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Zinc in PDB 5va0: Glucocorticoid Receptor Dna Binding Domain in Complex with Ap-1 Response Element From Vcam-1 Promoter

Protein crystallography data

The structure of Glucocorticoid Receptor Dna Binding Domain in Complex with Ap-1 Response Element From Vcam-1 Promoter, PDB code: 5va0 was solved by E.R.Weikum, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.48 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.442, 96.280, 105.223, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Glucocorticoid Receptor Dna Binding Domain in Complex with Ap-1 Response Element From Vcam-1 Promoter (pdb code 5va0). 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 in Complex with Ap-1 Response Element From Vcam-1 Promoter, PDB code: 5va0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5va0

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Zinc binding site 1 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Ap-1 Response Element From Vcam-1 Promoter


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 in Complex with Ap-1 Response Element From Vcam-1 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:30.7
occ:1.00
SG A:CYS424 2.3 30.1 1.0
SG A:CYS438 2.3 30.9 1.0
SG A:CYS421 2.3 32.1 1.0
SG A:CYS441 2.4 34.0 1.0
CB A:CYS441 3.2 29.3 1.0
CB A:CYS421 3.3 32.7 1.0
CB A:CYS424 3.4 27.6 1.0
CB A:CYS438 3.6 36.6 1.0
N A:CYS424 3.7 33.0 1.0
N A:CYS438 4.0 32.6 1.0
CA A:CYS424 4.1 34.7 1.0
N A:CYS441 4.3 29.1 1.0
NH1 A:ARG470 4.3 32.5 1.0
CA A:CYS441 4.3 31.5 1.0
CA A:CYS438 4.4 32.2 1.0
CB A:VAL423 4.5 34.7 1.0
CB A:ASP426 4.5 39.1 1.0
OG A:SER440 4.6 34.3 1.0
C A:VAL423 4.7 35.0 1.0
C A:CYS424 4.7 34.4 1.0
CA A:CYS421 4.7 33.6 1.0
CG1 A:VAL423 4.8 32.0 1.0
N A:SER425 4.8 32.1 1.0
N A:ASP426 4.9 35.7 1.0
NH2 A:ARG477 4.9 27.4 1.0
CA A:VAL423 4.9 34.7 1.0
O A:CYS438 4.9 31.9 1.0
C A:CYS438 4.9 31.0 1.0
N A:VAL423 5.0 30.4 1.0

Zinc binding site 2 out of 4 in 5va0

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Zinc binding site 2 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Ap-1 Response Element From Vcam-1 Promoter


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 in Complex with Ap-1 Response Element From Vcam-1 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:29.9
occ:1.00
SG A:CYS457 2.3 28.6 1.0
SG A:CYS463 2.3 29.5 1.0
SG A:CYS476 2.3 29.5 1.0
SG A:CYS473 2.4 30.3 1.0
CB A:CYS463 3.2 26.7 1.0
CB A:CYS473 3.3 30.2 1.0
CB A:CYS457 3.4 27.3 1.0
CB A:CYS476 3.4 23.0 1.0
O A:HOH707 3.8 27.0 1.0
CA A:CYS457 4.0 31.6 1.0
N A:CYS463 4.1 31.9 1.0
N A:CYS476 4.2 28.2 1.0
CA A:CYS463 4.3 27.6 1.0
CA A:CYS476 4.4 24.4 1.0
CA A:ASN461 4.4 34.1 1.0
N A:ASN461 4.5 33.8 1.0
O A:HOH702 4.6 31.2 1.0
N A:ALA458 4.7 27.7 1.0
N A:ASP462 4.7 34.2 1.0
CA A:CYS473 4.7 29.6 1.0
N A:GLY459 4.8 29.5 1.0
C A:CYS457 4.8 30.1 1.0
C A:ASN461 4.9 35.1 1.0
O A:HOH711 5.0 35.5 1.0
CB A:ALA475 5.0 26.5 1.0

