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Zinc in PDB 6cfn: Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain

Protein crystallography data

The structure of Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain, PDB code: 6cfn was solved by F.Frank, C.D.Okafor, E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.04 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.803, 65.432, 72.659, 71.27, 84.96, 68.44
R / Rfree (%) 19.5 / 24.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain (pdb code 6cfn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain, PDB code: 6cfn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 6cfn

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Zinc binding site 1 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


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 Dna-Free Glucocorticoid Receptor Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:51.6
occ:1.00
 SG A:CYS424 2.2 54.8 1.0
SG A:CYS441 2.3 62.3 1.0
SG A:CYS438 2.4 44.8 1.0
SG A:CYS421 2.5 63.9 1.0
CB A:CYS424 3.2 54.9 1.0
CB A:CYS421 3.3 43.5 1.0
CB A:CYS441 3.5 62.4 1.0
CB A:CYS438 3.5 51.5 1.0
N A:CYS424 3.7 55.2 1.0
N A:CYS438 4.0 46.0 1.0
CA A:CYS424 4.0 56.1 1.0
N A:CYS441 4.2 60.3 1.0
CA A:CYS438 4.3 52.2 1.0
CA A:CYS441 4.4 59.8 1.0
CB A:VAL423 4.5 54.7 1.0
C A:CYS424 4.7 57.4 1.0
C A:VAL423 4.8 48.9 1.0
NE A:ARG470 4.8 83.8 1.0
CA A:CYS421 4.8 59.9 1.0
N A:SER425 4.8 55.5 1.0
NH2 A:ARG477 4.9 57.3 1.0
C A:CYS438 5.0 60.7 1.0
O A:CYS438 5.0 67.5 1.0

Zinc binding site 2 out of 16 in 6cfn

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Zinc binding site 2 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


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 Dna-Free Glucocorticoid Receptor Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:47.6
occ:1.00
 SG A:CYS463 2.3 45.9 1.0
SG A:CYS473 2.4 44.4 1.0
SG A:CYS457 2.5 48.3 1.0
SG A:CYS476 2.5 44.5 1.0
CB A:CYS457 3.1 36.2 1.0
CB A:CYS476 3.4 33.4 1.0
CB A:CYS473 3.5 38.1 1.0
CB A:CYS463 3.6 36.9 1.0
O A:HOH703 3.7 61.4 1.0
CA A:CYS457 4.0 39.3 1.0
N A:CYS476 4.2 47.3 1.0
N A:CYS463 4.3 44.3 1.0
CA A:CYS476 4.3 41.9 1.0
CA A:ASN461 4.5 36.6 1.0
CA A:CYS463 4.6 37.2 1.0
N A:GLY459 4.6 58.9 1.0
N A:ASN461 4.6 41.9 1.0
C A:CYS457 4.7 48.1 1.0
N A:ASP462 4.8 44.5 1.0
N A:ALA458 4.9 46.0 1.0
CA A:CYS473 4.9 52.7 1.0
ND2 A:ASN461 4.9 43.3 1.0
C A:ASN461 5.0 42.7 1.0
CA A:GLY459 5.0 54.4 1.0

Zinc binding site 3 out of 16 in 6cfn

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Zinc binding site 3 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


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 Dna-Free Glucocorticoid Receptor Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:62.7
occ:1.00
 SG B:CYS441 2.2 53.6 1.0
SG B:CYS424 2.3 76.0 1.0
SG B:CYS438 2.4 59.8 1.0
SG B:CYS421 2.5 69.7 1.0
CB B:CYS424 3.2 57.5 1.0
CB B:CYS438 3.3 68.3 1.0
CB B:CYS441 3.4 59.6 1.0
CB B:CYS421 3.5 61.5 1.0
CG1 B:VAL423 3.7 77.2 1.0
NH1 B:ARG470 3.7 66.6 1.0
N B:CYS438 3.8 75.0 1.0
N B:CYS424 3.9 54.9 1.0
CA B:CYS424 4.1 60.9 1.0
CA B:CYS438 4.1 74.1 1.0
N B:CYS441 4.2 55.1 1.0
CA B:CYS441 4.4 56.0 1.0
CB B:ASP426 4.5 73.5 1.0
C B:CYS424 4.6 65.1 1.0
C B:CYS438 4.8 74.5 1.0
O B:CYS438 4.8 79.5 1.0
NH2 B:ARG477 4.8 57.5 1.0
N B:ASP426 4.8 70.2 1.0
C B:VAL423 4.9 56.4 1.0
N B:SER425 4.9 68.6 1.0
CA B:CYS421 5.0 62.6 1.0
CD B:ARG470 5.0 52.1 1.0
C B:THR437 5.0 65.0 1.0
CZ B:ARG470 5.0 61.2 1.0

Zinc binding site 4 out of 16 in 6cfn

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Zinc binding site 4 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


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 Dna-Free Glucocorticoid Receptor Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:45.2
occ:1.00
 SG B:CYS473 2.1 51.5 1.0
SG B:CYS463 2.2 64.3 1.0
SG B:CYS457 2.4 47.5 1.0
SG B:CYS476 2.6 46.4 1.0
CB B:CYS457 3.1 45.2 1.0
CB B:CYS473 3.1 41.8 1.0
CB B:CYS476 3.3 39.9 1.0
CB B:CYS463 3.6 60.6 1.0
CA B:CYS457 4.1 51.5 1.0
N B:CYS476 4.1 37.8 1.0
N B:CYS463 4.2 50.3 1.0
O B:HOH703 4.2 58.1 1.0
CA B:CYS476 4.3 46.9 1.0
CA B:ASN461 4.5 60.2 1.0
CA B:CYS463 4.5 49.2 1.0
CA B:CYS473 4.5 41.4 1.0
N B:ASN461 4.6 61.4 1.0
N B:GLY459 4.7 55.0 1.0
N B:ASP462 4.7 55.9 1.0
C B:CYS457 4.8 58.3 1.0
C B:ASN461 4.8 59.3 1.0
O B:CYS473 4.9 60.4 1.0
N B:ALA458 5.0 51.9 1.0

Zinc binding site 5 out of 16 in 6cfn

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Zinc binding site 5 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


Mono view


Stereo pair view

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

b:54.8
occ:1.00
 SG C:CYS424 2.2 61.8 1.0
SG C:CYS438 2.3 64.3 1.0
SG C:CYS421 2.4 71.2 1.0
SG C:CYS441 2.4 59.7 1.0
CB C:CYS424 2.9 58.8 1.0
CB C:CYS421 3.3 69.5 1.0
CB C:CYS438 3.4 62.2 1.0
CB C:CYS441 3.4 58.8 1.0
N C:CYS424 3.7 56.5 1.0
CG2 C:VAL423 3.8 62.4 1.0
CA C:CYS424 3.8 57.5 1.0
N C:CYS438 4.0 64.1 1.0
N C:CYS441 4.2 61.6 1.0
CA C:CYS438 4.3 55.0 1.0
NH1 C:ARG470 4.4 69.5 1.0
CA C:CYS441 4.4 57.3 1.0
C C:CYS424 4.5 67.0 1.0
CB C:ASP426 4.7 82.1 1.0
C C:VAL423 4.7 63.6 1.0
CA C:CYS421 4.7 76.9 1.0
N C:SER425 4.8 68.9 1.0
NH2 C:ARG477 4.8 58.2 1.0
N C:ASP426 4.9 65.3 1.0
C C:CYS438 5.0 60.1 1.0
CB C:VAL423 5.0 64.8 1.0

Zinc binding site 6 out of 16 in 6cfn

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Zinc binding site 6 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


Mono view


Stereo pair view

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

b:48.5
occ:1.00
 SG C:CYS463 2.3 46.1 1.0
SG C:CYS473 2.3 48.3 1.0
SG C:CYS457 2.4 39.9 1.0
SG C:CYS476 2.5 48.6 1.0
CB C:CYS473 3.1 30.7 1.0
CB C:CYS457 3.2 32.2 1.0
CB C:CYS463 3.3 60.2 1.0
CB C:CYS476 3.4 30.6 1.0
O C:HOH703 3.8 53.0 1.0
CA C:CYS457 4.1 39.7 1.0
N C:CYS476 4.1 38.5 1.0
N C:CYS463 4.3 55.0 1.0
CA C:CYS476 4.3 43.0 1.0
CA C:CYS463 4.4 54.3 1.0
CA C:CYS473 4.6 39.1 1.0
N C:GLY459 4.7 47.5 1.0
N C:ALA458 4.7 47.3 1.0
CA C:ASN461 4.7 42.4 1.0
C C:CYS457 4.7 43.2 1.0
N C:ASN461 4.8 47.7 1.0
O C:CYS473 4.9 53.7 1.0
N C:ASP462 4.9 38.3 1.0

Zinc binding site 7 out of 16 in 6cfn

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Zinc binding site 7 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


Mono view


Stereo pair view

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

b:58.1
occ:1.00
 SG D:CYS438 2.2 61.6 1.0
SG D:CYS424 2.2 57.1 1.0
SG D:CYS441 2.2 65.8 1.0
SG D:CYS421 2.4 68.5 1.0
CB D:CYS424 3.2 58.6 1.0
CB D:CYS421 3.3 57.8 1.0
CB D:CYS441 3.4 68.4 1.0
CB D:CYS438 3.5 64.8 1.0
N D:CYS424 3.7 48.5 1.0
CA D:CYS424 4.0 60.2 1.0
N D:CYS438 4.0 65.1 1.0
NH1 D:ARG470 4.1 59.7 1.0
N D:CYS441 4.2 58.6 1.0
CA D:CYS438 4.3 62.4 1.0
CA D:CYS441 4.4 70.1 1.0
CB D:VAL423 4.4 54.2 1.0
C D:CYS424 4.7 73.2 1.0
C D:VAL423 4.7 53.1 1.0
CA D:CYS421 4.7 60.0 1.0
CG1 D:VAL423 4.8 48.1 1.0
CG2 D:THR437 4.8 71.6 1.0
N D:SER425 4.8 70.4 1.0
C D:CYS438 4.9 67.0 1.0
CA D:VAL423 4.9 54.8 1.0
O D:CYS438 4.9 64.3 1.0
CB D:ASP426 5.0 73.0 1.0
N D:VAL423 5.0 58.7 1.0

