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Zinc in PDB 3g9o: Gr Dna-Binding Domain:Sgk 16BP Complex-9

Protein crystallography data

The structure of Gr Dna-Binding Domain:Sgk 16BP Complex-9, PDB code: 3g9o 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) 34.35 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.382, 38.470, 97.039, 90.00, 123.44, 90.00
R / Rfree (%) 17.7 / 20.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Gr Dna-Binding Domain:Sgk 16BP Complex-9 (pdb code 3g9o). 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:Sgk 16BP Complex-9, PDB code: 3g9o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3g9o

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Zinc binding site 1 out of 4 in the Gr Dna-Binding Domain:Sgk 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:Sgk 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn526

b:46.4
occ:1.00
SG B:CYS443 2.3 48.0 1.0
SG B:CYS457 2.3 47.0 1.0
SG B:CYS440 2.4 47.0 1.0
SG B:CYS460 2.4 40.7 1.0
CB B:CYS460 3.1 47.5 1.0
CB B:CYS440 3.2 63.6 1.0
CB B:CYS443 3.3 48.0 1.0
CB B:CYS457 3.5 52.6 1.0
N B:CYS443 3.7 44.7 1.0
N B:CYS457 3.9 54.9 1.0
CA B:CYS443 4.0 50.3 1.0
N B:CYS460 4.2 40.0 1.0
CA B:CYS460 4.2 43.1 1.0
NH1 B:ARG489 4.3 53.5 1.0
CA B:CYS457 4.3 52.6 1.0
CB B:VAL442 4.5 51.5 1.0
CB B:ASP445 4.5 65.0 1.0
OG B:SER459 4.6 52.1 1.0
C B:CYS443 4.7 54.8 1.0
CA B:CYS440 4.7 60.1 1.0
C B:VAL442 4.7 42.4 1.0
N B:SER444 4.8 55.0 1.0
N B:ASP445 4.8 60.0 1.0
C B:CYS457 4.9 52.3 1.0
O B:CYS457 4.9 49.5 1.0
CD B:ARG489 5.0 45.4 1.0
NH2 B:ARG496 5.0 35.4 1.0
CA B:VAL442 5.0 47.7 1.0
C B:THR456 5.0 59.3 1.0

Zinc binding site 2 out of 4 in 3g9o

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Zinc binding site 2 out of 4 in the Gr Dna-Binding Domain:Sgk 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:Sgk 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn527

b:29.2
occ:1.00
SG B:CYS476 2.3 26.3 1.0
SG B:CYS495 2.3 28.6 1.0
SG B:CYS482 2.3 32.0 1.0
SG B:CYS492 2.4 27.9 1.0
CB B:CYS482 3.2 34.7 1.0
CB B:CYS476 3.3 23.8 1.0
CB B:CYS495 3.3 27.2 1.0
CB B:CYS492 3.4 25.1 1.0
O B:HOH3 3.8 29.0 1.0
CA B:CYS476 4.0 21.7 1.0
N B:CYS482 4.0 31.1 1.0
O B:HOH1 4.1 31.5 1.0
N B:CYS495 4.2 26.7 1.0
CA B:CYS482 4.2 29.9 1.0
CA B:CYS495 4.3 29.6 1.0
N B:ASP481 4.6 27.0 1.0
O A:HOH32 4.6 40.3 1.0
CA B:ASN480 4.6 29.4 1.0
O B:HOH2 4.7 35.8 1.0
N B:ALA477 4.7 26.7 1.0
N B:ASN480 4.7 28.2 1.0
CA B:CYS492 4.8 26.3 1.0
C B:CYS476 4.8 23.0 1.0
N B:GLY478 4.9 27.5 1.0
C B:ASN480 4.9 32.1 1.0

Zinc binding site 3 out of 4 in 3g9o

Go back to Zinc Binding Sites List in 3g9o
Zinc binding site 3 out of 4 in the Gr Dna-Binding Domain:Sgk 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:Sgk 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn526

b:33.4
occ:1.00
SG A:CYS460 2.3 32.4 1.0
SG A:CYS443 2.3 33.8 1.0
SG A:CYS440 2.4 30.6 1.0
SG A:CYS457 2.4 33.0 1.0
CB A:CYS460 3.2 31.7 1.0
CB A:CYS440 3.3 36.5 1.0
CB A:CYS443 3.3 33.1 1.0
CB A:CYS457 3.6 33.3 1.0
N A:CYS443 3.7 32.1 1.0
N A:CYS457 3.9 32.6 1.0
CA A:CYS443 4.0 34.2 1.0
N A:CYS460 4.2 29.6 1.0
NH1 A:ARG489 4.2 37.6 1.0
CA A:CYS460 4.3 30.1 1.0
CA A:CYS457 4.3 33.5 1.0
OG A:SER459 4.4 36.8 1.0
CB A:VAL442 4.5 30.6 1.0
CB A:ASP445 4.5 49.9 1.0
C A:CYS443 4.6 42.7 1.0
C A:VAL442 4.7 33.5 1.0
CA A:CYS440 4.7 31.7 1.0
N A:SER444 4.8 39.0 1.0
C A:CYS457 4.9 36.1 1.0
N A:ASP445 4.9 45.8 1.0
O A:CYS457 4.9 32.5 1.0
NH2 A:ARG496 4.9 28.2 1.0
CD A:ARG489 5.0 28.2 1.0
CA A:VAL442 5.0 30.2 1.0

Zinc binding site 4 out of 4 in 3g9o

Go back to Zinc Binding Sites List in 3g9o
Zinc binding site 4 out of 4 in the Gr Dna-Binding Domain:Sgk 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:Sgk 16BP Complex-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn527

b:30.1
occ:1.00
SG A:CYS482 2.3 31.0 1.0
SG A:CYS476 2.3 28.9 1.0
SG A:CYS495 2.4 28.2 1.0
SG A:CYS492 2.4 28.0 1.0
CB A:CYS482 3.2 30.3 1.0
CB A:CYS476 3.3 31.2 1.0
CB A:CYS492 3.3 27.4 1.0
CB A:CYS495 3.5 27.2 1.0
O A:HOH7 3.8 33.7 1.0
N A:CYS482 4.0 33.3 1.0
CA A:CYS476 4.0 28.8 1.0
N A:CYS495 4.2 25.9 1.0
CA A:CYS482 4.2 32.3 1.0
CA A:ASN480 4.3 38.4 1.0
CA A:CYS495 4.4 24.2 1.0
N A:ASN480 4.5 35.5 1.0
O A:HOH11 4.6 31.5 1.0
O A:HOH21 4.6 45.7 1.0
N A:ASP481 4.6 31.5 1.0
N A:ALA477 4.7 32.3 1.0
O A:HOH32 4.7 40.3 1.0
CA A:CYS492 4.7 25.1 1.0
C A:ASN480 4.7 33.6 1.0
N A:GLY478 4.8 33.7 1.0
C A:CYS476 4.8 32.1 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 10:14:49 2020
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