 26.3 1.0
CB A:SER422 4.6 24.6 1.0
N A:GLY423 4.6 29.2 1.0
HB2 A:GLU416 4.6 37.5 1.0
H A:MET415 4.6 28.6 1.0
CB A:ILE413 4.7 21.3 1.0
CA A:CYS452 4.7 20.4 1.0
HD23 A:LEU418 4.8 36.8 1.0
O A:CYS411 4.8 29.4 1.0
HB3 A:TYR448 4.8 30.5 1.0
C A:ILE413 4.8 29.1 1.0
HA A:CYS414 4.8 29.4 1.0
HE2 A:HIS449 4.8 34.7 1.0
C A:CYS411 4.9 28.9 1.0
C A:CYS414 4.9 27.3 1.0
HA A:TYR448 4.9 25.4 1.0
HA A:CYS411 4.9 29.5 1.0
O A:GLU416 5.0 30.0 1.0
O A:HIS449 5.0 21.8 1.0
HA A:CYS452 5.0 24.6 1.0
N A:MET415 5.0 23.8 1.0
HD21 B:LEU590 5.0 34.3 1.0

Zinc binding site 2 out of 4 in 6y5p

Go back to Zinc Binding Sites List in 6y5p
Zinc binding site 2 out of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn709

b:26.2
occ:1.00
ND1 A:HIS446 2.0 27.7 1.0
SG A:CYS444 2.3 25.7 1.0
SG A:CYS468 2.3 24.8 1.0
SG A:CYS471 2.4 30.8 1.0
CE1 A:HIS446 2.9 27.8 1.0
HB2 A:CYS444 2.9 32.7 1.0
HE1 A:HIS446 3.0 33.4 1.0
HB2 A:HIS446 3.0 28.4 1.0
CG A:HIS446 3.1 24.0 1.0
CB A:CYS444 3.1 27.2 1.0
H A:CYS471 3.2 33.4 1.0
CB A:CYS468 3.2 20.2 1.0
HB3 A:CYS468 3.2 24.3 1.0
HB2 A:CYS468 3.2 24.3 1.0
HB3 A:CYS471 3.3 35.5 1.0
HB3 A:CYS444 3.4 32.7 1.0
CB A:CYS471 3.4 29.5 1.0
CB A:HIS446 3.5 23.6 1.0
HB A:THR470 3.6 32.1 1.0
H A:HIS446 3.7 28.4 1.0
N A:CYS471 3.8 27.8 1.0
HH A:TYR475 4.0 34.5 1.0
NE2 A:HIS446 4.0 32.1 1.0
HH A:TYR448 4.1 33.9 1.0
CD2 A:HIS446 4.1 33.1 1.0
HB3 A:HIS446 4.2 28.4 1.0
CA A:CYS471 4.2 28.5 1.0
HB2 A:CYS471 4.2 35.5 1.0
HB3 A:ALA473 4.3 34.8 1.0
HD23 A:LEU441 4.4 30.9 1.0
N A:HIS446 4.4 23.6 1.0
H A:THR470 4.5 30.5 1.0
H A:ALA473 4.5 31.9 1.0
CA A:CYS444 4.5 25.5 1.0
CB A:THR470 4.5 26.7 1.0
CA A:HIS446 4.6 26.2 1.0
CA A:CYS468 4.6 23.1 1.0
H A:LYS472 4.7 31.1 1.0
O A:HOH1046 4.7 45.3 1.0
HG22 A:THR470 4.7 44.2 1.0
C A:CYS444 4.8 24.0 1.0
HE2 A:TYR475 4.8 32.1 1.0
HE2 A:HIS446 4.8 38.6 1.0
OH A:TYR475 4.8 28.7 1.0
C A:THR470 4.8 32.7 1.0
OH A:TYR448 4.8 28.2 1.0
C A:CYS471 4.9 29.5 1.0
H A:CYS444 4.9 30.4 1.0
HA A:CYS468 4.9 27.8 1.0
HB3 A:LEU441 5.0 29.8 1.0
HB2 A:ALA473 5.0 34.8 1.0
HA A:CYS471 5.0 34.3 1.0

