Atomistry » Zinc » PDB 6xv1-6ya1 » 6xwg
Atomistry »
  Zinc »
    PDB 6xv1-6ya1 »
      6xwg »

Zinc in PDB 6xwg: Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element

Protein crystallography data

The structure of Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element, PDB code: 6xwg was solved by A.G.Mcewen, P.Poussin-Courmontagne, C.Peluso-Iltis, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.51 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.714, 56.714, 238.364, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 20.7

Other elements in 6xwg:

The structure of Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element (pdb code 6xwg). 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 the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element, PDB code: 6xwg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6xwg

Go back to Zinc Binding Sites List in 6xwg
Zinc binding site 1 out of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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 the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:62.9
occ:1.00
SG C:CYS135 2.2 64.7 1.0
SG C:CYS138 2.2 68.7 1.0
SG C:CYS152 2.4 59.5 1.0
SG C:CYS155 2.4 64.2 1.0
CB C:CYS155 3.3 59.4 1.0
CB C:CYS138 3.3 63.1 1.0
CB C:CYS135 3.3 64.2 1.0
CB C:CYS152 3.5 59.4 1.0
N C:CYS138 3.6 60.6 1.0
N C:CYS152 3.9 59.3 1.0
CA C:CYS138 4.0 62.5 1.0
CA C:CYS152 4.3 60.0 1.0
N C:CYS155 4.3 60.3 1.0
CA C:CYS155 4.4 58.4 1.0
CB C:ILE137 4.4 54.7 1.0
C C:ILE137 4.6 62.0 1.0
CA C:CYS135 4.7 65.1 1.0
CG2 C:ILE137 4.7 52.3 1.0
C C:CYS138 4.8 68.8 1.0
NH2 C:ARG191 4.9 49.7 1.0
CD C:ARG184 4.9 60.0 1.0
N C:GLY139 4.9 66.4 1.0
CA C:ILE137 4.9 54.8 1.0
NH1 C:ARG184 4.9 84.1 1.0
CB C:ASP140 4.9 72.2 1.0
CB C:SER151 5.0 60.5 1.0
C C:SER151 5.0 66.3 1.0

Zinc binding site 2 out of 4 in 6xwg

Go back to Zinc Binding Sites List in 6xwg
Zinc binding site 2 out of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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 the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:68.0
occ:1.00
SG C:CYS171 2.2 65.6 1.0
SG C:CYS187 2.2 58.1 1.0
SG C:CYS177 2.3 69.2 1.0
SG C:CYS190 2.5 56.1 1.0
CB C:CYS171 3.1 61.0 1.0
CB C:CYS187 3.1 54.5 1.0
CB C:CYS177 3.3 63.1 1.0
CB C:CYS190 3.7 49.8 1.0
CA C:CYS171 4.0 62.6 1.0
O C:HOH408 4.1 60.3 1.0
O C:HOH406 4.2 59.0 1.0
N C:CYS177 4.2 65.3 1.0
CA C:LYS175 4.2 63.2 1.0
N C:CYS190 4.3 50.5 1.0
CA C:CYS177 4.4 64.3 1.0
N C:LYS175 4.4 67.4 1.0
CA C:CYS187 4.6 54.9 1.0
CA C:CYS190 4.6 48.4 1.0
CD2 C:TYR189 4.7 54.5 1.0
C C:LYS175 4.7 67.4 1.0
CB C:TYR189 4.7 55.1 1.0
N C:ASP176 4.8 67.6 1.0
C C:CYS171 4.8 69.9 1.0
N C:ARG172 4.9 68.5 1.0

Zinc binding site 3 out of 4 in 6xwg

Go back to Zinc Binding Sites List in 6xwg
Zinc binding site 3 out of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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 the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:53.7
occ:1.00
SG D:CYS88 2.2 57.4 1.0
SG D:CYS108 2.3 58.0 1.0
SG D:CYS91 2.3 56.0 1.0
SG D:CYS105 2.4 48.6 1.0
CB D:CYS88 3.2 53.9 1.0
CB D:CYS91 3.3 52.1 1.0
CB D:CYS108 3.3 53.4 1.0
CB D:CYS105 3.5 46.1 1.0
N D:CYS91 3.6 49.3 1.0
CA D:CYS91 4.0 51.4 1.0
N D:CYS105 4.1 45.6 1.0
NH1 D:ARG137 4.2 51.6 1.0
N D:CYS108 4.3 54.1 1.0
CA D:CYS105 4.4 46.0 1.0
CA D:CYS108 4.4 53.5 1.0
CB D:VAL90 4.5 45.3 1.0
N D:GLN92 4.6 50.2 1.0
C D:CYS91 4.6 55.7 1.0
CA D:CYS88 4.6 53.5 1.0
CB D:ASP93 4.6 45.4 1.0
CD D:ARG137 4.7 51.7 1.0
NH2 D:ARG144 4.7 50.5 1.0
C D:VAL90 4.7 52.3 1.0
N D:ASP93 4.9 43.9 1.0
O D:CYS105 4.9 49.8 1.0
CA D:VAL90 5.0 44.7 1.0
C D:CYS105 5.0 51.2 1.0

Zinc binding site 4 out of 4 in 6xwg

Go back to Zinc Binding Sites List in 6xwg
Zinc binding site 4 out of 4 in the Crystal Structure of the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 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 the Human Rxr/Rar Dna-Binding Domain Heterodimer Bound to the Human RARB2 DR5 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:96.4
occ:1.00
SG D:CYS130 2.2 97.9 1.0
SG D:CYS140 2.2 83.3 1.0
SG D:CYS124 2.5 0.8 1.0
SG D:CYS143 2.6 77.9 1.0
CB D:CYS130 3.0 88.2 1.0
CB D:CYS140 3.0 77.7 1.0
CB D:CYS143 3.5 69.2 1.0
CB D:CYS124 3.8 99.4 1.0
CA D:CYS130 4.3 89.0 1.0
N D:CYS143 4.4 69.4 1.0
N D:CYS130 4.4 91.8 1.0
CA D:CYS124 4.4 0.1 1.0
CB D:ARG126 4.4 0.5 1.0
CA D:CYS140 4.5 74.9 1.0
CA D:CYS143 4.5 67.0 1.0
CA D:LYS128 4.7 97.4 1.0
N D:LYS128 4.7 0.1 1.0
CG D:ARG126 4.8 0.9 1.0
CD2 D:TYR142 4.9 79.2 1.0
C D:LYS128 5.0 99.2 1.0
N D:HIS125 5.0 0.6 1.0

Reference:

J.Osz, A.G.Mcewen, M.Bourguet, F.Przybilla, C.Peluso-Iltis, P.Poussin-Courmontagne, Y.Mely, S.Cianferani, C.M.Jeffries, D.I.Svergun, N.Rochel. Structural Basis For Dna Recognition and Allosteric Control of the Retinoic Acid Receptors Rar-Rxr. Nucleic Acids Res. V. 48 9969 2020.
ISSN: ESSN 1362-4962
PubMed: 32974652
DOI: 10.1093/NAR/GKAA697
Page generated: Thu Aug 21 21:19:04 2025

Last articles

Zn in 7FJI
Zn in 7FIR
Zn in 7FIQ
Zn in 7FIP
Zn in 7FGI
Zn in 7FGH
Zn in 7FGG
Zn in 7FH9
Zn in 7FH4
Zn in 7FB9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy