Zinc in PDB 6xwh: Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element

Protein crystallography data

The structure of Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element, PDB code: 6xwh 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) 22.22 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.705, 62.522, 53.635, 90.00, 104.84, 90.00
R / Rfree (%) 18.5 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element (pdb code 6xwh). 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 Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element, PDB code: 6xwh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6xwh

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Zinc binding site 1 out of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 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 Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:57.6
occ:1.00
SG C:CYS138 2.3 59.7 1.0
SG C:CYS152 2.3 54.4 1.0
SG C:CYS135 2.3 57.5 1.0
SG C:CYS155 2.3 51.0 1.0
CB C:CYS135 3.2 56.2 1.0
CB C:CYS155 3.3 45.9 1.0
CB C:CYS138 3.6 58.3 1.0
CB C:CYS152 3.6 50.5 1.0
N C:CYS138 3.9 58.8 1.0
N C:CYS152 4.0 48.8 1.0
N C:CYS155 4.1 49.1 1.0
NH1 C:ARG184 4.2 58.2 1.0
CA C:CYS138 4.3 60.0 1.0
CA C:CYS155 4.3 46.7 1.0
CB C:ASP140 4.4 61.0 1.0
CA C:CYS152 4.4 49.0 1.0
CB C:ILE137 4.6 57.6 1.0
CA C:CYS135 4.6 58.8 1.0
C C:ILE137 4.6 63.7 1.0
N C:ASP140 4.8 62.3 1.0
C C:CYS138 4.9 65.7 1.0
NH2 C:ARG191 4.9 49.3 1.0
N C:GLY139 4.9 61.1 1.0
CA C:ILE137 4.9 58.2 1.0
CD C:ARG184 5.0 55.0 1.0
N C:ILE137 5.0 58.5 1.0
C C:CYS152 5.0 52.8 1.0
O C:CYS152 5.0 53.3 1.0

Zinc binding site 2 out of 4 in 6xwh

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Zinc binding site 2 out of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 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 Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:0.4
occ:1.00
SG C:CYS171 2.2 94.8 1.0
SG C:CYS187 2.4 87.2 1.0
SG C:CYS177 2.5 96.9 1.0
SG C:CYS190 2.5 82.4 1.0
CB C:CYS171 3.2 90.2 1.0
CB C:CYS187 3.3 82.5 1.0
CB C:CYS177 3.5 89.4 1.0
CB C:CYS190 3.5 73.2 1.0
CA C:CYS171 4.0 92.4 1.0
N C:CYS190 4.2 71.2 1.0
CA C:LYS175 4.4 96.5 1.0
CA C:CYS190 4.4 70.1 1.0
N C:CYS177 4.4 94.3 1.0
CA C:CYS177 4.6 92.0 1.0
N C:LYS175 4.7 0.6 1.0
CD1 C:TYR189 4.7 80.7 1.0
CB C:TYR189 4.8 77.8 1.0
CA C:CYS187 4.8 79.5 1.0
C C:CYS171 4.8 0.6 1.0
N C:ARG172 4.8 0.3 1.0
N C:ASP176 4.9 0.9 1.0
C C:LYS175 4.9 0.5 1.0
N C:ASP173 4.9 0.2 1.0

Zinc binding site 3 out of 4 in 6xwh

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Zinc binding site 3 out of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 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 Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:49.9
occ:1.00
SG D:CYS152 2.2 49.0 1.0
SG D:CYS138 2.3 46.0 1.0
SG D:CYS155 2.4 46.7 1.0
SG D:CYS135 2.4 46.2 1.0
CB D:CYS155 3.3 44.5 1.0
CB D:CYS135 3.3 44.3 1.0
CB D:CYS138 3.3 43.2 1.0
CB D:CYS152 3.7 46.8 1.0
NH1 D:ARG184 3.7 57.3 1.0
N D:CYS138 3.8 48.3 1.0
N D:CYS152 4.1 46.8 1.0
CA D:CYS138 4.1 46.5 1.0
N D:CYS155 4.3 43.3 1.0
CA D:CYS155 4.4 44.0 1.0
CA D:CYS152 4.4 47.0 1.0
NH2 D:ARG191 4.6 39.9 1.0
CB D:ASP140 4.6 53.7 1.0
CB D:ILE137 4.7 48.6 1.0
C D:ILE137 4.7 54.0 1.0
CA D:CYS135 4.7 49.1 1.0
C D:CYS138 4.8 53.8 1.0
CD D:ARG184 4.8 45.3 1.0
N D:GLY139 4.8 52.0 1.0
CZ D:ARG184 4.9 59.9 1.0
N D:ASP140 4.9 54.5 1.0

Zinc binding site 4 out of 4 in 6xwh

Go back to Zinc Binding Sites List in 6xwh
Zinc binding site 4 out of 4 in the Crystal Structure of the Human Rxr Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 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 Dna-Binding Domain Homodimer Bound to the Human HOXB13 DR0 Response Element within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:65.0
occ:1.00
SG D:CYS187 2.3 59.4 1.0
SG D:CYS190 2.3 55.8 1.0
SG D:CYS177 2.4 61.2 1.0
SG D:CYS171 2.4 71.3 1.0
CB D:CYS177 3.4 55.0 1.0
CB D:CYS187 3.4 54.0 1.0
CB D:CYS171 3.5 67.4 1.0
CB D:CYS190 3.6 49.8 1.0
O D:HOH405 4.1 53.4 1.0
N D:CYS177 4.1 58.3 1.0
CA D:CYS171 4.2 66.3 1.0
N D:CYS190 4.2 52.0 1.0
CA D:LYS175 4.3 56.9 1.0
OD2 D:ASP173 4.4 83.3 1.0
CA D:CYS177 4.4 55.9 1.0
N D:ASP176 4.4 61.3 1.0
N D:LYS175 4.4 57.9 1.0
CA D:CYS190 4.5 50.1 1.0
C D:LYS175 4.6 64.0 1.0
CB D:ASP173 4.7 63.0 1.0
CD1 D:TYR189 4.7 57.2 1.0
CA D:CYS187 4.8 53.1 1.0
N D:ASP173 4.9 63.7 1.0
CB D:TYR189 4.9 54.2 1.0
N D:ARG172 4.9 66.6 1.0
C D:CYS171 5.0 71.6 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 13:12:57 2020

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