Zinc binding site 3 out of 4 in 6y5p

Go back to Zinc Binding Sites List in 6y5p
Zinc binding site 3 out of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:50.3
occ:1.00
ND1 B:HIS446 2.0 60.3 1.0
SG B:CYS471 2.1 54.0 1.0
SG B:CYS444 2.3 0.4 1.0
SG B:CYS468 2.4 87.2 1.0
HB2 B:CYS444 2.4 75.1 1.0
CB B:CYS444 2.8 62.5 1.0
HB2 B:HIS446 2.9 53.0 1.0
CE1 B:HIS446 2.9 60.3 1.0
HB3 B:CYS444 3.1 75.1 1.0
CG B:HIS446 3.1 59.0 1.0
HE1 B:HIS446 3.1 72.5 1.0
H B:CYS471 3.2 63.0 1.0
HB3 B:CYS468 3.2 62.5 1.0
CB B:CYS468 3.2 52.1 1.0
HB2 B:CYS468 3.3 62.5 1.0
HB3 B:CYS471 3.3 57.1 1.0
CB B:CYS471 3.4 47.5 1.0
CB B:HIS446 3.5 44.1 1.0
HB B:THR470 3.7 53.2 1.0
H B:HIS446 3.8 58.8 1.0
N B:CYS471 3.9 52.4 1.0
HB3 B:HIS446 4.0 53.0 1.0
HB3 B:ALA473 4.1 60.8 1.0
NE2 B:HIS446 4.1 62.0 1.0
HH B:TYR448 4.1 59.4 1.0
HB2 B:CYS471 4.1 57.1 1.0
CD2 B:HIS446 4.2 57.4 1.0
CA B:CYS471 4.2 45.2 1.0
HH B:TYR475 4.2 87.1 1.0
HD12 B:LEU441 4.2 53.6 1.0
CA B:CYS444 4.2 53.0 1.0
H B:ALA473 4.4 57.1 1.0
N B:HIS446 4.5 48.9 1.0
H B:THR470 4.5 70.3 1.0
C B:CYS444 4.6 56.3 1.0
CB B:THR470 4.6 44.3 1.0
HD13 B:LEU441 4.6 53.6 1.0
HG22 B:THR470 4.6 63.1 1.0
CA B:HIS446 4.7 43.7 1.0
CA B:CYS468 4.7 41.5 1.0
HB2 B:ALA473 4.7 60.8 1.0
O B:CYS444 4.7 66.7 1.0
HA B:CYS444 4.7 63.6 1.0
H B:LYS472 4.7 78.7 1.0
HB2 B:LEU441 4.8 60.2 1.0
C B:CYS471 4.8 51.8 1.0
HE1 B:TYR475 4.8 60.8 1.0
CB B:ALA473 4.8 50.6 1.0
HE2 B:HIS446 4.8 74.5 1.0
OH B:TYR448 4.9 49.4 1.0
CD1 B:LEU441 4.9 44.6 1.0
H B:CYS444 4.9 70.2 1.0
C B:THR470 4.9 55.9 1.0
HA B:CYS468 5.0 49.8 1.0
OH B:TYR475 5.0 72.5 1.0
N B:LYS472 5.0 65.5 1.0
HA B:CYS471 5.0 54.3 1.0

Zinc binding site 4 out of 4 in 6y5p

Go back to Zinc Binding Sites List in 6y5p
Zinc binding site 4 out of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:71.6
occ:1.00
SG B:CYS411 2.0 47.0 1.0
ND1 B:HIS449 2.2 45.9 1.0
SG B:CYS452 2.3 49.0 1.0
SG B:CYS414 2.4 60.0 1.0
HB2 B:HIS449 2.7 58.6 1.0
HB3 B:CYS414 2.9 48.8 1.0
HB3 B:CYS411 3.0 57.7 1.0
H B:CYS414 3.1 43.9 1.0
CB B:CYS411 3.1 48.0 1.0
CG B:HIS449 3.1 44.7 1.0
CE1 B:HIS449 3.2 43.5 1.0
HB2 B:CYS452 3.2 50.1 1.0
CB B:CYS414 3.2 40.6 1.0
CB B:CYS452 3.3 41.7 1.0
HA B:SER422 3.3 60.5 1.0
HE1 B:HIS449 3.4 52.2 1.0
H B:HIS449 3.4 53.5 1.0
HB2 B:CYS411 3.4 57.7 1.0
CB B:HIS449 3.4 48.8 1.0
HB3 B:CYS452 3.5 50.1 1.0
H B:GLY423 3.7 60.3 1.0
N B:CYS414 3.8 36.5 1.0
HB2 B:SER422 3.8 64.3 1.0
HB B:ILE413 3.9 43.6 1.0
HB2 B:CYS414 4.0 48.8 1.0
HB3 B:HIS449 4.1 58.6 1.0
CA B:CYS414 4.1 36.0 1.0
N B:HIS449 4.1 44.5 1.0
OG B:SER422 4.1 60.7 1.0
CA B:SER422 4.2 50.4 1.0
NE2 B:HIS449 4.2 50.9 1.0
CD2 B:HIS449 4.2 47.6 1.0
CB B:SER422 4.2 53.5 1.0
CA B:HIS449 4.4 47.0 1.0
N B:GLY423 4.5 50.2 1.0
H B:GLU416 4.5 71.9 1.0
H B:CYS452 4.5 53.8 1.0
HG B:SER422 4.5 72.9 1.0
CA B:CYS411 4.5 41.4 1.0
H B:ILE413 4.6 44.3 1.0
CA B:CYS452 4.6 36.7 1.0
HB2 B:GLU416 4.7 56.6 1.0
H B:MET415 4.7 47.5 1.0
HD21 A:LEU590 4.8 50.8 1.0
CB B:ILE413 4.8 36.3 1.0
HB3 B:TYR448 4.8 46.3 1.0
HA B:CYS414 4.9 43.3 1.0
O B:CYS411 4.9 45.3 1.0
HA B:CYS452 4.9 44.1 1.0
C B:CYS414 4.9 49.3 1.0
C B:CYS411 4.9 40.9 1.0
O B:HIS449 4.9 43.6 1.0
C B:SER422 4.9 48.6 1.0
C B:ILE413 4.9 37.2 1.0
HD23 B:LEU418 4.9 63.9 1.0
HE2 B:HIS449 5.0 61.2 1.0
N B:CYS452 5.0 44.8 1.0
HA B:CYS411 5.0 49.8 1.0
O B:GLU416 5.0 48.0 1.0

Reference:

C.Chatrin, M.Gabrielsen, L.Buetow, M.A.Nakasone, S.F.Ahmed, D.Sumpton, G.J.Sibbet, B.O.Smith, D.T.Huang. Structural Insights Into Adp-Ribosylation of Ubiquitin By Deltex Family E3 Ubiquitin Ligases. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 32948590
DOI: 10.1126/SCIADV.ABC0418
Page generated: Wed Dec 16 13:15:01 2020

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