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Zinc in PDB 5cc1: S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex

Protein crystallography data

The structure of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex, PDB code: 5cc1 was solved by W.H.Hudson, E.A.Weikum, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.41 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.721, 39.122, 132.099, 90.00, 101.10, 90.00
R / Rfree (%) 24.5 / 27.9

Zinc Binding Sites:

The binding sites of Zinc atom in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex (pdb code 5cc1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex, PDB code: 5cc1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5cc1

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Zinc binding site 1 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:52.1
occ:1.00
SG A:CYS421 2.2 48.2 1.0
SG A:CYS424 2.3 56.2 1.0
SG A:CYS438 2.4 53.8 1.0
SG A:CYS441 2.4 53.6 1.0
CB A:CYS421 3.2 52.1 1.0
CB A:CYS441 3.3 46.0 1.0
CB A:CYS438 3.4 54.8 1.0
CB A:CYS424 3.5 53.0 1.0
N A:CYS424 3.5 53.2 1.0
N A:CYS438 3.9 56.0 1.0
CA A:CYS424 4.0 54.7 1.0
CA A:CYS438 4.2 55.7 1.0
NH1 A:ARG470 4.3 52.1 1.0
CB A:VAL423 4.4 53.5 1.0
N A:CYS441 4.4 49.6 1.0
CA A:CYS441 4.5 48.5 1.0
CB A:ASP426 4.6 59.7 1.0
C A:VAL423 4.6 58.4 1.0
CA A:CYS421 4.6 53.0 1.0
OG A:SER440 4.7 51.4 1.0
C A:CYS424 4.7 59.0 1.0
N A:GLY425 4.8 60.2 1.0
CA A:VAL423 4.8 54.1 1.0
C A:CYS438 4.9 53.8 1.0
N A:VAL423 4.9 51.1 1.0
O A:CYS438 4.9 54.0 1.0
N A:ASP426 4.9 59.4 1.0
C A:THR437 5.0 55.8 1.0

Zinc binding site 2 out of 8 in 5cc1

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Zinc binding site 2 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:43.1
occ:1.00
SG A:CYS457 2.2 46.0 1.0
SG A:CYS463 2.3 45.2 1.0
SG A:CYS473 2.3 42.5 1.0
SG A:CYS476 2.3 40.4 1.0
CB A:CYS463 3.2 40.7 1.0
CB A:CYS457 3.3 45.1 1.0
CB A:CYS473 3.4 42.0 1.0
CB A:CYS476 3.5 41.2 1.0
N A:CYS463 4.0 43.4 1.0
CA A:CYS457 4.0 49.3 1.0
CA A:ASN461 4.1 44.9 1.0
CA A:CYS463 4.2 44.5 1.0
N A:CYS476 4.2 41.1 1.0
N A:ASN461 4.3 47.9 1.0
CA A:CYS476 4.5 37.3 1.0
C A:ASN461 4.6 50.9 1.0
N A:ALA458 4.7 45.8 1.0
N A:GLY459 4.7 44.9 1.0
N A:ASP462 4.8 51.3 1.0
CA A:CYS473 4.8 43.8 1.0
C A:CYS457 4.8 48.7 1.0

Zinc binding site 3 out of 8 in 5cc1

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Zinc binding site 3 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:65.8
occ:1.00
SG B:CYS424 2.2 68.1 1.0
SG B:CYS441 2.3 66.3 1.0
SG B:CYS421 2.4 68.9 1.0
SG B:CYS438 2.4 67.2 1.0
CB B:CYS424 3.2 63.0 1.0
CB B:CYS421 3.2 73.9 1.0
CB B:CYS441 3.3 68.1 1.0
CB B:CYS438 3.4 71.4 1.0
N B:CYS424 3.5 67.0 1.0
CA B:CYS424 3.8 66.5 1.0
N B:CYS438 4.0 68.9 1.0
CA B:CYS438 4.3 68.1 1.0
CB B:VAL423 4.4 64.8 1.0
N B:CYS441 4.4 62.0 1.0
CA B:CYS441 4.4 63.7 1.0
CB B:ASP426 4.5 73.5 1.0
C B:CYS424 4.5 69.9 1.0
OG B:SER440 4.6 67.8 1.0
NH1 B:ARG470 4.6 65.6 1.0
C B:VAL423 4.6 68.5 1.0
N B:GLY425 4.6 70.5 1.0
CA B:CYS421 4.7 74.9 1.0
N B:ASP426 4.7 76.4 1.0
C B:CYS438 4.9 67.2 1.0
CA B:VAL423 4.9 65.5 1.0
O B:CYS438 4.9 69.7 1.0
CG1 B:VAL423 4.9 63.9 1.0
N B:VAL423 5.0 68.3 1.0

