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Zinc in PDB 3g9j: Gr Dna Binding Domain:Pal, 18BP Complex-36

Protein crystallography data

The structure of Gr Dna Binding Domain:Pal, 18BP Complex-36, PDB code: 3g9j 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) 49.13 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.069, 102.096, 112.076, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Gr Dna Binding Domain:Pal, 18BP Complex-36 (pdb code 3g9j). 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:Pal, 18BP Complex-36, PDB code: 3g9j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3g9j

Go back to Zinc Binding Sites List in 3g9j
Zinc binding site 1 out of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36


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:Pal, 18BP Complex-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1514

b:45.3
occ:1.00
SG A:CYS460 2.3 43.8 1.0
SG A:CYS443 2.3 48.4 1.0
SG A:CYS440 2.4 48.8 1.0
SG A:CYS457 2.4 48.2 1.0
CB A:CYS460 3.2 45.4 1.0
CB A:CYS443 3.2 53.2 1.0
CB A:CYS440 3.3 54.5 1.0
CB A:CYS457 3.6 58.3 0.9
N A:CYS443 3.7 52.1 1.0
CA A:CYS443 4.0 47.8 1.0
N A:CYS457 4.0 49.7 1.0
N A:CYS460 4.3 36.6 1.0
CA A:CYS457 4.3 58.2 1.0
CA A:CYS460 4.3 39.7 1.0
NH1 A:ARG489 4.4 66.7 1.0
CB A:VAL442 4.4 51.8 1.0
C A:CYS443 4.6 54.5 1.0
OG A:SER459 4.6 42.1 1.0
C A:VAL442 4.6 55.4 1.0
CB A:ASP445 4.7 74.7 1.0
CA A:CYS440 4.8 55.4 1.0
N A:SER444 4.8 50.7 1.0
CD A:ARG489 4.8 52.6 1.0
CG1 A:VAL442 4.9 36.8 1.0
N A:ASP445 4.9 43.2 1.0
NH2 A:ARG496 4.9 40.1 1.0
C A:CYS457 4.9 48.8 1.0
CA A:VAL442 4.9 54.4 1.0
O A:CYS457 4.9 43.7 1.0
N A:VAL442 5.0 58.1 1.0

Zinc binding site 2 out of 4 in 3g9j

Go back to Zinc Binding Sites List in 3g9j
Zinc binding site 2 out of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36


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:Pal, 18BP Complex-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1515

b:36.5
occ:1.00
SG A:CYS482 2.2 31.6 1.0
SG A:CYS476 2.3 33.3 1.0
SG A:CYS492 2.4 36.7 1.0
SG A:CYS495 2.4 41.3 1.0
CB A:CYS482 3.1 27.6 1.0
CB A:CYS476 3.3 30.6 1.0
CB A:CYS492 3.3 26.9 1.0
CB A:CYS495 3.4 24.1 1.0
O A:HOH3 3.7 29.1 1.0
N A:CYS482 3.9 40.6 1.0
CA A:CYS476 3.9 25.9 0.9
CA A:CYS482 4.1 41.1 1.0
N A:CYS495 4.2 32.8 1.0
O A:HOH526 4.3 37.4 1.0
CA A:CYS495 4.4 31.3 1.0
CA A:ASN480 4.5 41.6 1.0
N A:ALA477 4.5 29.0 1.0
O B:HOH8 4.6 39.8 1.0
N A:ASP481 4.6 33.9 1.0
N A:ASN480 4.6 43.8 1.0
C A:CYS476 4.7 33.8 1.0
N A:GLY478 4.8 33.4 1.0
CA A:CYS492 4.8 24.7 1.0
C A:ASN480 4.9 46.7 1.0
O A:HOH28 5.0 45.4 1.0

Zinc binding site 3 out of 4 in 3g9j

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Zinc binding site 3 out of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36


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:Pal, 18BP Complex-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1512

b:41.4
occ:1.00
SG B:CYS460 2.2 34.8 1.0
SG B:CYS440 2.3 36.9 1.0
SG B:CYS443 2.4 45.4 1.0
SG B:CYS457 2.4 47.5 1.0
CB B:CYS460 3.1 33.2 1.0
CB B:CYS440 3.2 52.3 1.0
CB B:CYS443 3.4 43.0 0.9
N B:CYS443 3.6 44.7 1.0
CB B:CYS457 3.7 50.0 1.0
N B:CYS457 3.7 40.8 1.0
CA B:CYS443 4.0 44.4 1.0
N B:CYS460 4.1 31.4 1.0
CA B:CYS460 4.2 34.6 1.0
NH1 B:ARG489 4.3 41.1 1.0
CA B:CYS457 4.3 45.8 1.0
OG B:SER459 4.4 39.3 1.0
CB B:VAL442 4.5 46.1 1.0
CB B:ASP445 4.5 61.1 1.0
C B:VAL442 4.7 53.0 1.0
CA B:CYS440 4.7 49.2 1.0
C B:CYS443 4.7 49.9 1.0
N B:ASP445 4.8 53.0 1.0
O B:CYS457 4.8 43.5 1.0
C B:THR456 4.8 49.9 1.0
N B:SER444 4.8 53.0 1.0
C B:CYS457 4.9 35.4 1.0
NH2 B:ARG496 4.9 36.7 1.0
CB B:THR456 4.9 45.7 1.0
CA B:THR456 5.0 44.6 1.0
CA B:VAL442 5.0 49.2 1.0

Zinc binding site 4 out of 4 in 3g9j

Go back to Zinc Binding Sites List in 3g9j
Zinc binding site 4 out of 4 in the Gr Dna Binding Domain:Pal, 18BP Complex-36


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:Pal, 18BP Complex-36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1513

b:34.2
occ:0.98
SG B:CYS482 2.2 30.2 1.0
SG B:CYS476 2.3 35.7 1.0
SG B:CYS492 2.3 34.1 1.0
SG B:CYS495 2.4 36.1 1.0
CB B:CYS482 3.3 27.1 1.0
CB B:CYS492 3.4 35.3 1.0
CB B:CYS495 3.4 28.1 1.0
CB B:CYS476 3.4 29.5 1.0
O B:HOH4 3.8 33.4 1.0
N B:CYS482 4.0 36.0 1.0
CA B:CYS476 4.0 35.2 1.0
N B:CYS495 4.2 29.1 1.0
CA B:CYS482 4.2 32.3 1.0
CA B:ASN480 4.4 45.6 1.0
CA B:CYS495 4.4 29.6 1.0
N B:ASN480 4.5 39.0 1.0
O B:HOH13 4.5 38.2 1.0
O B:HOH20 4.6 45.2 1.0
N B:ASP481 4.7 31.9 1.0
N B:ALA477 4.7 36.6 1.0
CA B:CYS492 4.8 31.9 1.0
N B:GLY478 4.8 31.4 0.9
C B:ASN480 4.8 38.2 1.0
C B:CYS476 4.8 39.8 1.0
O B:HOH8 4.9 39.8 1.0
CB B:ALA494 5.0 25.2 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 10:14:38 2020
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