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Zinc in PDB 3g9m: Gr Dna-Binding Domain:Sgk 16BP Complex-44

Protein crystallography data

The structure of Gr Dna-Binding Domain:Sgk 16BP Complex-44, PDB code: 3g9m 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) 30.61 / 1.61
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.058, 38.713, 96.475, 90.00, 123.71, 90.00
R / Rfree (%) 18.7 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Gr Dna-Binding Domain:Sgk 16BP Complex-44 (pdb code 3g9m). 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-44, PDB code: 3g9m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3g9m

Go back to Zinc Binding Sites List in 3g9m
Zinc binding site 1 out of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44


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-44 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn526

b:27.2
occ:1.00
SG A:CYS460 2.3 26.1 1.0
SG A:CYS443 2.3 29.2 1.0
SG A:CYS440 2.3 25.7 1.0
SG A:CYS457 2.3 28.1 1.0
CB A:CYS460 3.2 25.0 1.0
CB A:CYS440 3.3 31.1 1.0
CB A:CYS443 3.4 25.5 1.0
CB A:CYS457 3.7 22.7 1.0
N A:CYS443 3.7 27.7 1.0
N A:CYS457 3.9 25.5 1.0
CA A:CYS443 4.1 25.9 1.0
N A:CYS460 4.2 23.1 1.0
CA A:CYS460 4.3 26.3 1.0
NH1 A:ARG489 4.3 31.4 1.0
CA A:CYS457 4.3 25.9 1.0
OG A:SER459 4.5 28.2 1.0
CB A:VAL442 4.5 22.9 1.0
CB A:ASP445 4.5 37.3 1.0
C A:VAL442 4.7 30.1 1.0
C A:CYS443 4.7 38.1 1.0
CA A:CYS440 4.7 32.7 1.0
N A:SER444 4.8 30.9 1.0
N A:ASP445 4.8 40.0 1.0
O A:CYS457 4.8 26.0 1.0
NH2 A:ARG496 4.9 24.8 1.0
C A:CYS457 4.9 26.8 1.0
CD A:ARG489 4.9 29.5 1.0
CA A:VAL442 5.0 28.7 1.0
N A:VAL442 5.0 27.5 1.0

Zinc binding site 2 out of 4 in 3g9m

Go back to Zinc Binding Sites List in 3g9m
Zinc binding site 2 out of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44


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-44 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn527

b:21.8
occ:1.00
SG A:CYS482 2.3 22.1 1.0
SG A:CYS492 2.3 21.3 1.0
SG A:CYS495 2.3 22.5 1.0
SG A:CYS476 2.4 22.5 1.0
CB A:CYS482 3.2 25.1 1.0
CB A:CYS492 3.3 22.1 1.0
CB A:CYS476 3.4 19.8 1.0
CB A:CYS495 3.5 18.7 1.0
O1 A:EDO1 3.7 24.2 1.0
N A:CYS482 4.0 21.8 1.0
CA A:CYS476 4.0 23.5 1.0
C1 A:EDO1 4.1 40.0 1.0
N A:CYS495 4.1 20.9 1.0
CA A:CYS482 4.2 24.3 1.0
CA A:CYS495 4.4 19.3 1.0
CA A:ASN480 4.4 26.6 1.0
N A:ASN480 4.5 26.7 1.0
O A:HOH7 4.6 23.6 1.0
C2 A:EDO1 4.6 46.2 1.0
N A:ASP481 4.6 23.6 1.0
N A:ALA477 4.7 20.4 1.0
O A:HOH32 4.7 37.4 1.0
CA A:CYS492 4.8 18.2 1.0
C A:ASN480 4.8 25.1 1.0
N A:GLY478 4.8 24.5 1.0
O2 A:EDO1 4.8 28.3 1.0
C A:CYS476 4.8 25.8 1.0

Zinc binding site 3 out of 4 in 3g9m

Go back to Zinc Binding Sites List in 3g9m
Zinc binding site 3 out of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44


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-44 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn526

b:32.5
occ:1.00
SG B:CYS443 2.3 32.9 1.0
SG B:CYS460 2.3 31.0 1.0
SG B:CYS440 2.4 33.0 1.0
SG B:CYS457 2.4 34.0 1.0
CB B:CYS460 3.2 30.2 1.0
CB B:CYS440 3.3 34.2 1.0
CB B:CYS443 3.3 29.8 1.0
CB B:CYS457 3.6 29.9 1.0
N B:CYS443 3.8 31.0 1.0
N B:CYS457 3.9 34.9 1.0
CA B:CYS443 4.1 34.6 1.0
N B:CYS460 4.2 28.1 1.0
CA B:CYS460 4.3 27.3 1.0
CA B:CYS457 4.3 31.7 1.0
NH1 B:ARG489 4.4 38.9 1.0
OG B:SER459 4.5 34.9 1.0
CB B:VAL442 4.5 34.9 1.0
CB B:ASP445 4.6 39.2 1.0
C B:CYS443 4.7 37.2 1.0
CA B:CYS440 4.7 35.8 1.0
C B:VAL442 4.8 30.2 1.0
O B:CYS457 4.8 32.4 1.0
NH2 B:ARG496 4.8 26.9 1.0
N B:SER444 4.8 40.3 1.0
C B:CYS457 4.9 31.7 1.0
CD B:ARG489 4.9 30.4 1.0
N B:ASP445 4.9 44.0 1.0

Zinc binding site 4 out of 4 in 3g9m

Go back to Zinc Binding Sites List in 3g9m
Zinc binding site 4 out of 4 in the Gr Dna-Binding Domain:Sgk 16BP Complex-44


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-44 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn527

b:22.2
occ:1.00
SG B:CYS482 2.3 22.9 1.0
SG B:CYS476 2.3 21.2 1.0
SG B:CYS492 2.4 21.8 1.0
SG B:CYS495 2.4 23.4 1.0
CB B:CYS482 3.2 23.0 1.0
CB B:CYS492 3.3 18.6 1.0
CB B:CYS495 3.3 18.9 1.0
CB B:CYS476 3.4 18.7 1.0
O A:HOH529 3.8 22.1 1.0
N B:CYS482 3.9 25.7 1.0
CA B:CYS476 4.0 19.7 1.0
O B:HOH11 4.1 24.2 1.0
N B:CYS495 4.1 21.2 1.0
CA B:CYS482 4.2 24.2 1.0
CA B:CYS495 4.3 20.7 1.0
O2 A:EDO1 4.5 28.3 1.0
CA B:ASN480 4.6 23.7 1.0
N B:ASP481 4.6 23.4 1.0
N B:ASN480 4.7 22.3 1.0
O B:HOH14 4.7 28.0 1.0
N B:ALA477 4.7 20.5 1.0
CA B:CYS492 4.7 20.8 1.0
C B:CYS476 4.8 19.9 1.0
C B:ASN480 4.9 27.2 1.0
N B:GLY478 4.9 22.1 1.0
CB B:ALA494 5.0 21.6 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: Wed Dec 16 04:20:14 2020

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