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: Wed Dec 16 13:12:53 2020

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