Zinc binding site 3 out of 4 in 5va0

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Zinc binding site 3 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Ap-1 Response Element From Vcam-1 Promoter


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 in Complex with Ap-1 Response Element From Vcam-1 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:30.0
occ:1.00
SG B:CYS473 2.3 30.3 1.0
SG B:CYS476 2.3 33.9 1.0
SG B:CYS457 2.4 25.5 1.0
SG B:CYS463 2.4 28.7 1.0
CB B:CYS463 3.1 26.5 1.0
CB B:CYS473 3.3 27.5 1.0
CB B:CYS457 3.3 23.1 1.0
CB B:CYS476 3.3 29.4 1.0
O B:HOH708 3.7 29.5 1.0
N B:CYS463 4.0 35.3 1.0
O B:HOH710 4.1 35.2 1.0
CA B:CYS457 4.1 25.9 1.0
CA B:CYS463 4.1 33.5 1.0
N B:CYS476 4.2 33.3 1.0
CA B:CYS476 4.4 29.5 1.0
CA B:ASN461 4.5 29.3 1.0
N B:ASP462 4.6 31.2 1.0
N B:ASN461 4.6 32.1 1.0
CA B:CYS473 4.7 32.0 1.0
N B:ALA458 4.8 23.4 1.0
C B:ASN461 4.8 32.3 1.0
C B:CYS457 4.9 28.5 1.0
N B:GLY459 5.0 27.7 1.0

Zinc binding site 4 out of 4 in 5va0

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Zinc binding site 4 out of 4 in the Glucocorticoid Receptor Dna Binding Domain in Complex with Ap-1 Response Element From Vcam-1 Promoter


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 in Complex with Ap-1 Response Element From Vcam-1 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:39.6
occ:1.00
SG B:CYS421 2.3 41.0 1.0
SG B:CYS424 2.3 37.5 1.0
SG B:CYS441 2.3 37.3 1.0
SG B:CYS438 2.4 37.9 1.0
CB B:CYS441 3.2 35.1 1.0
CB B:CYS421 3.3 45.4 1.0
CB B:CYS424 3.3 40.4 1.0
CB B:CYS438 3.5 40.0 1.0
N B:CYS424 3.7 40.5 1.0
N B:CYS438 3.9 40.5 1.0
CA B:CYS424 4.0 42.8 1.0
N B:CYS441 4.3 33.6 1.0
CA B:CYS438 4.3 38.9 1.0
NH1 B:ARG470 4.3 38.4 1.0
CA B:CYS441 4.3 39.3 1.0
CB B:VAL423 4.4 43.0 1.0
OG B:SER440 4.4 41.4 1.0
C B:VAL423 4.7 42.5 1.0
CB B:ASP426 4.7 44.3 1.0
CA B:CYS421 4.7 44.6 1.0
C B:CYS424 4.7 43.6 1.0
CG1 B:VAL423 4.8 35.4 1.0
N B:SER425 4.9 44.5 1.0
CA B:VAL423 4.9 45.0 1.0
C B:CYS438 4.9 38.6 1.0
N B:ASP426 4.9 44.8 1.0
N B:VAL423 4.9 41.8 1.0
NH2 B:ARG477 5.0 31.8 1.0
O B:CYS438 5.0 39.2 1.0

Reference:

E.R.Weikum, I.M.S.De Vera, J.C.Nwachukwu, W.H.Hudson, K.W.Nettles, D.J.Kojetin, E.A.Ortlund. Tethering Not Required: the Glucocorticoid Receptor Binds Directly to Activator Protein-1 Recognition Motifs to Repress Inflammatory Genes. Nucleic Acids Res. V. 45 8596 2017.
ISSN: ESSN 1362-4962
PubMed: 28591827
DOI: 10.1093/NAR/GKX509
Page generated: Wed Dec 16 11:07:47 2020

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