Atomistry » Zinc » PDB 1yjo-1z3i » 1ynw
Atomistry »
  Zinc »
    PDB 1yjo-1z3i »
      1ynw »

Zinc in PDB 1ynw: Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element

Protein crystallography data

The structure of Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element, PDB code: 1ynw was solved by P.L.Shaffer, D.T.Gewirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.104, 57.049, 73.438, 90.00, 110.31, 90.00
R / Rfree (%) 23.2 / 28.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element (pdb code 1ynw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element, PDB code: 1ynw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ynw

Go back to Zinc Binding Sites List in 1ynw
Zinc binding site 1 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn150

b:92.9
occ:1.00
SG A:CYS24 2.5 0.9 1.0
SG A:CYS44 2.5 94.2 1.0
SG A:CYS41 2.6 81.5 1.0
SG A:CYS27 2.7 0.3 1.0
CB A:CYS41 3.2 84.4 1.0
CB A:CYS44 3.2 92.6 1.0
CB A:CYS24 3.3 0.7 1.0
CB A:CYS27 3.6 0.5 1.0
N A:CYS27 3.6 0.1 1.0
N A:CYS41 3.6 84.3 1.0
CB A:VAL26 4.0 0.9 1.0
CA A:CYS41 4.0 83.9 1.0
CA A:CYS27 4.1 0.4 1.0
CG1 A:VAL26 4.1 0.3 1.0
N A:CYS44 4.2 90.8 1.0
CA A:CYS44 4.3 92.6 1.0
CB A:ASP29 4.5 97.8 1.0
C A:VAL26 4.6 0.6 1.0
CA A:VAL26 4.7 0.9 1.0
CA A:CYS24 4.7 0.2 1.0
O A:CYS41 4.7 82.8 1.0
N A:VAL26 4.7 0.8 1.0
C A:CYS27 4.7 0.8 1.0
C A:CYS41 4.7 83.3 1.0
C A:THR40 4.8 85.2 1.0
NH1 A:ARG73 4.8 95.3 1.0
NH2 A:ARG80 4.9 88.9 1.0
CB A:THR40 5.0 85.7 1.0

Zinc binding site 2 out of 4 in 1ynw

Go back to Zinc Binding Sites List in 1ynw
Zinc binding site 2 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn151

b:0.6
occ:1.00
SG A:CYS66 2.3 0.3 1.0
SG A:CYS76 2.4 94.3 1.0
SG A:CYS79 2.4 0.3 1.0
SG A:CYS60 2.4 0.3 1.0
CB A:CYS60 2.7 0.3 1.0
CB A:CYS79 3.3 97.8 1.0
CB A:CYS76 3.6 97.1 1.0
N A:ASP65 3.8 0.8 1.0
N A:CYS66 3.9 0.8 1.0
CA A:CYS60 3.9 0.2 1.0
CB A:CYS66 4.0 0.7 1.0
CA A:GLY64 4.1 0.1 1.0
N A:CYS79 4.2 94.3 1.0
C A:GLY64 4.3 0.1 1.0
CA A:CYS79 4.3 96.0 1.0
N A:GLY64 4.5 0.9 1.0
CA A:CYS66 4.6 0.5 1.0
C A:CYS60 4.6 0.4 1.0
CB A:ALA62 4.6 0.6 1.0
CA A:ASP65 4.7 0.1 1.0
C A:ASP65 4.8 0.6 1.0
CA A:CYS76 5.0 97.8 1.0
N A:CYS60 5.0 0.4 1.0

Zinc binding site 3 out of 4 in 1ynw

Go back to Zinc Binding Sites List in 1ynw
Zinc binding site 3 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn350

b:99.7
occ:1.00
SG B:CYS255 2.2 89.4 1.0
SG B:CYS235 2.4 0.1 1.0
SG B:CYS238 2.5 0.5 1.0
SG B:CYS252 2.6 93.1 1.0
N B:CYS238 3.0 0.5 1.0
CB B:CYS238 3.1 0.6 1.0
CB B:CYS255 3.2 93.7 1.0
CB B:CYS235 3.3 0.6 1.0
CA B:CYS238 3.5 0.7 1.0
CB B:CYS252 3.6 94.6 1.0
N B:CYS252 3.9 94.8 1.0
CB B:ILE237 3.9 0.7 1.0
C B:ILE237 4.1 0.3 1.0
N B:GLY239 4.2 0.0 1.0
C B:CYS238 4.2 0.9 1.0
N B:CYS255 4.2 94.6 1.0
CA B:CYS255 4.3 94.1 1.0
CA B:CYS252 4.3 93.6 1.0
CA B:ILE237 4.5 0.6 1.0
NH2 B:ARG291 4.5 89.1 1.0
CA B:CYS235 4.7 0.7 1.0
N B:ILE237 4.7 0.8 1.0
CG1 B:ILE237 4.7 0.3 1.0
CG2 B:ILE237 4.8 0.0 1.0
NH1 B:ARG284 4.8 97.6 1.0
O B:CYS235 4.9 0.6 1.0
C B:SER251 4.9 96.3 1.0
C B:CYS235 5.0 0.7 1.0
N B:ASP240 5.0 0.5 1.0
CB B:ASP240 5.0 0.4 1.0

Zinc binding site 4 out of 4 in 1ynw

Go back to Zinc Binding Sites List in 1ynw
Zinc binding site 4 out of 4 in the Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Vitamin D Receptor and 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound to A DR3 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn351

b:0.6
occ:1.00
SG B:CYS287 2.2 0.9 1.0
SG B:CYS277 2.5 0.5 1.0
SG B:CYS271 2.6 0.5 1.0
CB B:CYS287 2.7 0.2 1.0
SG B:CYS290 2.8 0.6 1.0
CB B:CYS271 3.8 0.1 1.0
CB B:CYS290 3.8 0.4 1.0
CB B:CYS277 3.9 0.8 1.0
CA B:CYS271 3.9 0.4 1.0
N B:ARG272 3.9 0.8 1.0
CA B:CYS287 4.2 0.8 1.0
C B:CYS271 4.4 0.4 1.0
N B:CYS290 4.5 0.1 1.0
N B:ASP273 4.5 0.6 1.0
CA B:CYS290 4.8 0.8 1.0
C B:CYS287 4.8 0.7 1.0
O B:CYS287 4.9 0.9 1.0
CA B:LYS275 4.9 0.5 1.0
N B:LYS275 4.9 0.3 1.0
CA B:ARG272 4.9 0.9 1.0
CB B:ARG272 4.9 0.3 1.0
CD2 B:TYR289 5.0 0.1 1.0
CB B:TYR289 5.0 0.2 1.0

Reference:

P.L.Shaffer, D.T.Gewirth. Structural Analysis of Rxr-Vdr Interactions on DR3 Dna J.Steroid Biochem.Mol.Biol. V.9-90 215 2004.
ISSN: ISSN 0960-0760
PubMed: 15225774
DOI: 10.1016/J.JSBMB.2004.03.084
Page generated: Wed Dec 16 03:14:49 2020

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy