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Zinc in PDB 3fyl: Gr Dna Binding Domain:Cgt Complex

Protein crystallography data

The structure of Gr Dna Binding Domain:Cgt Complex, PDB code: 3fyl was solved by M.A.Pufall, K.R.Yamamoto, S.H.Meijsing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.24 / 1.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.445, 37.770, 96.679, 90.00, 123.50, 90.00
R / Rfree (%) 19.6 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Gr Dna Binding Domain:Cgt Complex (pdb code 3fyl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Gr Dna Binding Domain:Cgt Complex, PDB code: 3fyl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3fyl

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Zinc binding site 1 out of 4 in the Gr Dna Binding Domain:Cgt Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gr Dna Binding Domain:Cgt Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn526

b:30.4
occ:0.56
SG A:CYS460 2.2 27.6 0.5
SG A:CYS440 2.3 29.7 0.6
SG A:CYS443 2.3 34.1 0.7
SG A:CYS457 2.4 36.3 0.7
CB A:CYS460 3.2 33.6 0.8
CB A:CYS440 3.2 41.5 1.0
CB A:CYS443 3.3 35.6 0.7
CB A:CYS457 3.7 40.3 0.8
N A:CYS443 3.7 41.2 1.0
N A:CYS457 3.9 41.4 1.0
CA A:CYS443 4.1 33.4 0.7
N A:CYS460 4.1 23.1 0.5
NH1 A:ARG489 4.2 37.1 0.8
CA A:CYS460 4.2 27.9 0.8
CA A:CYS457 4.4 34.8 0.8
OG A:SER459 4.4 29.8 0.5
CB A:VAL442 4.4 28.1 0.8
CB A:ASP445 4.6 48.6 1.0
CA A:CYS440 4.7 39.1 1.0
C A:CYS443 4.7 44.6 1.0
C A:VAL442 4.7 42.7 1.0
N A:SER444 4.8 34.5 0.7
O A:CYS457 4.9 32.8 0.7
C A:CYS457 4.9 36.3 1.0
N A:ASP445 4.9 45.8 0.7
NH2 A:ARG496 4.9 22.2 0.5
CD A:ARG489 4.9 23.9 0.5
CB A:THR456 5.0 38.9 1.0
CA A:VAL442 5.0 29.4 0.8
N A:VAL442 5.0 23.1 0.6

Zinc binding site 2 out of 4 in 3fyl

Go back to Zinc Binding Sites List in 3fyl
Zinc binding site 2 out of 4 in the Gr Dna Binding Domain:Cgt Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gr Dna Binding Domain:Cgt Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn527

b:28.4
occ:0.64
SG A:CYS482 2.2 24.7 0.5
SG A:CYS476 2.3 34.8 1.0
SG A:CYS495 2.3 23.9 0.6
SG A:CYS492 2.4 23.9 0.5
CB A:CYS482 3.2 29.2 0.7
CB A:CYS492 3.2 31.4 1.0
CB A:CYS476 3.3 33.7 1.0
CB A:CYS495 3.4 36.0 1.0
O A:HOH4 3.8 37.7 1.0
N A:CYS482 3.9 29.9 0.6
CA A:CYS476 4.0 27.0 0.7
N A:CYS495 4.2 24.5 0.6
CA A:CYS482 4.2 33.9 1.0
CA A:CYS495 4.4 30.1 1.0
O A:HOH58 4.4 53.1 1.0
CA A:ASN480 4.4 38.0 0.8
N A:ASP481 4.5 29.2 0.7
N A:ASN480 4.6 43.2 1.0
O A:HOH7 4.6 33.2 1.0
O A:HOH2 4.7 39.5 1.0
CA A:CYS492 4.7 23.6 0.6
C A:ASN480 4.7 36.3 0.9
N A:GLY478 4.8 34.6 0.8
N A:ALA477 4.8 25.7 0.5
C A:CYS476 4.9 26.2 0.7

Zinc binding site 3 out of 4 in 3fyl

Go back to Zinc Binding Sites List in 3fyl
Zinc binding site 3 out of 4 in the Gr Dna Binding Domain:Cgt Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Gr Dna Binding Domain:Cgt Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn526

b:50.5
occ:1.00
SG B:CYS460 2.3 42.0 0.8
SG B:CYS457 2.3 51.8 1.0
SG B:CYS443 2.3 49.9 1.0
SG B:CYS440 2.4 41.4 0.6
CB B:CYS460 3.1 35.9 0.7
CB B:CYS440 3.2 48.8 1.0
CB B:CYS443 3.4 50.9 1.0
CB B:CYS457 3.6 46.8 1.0
N B:CYS443 3.8 47.7 1.0
N B:CYS457 3.9 53.0 1.0
CA B:CYS443 4.1 46.3 0.9
N B:CYS460 4.2 40.0 0.8
CA B:CYS460 4.2 42.5 0.9
CA B:CYS457 4.4 49.6 1.0
NH1 B:ARG489 4.4 44.0 0.8
CB B:ASP445 4.5 49.4 0.8
OG B:SER459 4.5 37.6 0.5
CB B:VAL442 4.5 37.6 0.6
CA B:CYS440 4.7 53.1 1.0
C B:CYS443 4.7 53.2 1.0
N B:ASP445 4.8 55.2 0.8
C B:VAL442 4.8 47.7 1.0
N B:SER444 4.8 52.3 1.0
NH2 B:ARG496 4.8 34.0 0.6
CD B:ARG489 4.9 43.8 1.0
C B:CYS457 5.0 52.8 1.0
O B:CYS457 5.0 53.2 1.0
CG1 B:VAL442 5.0 35.1 0.6

Zinc binding site 4 out of 4 in 3fyl

Go back to Zinc Binding Sites List in 3fyl
Zinc binding site 4 out of 4 in the Gr Dna Binding Domain:Cgt Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Gr Dna Binding Domain:Cgt Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn527

b:35.3
occ:1.00
SG B:CYS482 2.2 29.4 0.7
SG B:CYS476 2.3 26.5 0.7
SG B:CYS495 2.3 20.2 0.5
SG B:CYS492 2.4 23.4 0.5
CB B:CYS482 3.2 31.7 0.8
CB B:CYS495 3.3 33.7 1.0
CB B:CYS492 3.3 25.8 0.7
CB B:CYS476 3.4 18.5 0.5
O A:HOH13 3.8 32.8 1.0
N B:CYS482 3.9 37.3 0.8
CA B:CYS476 4.0 21.4 0.6
N B:CYS495 4.1 24.9 0.6
CA B:CYS482 4.2 37.6 1.0
O B:HOH11 4.2 38.0 1.0
CA B:CYS495 4.3 38.0 1.0
O A:HOH2 4.5 39.5 1.0
N B:ASP481 4.6 22.8 0.5
CA B:ASN480 4.6 37.1 1.0
N B:ASN480 4.7 25.5 0.6
CA B:CYS492 4.7 28.3 0.8
N B:ALA477 4.8 18.1 0.5
N B:GLY478 4.8 20.4 0.5
O B:HOH32 4.8 44.1 1.0
C B:CYS476 4.9 25.2 0.8
C B:ASN480 4.9 34.8 0.8
CB B:ALA494 4.9 33.2 0.8

Reference:

S.H.Meijsing, M.A.Pufall, A.Y.So, D.L.Bates, L.Chen, K.R.Yamamoto. Dna Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity. Science V. 324 407 2009.
ISSN: ISSN 0036-8075
PubMed: 19372434
DOI: 10.1126/SCIENCE.1164265
Page generated: Sat Sep 26 10:11:41 2020
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