Zinc binding site 8 out of 16 in 6cfn

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Zinc binding site 8 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


Mono view


Stereo pair view

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

b:47.2
occ:1.00
 SG D:CYS463 2.2 46.2 1.0
SG D:CYS473 2.3 51.4 1.0
SG D:CYS476 2.4 52.0 1.0
SG D:CYS457 2.4 41.1 1.0
CB D:CYS457 3.1 36.5 1.0
CB D:CYS463 3.2 47.1 1.0
CB D:CYS473 3.3 41.1 1.0
CB D:CYS476 3.3 37.1 1.0
CA D:CYS457 3.9 51.9 1.0
O D:HOH701 3.9 55.3 1.0
N D:CYS476 4.0 54.7 1.0
N D:CYS463 4.1 54.9 1.0
CA D:CYS476 4.2 50.5 1.0
CA D:CYS463 4.3 55.2 1.0
CA D:ASN461 4.5 57.7 1.0
N D:ASN461 4.6 61.4 1.0
C D:CYS457 4.6 52.4 1.0
CA D:CYS473 4.7 46.5 1.0
N D:ASP462 4.8 75.3 1.0
N D:ALA458 4.8 49.7 1.0
N D:GLY459 4.8 60.6 1.0
CB E:ALA458 5.0 25.4 1.0
C D:ASN461 5.0 65.7 1.0

Zinc binding site 9 out of 16 in 6cfn

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Zinc binding site 9 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:53.4
occ:1.00
 SG E:CYS438 2.2 66.7 1.0
SG E:CYS424 2.3 55.3 1.0
SG E:CYS441 2.3 63.5 1.0
SG E:CYS421 2.4 74.4 1.0
CB E:CYS424 2.5 57.9 1.0
CB E:CYS441 3.3 64.4 1.0
CB E:CYS421 3.3 56.3 1.0
CB E:CYS438 3.4 67.3 1.0
CA E:CYS424 3.8 62.6 1.0
N E:CYS438 3.9 59.4 1.0
N E:CYS424 3.9 66.9 1.0
N E:CYS441 4.2 62.4 1.0
CA E:CYS438 4.2 59.2 1.0
OG E:SER440 4.3 80.0 1.0
CA E:CYS441 4.3 57.6 1.0
C E:CYS424 4.5 68.2 1.0
CB E:ASP426 4.6 85.6 1.0
NH1 E:ARG470 4.6 81.2 1.0
CB E:VAL423 4.7 57.2 1.0
CD E:ARG470 4.8 80.9 1.0
CA E:CYS421 4.8 61.4 1.0
N E:SER425 4.8 73.4 1.0
NH2 E:ARG477 4.8 64.0 1.0
C E:VAL423 4.9 66.6 1.0
C E:CYS438 4.9 55.2 1.0
N E:ASP426 5.0 72.0 1.0

Zinc binding site 10 out of 16 in 6cfn

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Zinc binding site 10 out of 16 in the Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Dna-Free Glucocorticoid Receptor Dna Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn602

b:45.9
occ:1.00
 SG E:CYS457 2.3 41.6 1.0
SG E:CYS473 2.3 37.7 1.0
SG E:CYS463 2.3 44.2 1.0
SG E:CYS476 2.4 47.1 1.0
CB E:CYS457 3.3 38.5 1.0
CB E:CYS463 3.3 41.1 1.0
CB E:CYS476 3.3 35.5 1.0
CB E:CYS473 3.4 40.7 1.0
N E:CYS476 4.0 45.7 1.0
CA E:CYS457 4.1 44.0 1.0
N E:CYS463 4.2 48.9 1.0
CA E:CYS476 4.2 51.7 1.0
CA E:CYS463 4.3 43.2 1.0
O E:HOH701 4.5 41.1 1.0
CB D:ALA458 4.6 35.6 1.0
CA E:ASN461 4.6 41.1 1.0
N E:ASN461 4.7 41.1 1.0
N E:ASP462 4.7 47.4 1.0
N E:GLY459 4.8 53.1 1.0
CA E:CYS473 4.8 46.9 1.0
C E:CYS457 4.9 41.1 1.0
N E:ALA458 4.9 35.5 1.0
O E:CYS473 5.0 47.2 1.0
CB E:ALA475 5.0 41.1 1.0
C E:ASN461 5.0 50.2 1.0

Reference:

F.Frank, C.D.Okafor, E.A.Ortlund. The First Crystal Structure of A Dna-Free Nuclear Receptor Dna Binding Domain Sheds Light on Dna-Driven Allostery in the Glucocorticoid Receptor. Sci Rep V. 8 13497 2018.
ISSN: ESSN 2045-2322
PubMed: 30201977
DOI: 10.1038/S41598-018-31812-9
Page generated: Mon Oct 28 18:49:44 2024

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