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Zinc in PDB 3g97: Gr Dna-Binding Domain:Gilz 16BP Complex-9

Protein crystallography data

The structure of Gr Dna-Binding Domain:Gilz 16BP Complex-9, PDB code: 3g97 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) 34.55 / 2.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.823, 38.589, 97.120, 90.00, 122.89, 90.00
R / Rfree (%) 20.3 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Gr Dna-Binding Domain:Gilz 16BP Complex-9 (pdb code 3g97). 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:Gilz 16BP Complex-9, PDB code: 3g97:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3g97

Go back to Zinc Binding Sites List in 3g97
Zinc binding site 1 out of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9


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:Gilz 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn526

b:97.0
occ:1.00
SG B:CYS460 2.4 88.9 1.0
SG B:CYS440 2.5 0.9 1.0
SG B:CYS443 2.5 99.2 1.0
SG B:CYS457 2.7 0.3 1.0
CB B:CYS460 3.3 80.6 1.0
CB B:CYS440 3.3 0.5 1.0
CB B:CYS457 3.4 96.2 1.0
N B:CYS443 3.4 0.6 1.0
CB B:CYS443 3.4 0.9 1.0
N B:CYS457 3.6 97.3 1.0
CA B:CYS443 3.9 0.3 1.0
CA B:CYS457 4.1 99.4 1.0
CB B:VAL442 4.3 87.0 1.0
C B:CYS443 4.4 0.1 1.0
CA B:CYS460 4.5 80.0 1.0
CB B:ASP445 4.5 0.5 1.0
N B:CYS460 4.5 85.8 1.0
C B:VAL442 4.5 94.6 1.0
N B:SER444 4.6 0.9 1.0
C B:THR456 4.7 99.9 1.0
N B:ASP445 4.7 0.7 1.0
C B:CYS457 4.8 96.9 1.0
CA B:CYS440 4.8 0.3 1.0
OG B:SER459 4.8 93.7 1.0
CA B:VAL442 4.8 92.6 1.0
CA B:THR456 4.8 98.7 1.0
NH1 B:ARG489 4.8 0.6 1.0
O B:CYS457 4.8 93.6 1.0
N B:VAL442 4.9 98.4 1.0
CB B:THR456 4.9 95.8 1.0
O B:CYS443 5.0 0.1 1.0

Zinc binding site 2 out of 4 in 3g97

Go back to Zinc Binding Sites List in 3g97
Zinc binding site 2 out of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9


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:Gilz 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn527

b:47.8
occ:1.00
SG B:CYS482 2.2 42.7 1.0
SG B:CYS476 2.2 41.0 1.0
SG B:CYS492 2.3 43.6 1.0
SG B:CYS495 2.5 52.0 1.0
CB B:CYS482 3.2 45.8 1.0
CB B:CYS492 3.4 43.1 1.0
CB B:CYS495 3.4 36.4 1.0
CB B:CYS476 3.4 32.4 1.0
O B:HOH34 3.7 52.3 1.0
N B:CYS482 3.9 48.0 1.0
CA B:CYS476 4.0 38.5 1.0
O B:HOH13 4.1 40.2 1.0
CA B:CYS482 4.1 45.2 1.0
N B:CYS495 4.3 46.6 1.0
CA B:CYS495 4.4 47.3 1.0
O2 A:EDO1 4.5 46.1 1.0
N B:ASP481 4.6 49.7 1.0
O B:HOH14 4.6 57.2 1.0
N B:ASN480 4.6 44.0 1.0
CA B:ASN480 4.6 48.8 1.0
N B:ALA477 4.6 35.4 1.0
N B:GLY478 4.8 47.1 1.0
CA B:CYS492 4.8 43.8 1.0
C B:CYS476 4.8 37.9 1.0
C B:ASN480 4.9 50.8 1.0

Zinc binding site 3 out of 4 in 3g97

Go back to Zinc Binding Sites List in 3g97
Zinc binding site 3 out of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9


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:Gilz 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn526

b:62.5
occ:1.00
SG A:CYS460 2.2 56.7 1.0
SG A:CYS457 2.3 77.1 1.0
SG A:CYS443 2.3 60.8 1.0
SG A:CYS440 2.6 53.8 1.0
CB A:CYS443 3.0 58.7 1.0
CB A:CYS440 3.1 53.5 1.0
CB A:CYS460 3.4 51.8 1.0
CG2 A:VAL442 3.7 68.6 1.0
N A:CYS443 3.7 72.4 1.0
CB A:CYS457 3.7 68.4 1.0
CA A:CYS443 3.9 64.7 1.0
N A:CYS457 3.9 69.4 1.0
OG A:SER459 4.0 67.0 1.0
N A:CYS460 4.3 41.8 1.0
CA A:CYS457 4.4 62.9 1.0
CA A:CYS460 4.4 33.1 1.0
C A:CYS443 4.4 73.3 1.0
CB A:ASP445 4.5 78.5 1.0
CA A:CYS440 4.6 59.5 1.0
N A:ASP445 4.6 75.0 1.0
N A:SER444 4.7 78.0 1.0
O A:CYS457 4.7 51.6 1.0
C A:VAL442 4.8 66.4 1.0
NH2 A:ARG496 4.8 63.1 1.0
C A:CYS457 4.8 58.1 1.0
CD A:ARG489 4.9 72.2 1.0
NH1 A:ARG489 5.0 53.4 1.0

Zinc binding site 4 out of 4 in 3g97

Go back to Zinc Binding Sites List in 3g97
Zinc binding site 4 out of 4 in the Gr Dna-Binding Domain:Gilz 16BP Complex-9


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:Gilz 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn527

b:40.6
occ:1.00
SG A:CYS482 2.2 44.2 1.0
SG A:CYS476 2.3 38.8 1.0
SG A:CYS492 2.3 41.0 1.0
SG A:CYS495 2.4 43.6 1.0
CB A:CYS482 3.2 57.6 1.0
CB A:CYS495 3.3 32.3 1.0
CB A:CYS492 3.4 36.6 1.0
CB A:CYS476 3.4 29.2 1.0
C1 A:EDO1 3.7 50.9 1.0
N A:CYS482 3.9 44.2 1.0
CA A:CYS476 4.0 38.3 1.0
N A:CYS495 4.1 27.6 1.0
CA A:CYS482 4.2 49.1 1.0
CA A:CYS495 4.3 31.8 1.0
CA A:ASN480 4.3 45.8 1.0
N A:ASN480 4.4 55.7 1.0
O A:HOH529 4.5 35.7 1.0
O1 A:EDO1 4.6 47.6 1.0
N A:ASP481 4.6 37.0 1.0
O2 A:EDO1 4.7 46.1 1.0
N A:ALA477 4.7 46.4 1.0
O A:HOH7 4.7 54.0 1.0
C A:ASN480 4.8 42.6 1.0
CA A:CYS492 4.8 37.5 1.0
C A:CYS476 4.8 48.5 1.0
C2 A:EDO1 4.8 57.1 1.0
N A:GLY478 4.8 46.7 1.0
CB A:ALA494 4.9 41.8 1.0

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 10:14:12 2020
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