Zinc binding site 4 out of 8 in 5cc1

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Zinc binding site 4 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:45.8
occ:1.00
SG B:CYS457 2.3 47.3 1.0
SG B:CYS463 2.3 49.6 1.0
SG B:CYS473 2.3 45.8 1.0
SG B:CYS476 2.3 46.7 1.0
CB B:CYS463 3.1 49.1 1.0
CB B:CYS457 3.2 44.8 1.0
CB B:CYS473 3.2 42.7 1.0
CB B:CYS476 3.4 48.3 1.0
CA B:CYS457 3.9 42.7 1.0
N B:CYS463 4.0 52.0 1.0
CA B:CYS463 4.2 48.3 1.0
N B:CYS476 4.2 46.7 1.0
CA B:CYS476 4.4 47.6 1.0
CA B:ASN461 4.6 46.4 1.0
CA B:CYS473 4.6 48.1 1.0
N B:ASN461 4.7 44.7 1.0
N B:ALA458 4.7 40.9 1.0
C B:CYS457 4.8 45.2 1.0
N B:ASP462 4.8 52.6 1.0
N B:GLY459 4.8 44.9 1.0
C B:ASN461 4.9 49.9 1.0

Zinc binding site 5 out of 8 in 5cc1

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Zinc binding site 5 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn601

b:52.8
occ:1.00
SG W:CYS421 2.1 46.9 1.0
SG W:CYS438 2.3 53.3 1.0
SG W:CYS424 2.4 55.7 1.0
SG W:CYS441 2.4 53.6 1.0
CB W:CYS421 3.2 52.9 1.0
CB W:CYS441 3.3 45.8 1.0
CB W:CYS438 3.4 54.1 1.0
CB W:CYS424 3.4 52.3 1.0
N W:CYS424 3.5 52.9 1.0
N W:CYS438 3.9 55.3 1.0
CA W:CYS424 4.0 54.7 1.0
CA W:CYS438 4.2 55.5 1.0
NH1 W:ARG470 4.3 51.8 1.0
CB W:VAL423 4.3 53.5 1.0
N W:CYS441 4.4 49.8 1.0
CA W:CYS441 4.5 48.3 1.0
CB W:ASP426 4.5 59.5 1.0
C W:VAL423 4.6 58.2 1.0
CA W:CYS421 4.6 52.3 1.0
OG W:SER440 4.6 51.9 1.0
C W:CYS424 4.7 58.6 1.0
N W:GLY425 4.8 60.2 1.0
CA W:VAL423 4.8 53.9 1.0
N W:VAL423 4.9 51.3 1.0
C W:CYS438 4.9 53.6 1.0
O W:CYS438 4.9 54.4 1.0
N W:ASP426 4.9 59.7 1.0

Zinc binding site 6 out of 8 in 5cc1

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Zinc binding site 6 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn602

b:42.7
occ:1.00
SG W:CYS457 2.3 46.6 1.0
SG W:CYS463 2.3 45.0 1.0
SG W:CYS473 2.3 44.5 1.0
SG W:CYS476 2.3 40.1 1.0
CB W:CYS463 3.2 41.0 1.0
CB W:CYS457 3.3 44.8 1.0
CB W:CYS473 3.4 40.7 1.0
CB W:CYS476 3.5 41.1 1.0
N W:CYS463 4.0 43.8 1.0
CA W:CYS457 4.0 48.7 1.0
CA W:ASN461 4.2 45.6 1.0
CA W:CYS463 4.2 43.5 1.0
N W:CYS476 4.2 41.4 1.0
N W:ASN461 4.3 48.4 1.0
CA W:CYS476 4.4 37.1 1.0
C W:ASN461 4.7 49.9 1.0
N W:ALA458 4.7 46.3 1.0
N W:GLY459 4.7 44.4 1.0
CA W:CYS473 4.8 44.0 1.0
C W:CYS457 4.8 48.9 1.0
N W:ASP462 4.8 50.0 1.0

