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Zinc in PDB 5e69: Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex

Protein crystallography data

The structure of Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex, PDB code: 5e69 was solved by W.H.Hudson, E.A.Rye, A.G.Herbst, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.27 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.165, 97.176, 103.265, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex (pdb code 5e69). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex, PDB code: 5e69:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5e69

Go back to Zinc Binding Sites List in 5e69
Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:34.7
occ:1.00
SG A:CYS424 2.2 37.9 1.0
SG A:CYS421 2.3 35.0 1.0
SG A:CYS438 2.4 37.7 1.0
SG A:CYS441 2.4 35.3 1.0
CB A:CYS441 3.2 32.8 1.0
CB A:CYS421 3.3 37.5 1.0
CB A:CYS424 3.4 38.3 1.0
N A:CYS424 3.6 38.5 1.0
CB A:CYS438 3.6 39.2 1.0
N A:CYS438 3.9 36.1 1.0
CA A:CYS424 4.0 38.5 1.0
CB A:VAL423 4.3 33.9 1.0
NH1 A:ARG470 4.3 40.3 1.0
CA A:CYS438 4.4 39.2 1.0
N A:CYS441 4.4 33.2 1.0
CA A:CYS441 4.4 34.3 1.0
CB A:ASP426 4.7 44.8 1.0
OG A:SER440 4.7 41.8 1.0
C A:VAL423 4.7 40.0 1.0
C A:CYS424 4.7 38.9 1.0
CA A:CYS421 4.8 40.3 1.0
N A:SER425 4.8 39.9 1.0
NH2 A:ARG477 4.9 34.3 1.0
N A:ASP426 4.9 41.5 1.0
CA A:VAL423 4.9 37.2 1.0
CG1 A:VAL423 4.9 35.0 1.0
N A:VAL423 4.9 37.8 1.0
C A:CYS438 5.0 39.1 1.0

Zinc binding site 2 out of 4 in 5e69

Go back to Zinc Binding Sites List in 5e69
Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:33.2
occ:1.00
O A:HOH733 2.1 66.9 1.0
SG A:CYS457 2.3 36.0 1.0
SG A:CYS473 2.3 33.8 1.0
SG A:CYS476 2.3 31.9 1.0
SG A:CYS463 2.4 37.2 1.0
CB A:CYS463 3.2 35.4 1.0
CB A:CYS457 3.3 35.5 1.0
CB A:CYS473 3.4 34.3 1.0
CB A:CYS476 3.4 29.8 1.0
O B:HOH725 3.9 37.5 1.0
CA A:CYS457 4.0 37.8 1.0
N A:CYS463 4.1 37.4 1.0
N A:CYS476 4.2 29.6 1.0
CA A:CYS463 4.3 39.5 1.0
CA A:ASN461 4.3 40.2 1.0
O A:HOH711 4.3 38.7 1.0
CA A:CYS476 4.4 27.9 1.0
O A:HOH737 4.5 44.3 1.0
N A:ASN461 4.5 37.1 1.0
N A:ALA458 4.8 36.8 1.0
CA A:CYS473 4.8 37.3 1.0
C A:ASN461 4.8 39.1 1.0
N A:GLY459 4.8 36.3 1.0
C A:CYS457 4.8 37.9 1.0
O A:HOH709 4.9 34.0 1.0
CB A:ALA475 5.0 35.0 1.0
N A:ASP462 5.0 38.9 1.0

Zinc binding site 3 out of 4 in 5e69

Go back to Zinc Binding Sites List in 5e69
Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:34.2
occ:1.00
SG B:CYS473 2.3 35.0 1.0
SG B:CYS457 2.3 30.8 1.0
SG B:CYS476 2.3 34.1 1.0
SG B:CYS463 2.4 35.0 1.0
CB B:CYS463 3.2 35.3 1.0
CB B:CYS457 3.2 29.9 1.0
CB B:CYS473 3.3 40.3 1.0
CB B:CYS476 3.4 36.1 1.0
O B:HOH724 3.9 32.8 1.0
CA B:CYS457 4.0 31.1 1.0
N B:CYS463 4.1 37.1 1.0
O B:HOH701 4.1 38.0 1.0
N B:CYS476 4.2 34.3 1.0
CA B:CYS463 4.3 38.4 1.0
CA B:CYS476 4.4 32.6 1.0
CA B:ASN461 4.5 34.1 1.0
N B:ASN461 4.6 32.8 1.0
CA B:CYS473 4.7 37.4 1.0
O A:HOH737 4.8 44.3 1.0
C B:ASN461 4.8 36.3 1.0
C B:CYS457 4.8 32.1 1.0
N B:ALA458 4.8 30.2 1.0
N B:GLY459 4.9 36.5 1.0
N B:ASP462 4.9 38.5 1.0
O B:HOH719 4.9 38.5 1.0
CB B:ALA475 5.0 36.5 1.0

Zinc binding site 4 out of 4 in 5e69

Go back to Zinc Binding Sites List in 5e69
Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Glucocorticoid Receptor Dna Binding Domain - IL8 Nf-Kb Response Element Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:43.0
occ:1.00
SG B:CYS424 2.2 48.7 1.0
SG B:CYS421 2.3 46.4 1.0
SG B:CYS441 2.4 44.0 1.0
SG B:CYS438 2.4 48.5 1.0
CB B:CYS441 3.2 43.4 1.0
CB B:CYS421 3.2 49.2 1.0
CB B:CYS424 3.3 44.4 1.0
N B:CYS424 3.6 44.4 1.0
CB B:CYS438 3.6 48.9 1.0
CA B:CYS424 3.9 47.9 1.0
N B:CYS438 4.0 46.8 1.0
NH1 B:ARG470 4.3 48.1 1.0
N B:CYS441 4.3 41.8 1.0
CA B:CYS441 4.3 41.9 1.0
CA B:CYS438 4.3 47.3 1.0
CB B:VAL423 4.4 43.4 1.0
OG B:SER440 4.5 49.3 1.0
C B:CYS424 4.6 47.9 1.0
C B:VAL423 4.7 46.7 1.0
CA B:CYS421 4.7 49.2 1.0
CB B:ASP426 4.7 52.2 1.0
N B:SER425 4.8 48.5 1.0
N B:ASP426 4.9 49.0 1.0
NH2 B:ARG477 4.9 43.7 1.0
CA B:VAL423 4.9 46.6 1.0
N B:VAL423 5.0 46.8 1.0
C B:CYS438 5.0 45.4 1.0
CG1 B:VAL423 5.0 45.4 1.0

Reference:

W.H.Hudson, I.M.S.Vera, J.C.Nwachukwu, E.R.Weikum, A.G.Herbst, Q.Yang, D.L.Bain, K.W.Nettles, D.J.Kojetin, E.A.Ortlund. Cryptic Glucocorticoid Receptor-Binding Sites Pervade Genomic Nf-Kappa B Response Elements. Nat Commun V. 9 1337 2018.
ISSN: ESSN 2041-1723
PubMed: 29626214
DOI: 10.1038/S41467-018-03780-1
Page generated: Wed Dec 16 06:09:06 2020

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