Zinc binding site 7 out of 8 in 5cc1

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Zinc binding site 7 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn601

b:65.9
occ:1.00
SG X:CYS424 2.2 68.7 1.0
SG X:CYS441 2.3 66.3 1.0
SG X:CYS421 2.4 69.3 1.0
SG X:CYS438 2.5 67.4 1.0
CB X:CYS424 3.2 63.0 1.0
CB X:CYS421 3.3 73.9 1.0
CB X:CYS441 3.3 68.3 1.0
CB X:CYS438 3.4 71.1 1.0
N X:CYS424 3.5 68.1 1.0
CA X:CYS424 3.9 67.1 1.0
N X:CYS438 4.0 68.9 1.0
CA X:CYS438 4.3 68.0 1.0
CB X:VAL423 4.4 65.0 1.0
N X:CYS441 4.4 61.9 1.0
CA X:CYS441 4.4 63.6 1.0
CB X:ASP426 4.5 73.8 1.0
C X:CYS424 4.5 70.5 1.0
OG X:SER440 4.6 67.8 1.0
NH1 X:ARG470 4.6 65.2 1.0
C X:VAL423 4.6 69.8 1.0
N X:GLY425 4.6 71.5 1.0
N X:ASP426 4.7 76.5 1.0
CA X:CYS421 4.7 74.6 1.0
C X:CYS438 4.9 66.8 1.0
CA X:VAL423 4.9 66.5 1.0
O X:CYS438 4.9 69.4 1.0
CG1 X:VAL423 4.9 64.5 1.0
N X:VAL423 5.0 69.4 1.0

Zinc binding site 8 out of 8 in 5cc1

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Zinc binding site 8 out of 8 in the S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of S425G Glucocorticoid Receptor Dna Binding Domain - (+)Gre Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn602

b:46.9
occ:1.00
SG X:CYS473 2.2 46.0 1.0
SG X:CYS457 2.2 46.1 1.0
SG X:CYS463 2.3 49.5 1.0
SG X:CYS476 2.3 46.3 1.0
CB X:CYS463 3.1 47.5 1.0
CB X:CYS457 3.2 44.3 1.0
CB X:CYS473 3.2 44.8 1.0
CB X:CYS476 3.4 48.3 1.0
N X:CYS463 3.9 52.1 1.0
CA X:CYS457 4.0 43.8 1.0
CA X:CYS463 4.1 48.7 1.0
N X:CYS476 4.2 46.7 1.0
CA X:CYS476 4.4 47.4 1.0
CA X:ASN461 4.6 46.9 1.0
CA X:CYS473 4.6 48.0 1.0
N X:ASN461 4.7 45.3 1.0
N X:ALA458 4.8 41.2 1.0
N X:ASP462 4.8 52.3 1.0
N X:GLY459 4.8 44.9 1.0
C X:CYS457 4.8 45.6 1.0
C X:ASN461 4.8 50.0 1.0

Reference:

W.H.Hudson, B.R.Kossmann, I.M.De Vera, S.W.Chuo, E.R.Weikum, G.N.Eick, J.W.Thornton, I.N.Ivanov, D.J.Kojetin, E.A.Ortlund. Distal Substitutions Drive Divergent Dna Specificity Among Paralogous Transcription Factors Through Subdivision of Conformational Space. Proc.Natl.Acad.Sci.Usa V. 113 326 2016.
ISSN: ESSN 1091-6490
PubMed: 26715749
DOI: 10.1073/PNAS.1518960113
Page generated: Wed Dec 16 06:06:37 2020

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