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Zinc in PDB 3g9i: Gr Dna Binding Domain: Pal Complex-35

Protein crystallography data

The structure of Gr Dna Binding Domain: Pal Complex-35, PDB code: 3g9i 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) 48.81 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.513, 37.648, 95.448, 90.00, 123.08, 90.00
R / Rfree (%) 17 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Gr Dna Binding Domain: Pal Complex-35 (pdb code 3g9i). 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 Complex-35, PDB code: 3g9i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3g9i

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Zinc binding site 1 out of 4 in the Gr Dna Binding Domain: Pal Complex-35


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 Complex-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn526

b:46.4
occ:1.00
SG A:CYS443 2.2 44.2 1.0
SG A:CYS457 2.3 46.5 1.0
SG A:CYS460 2.3 40.5 1.0
SG A:CYS440 2.4 47.9 1.0
CB A:CYS460 3.1 38.8 1.0
CB A:CYS440 3.3 55.4 1.0
CB A:CYS443 3.3 43.1 1.0
CB A:CYS457 3.5 48.4 1.0
N A:CYS443 3.7 41.8 1.0
N A:CYS457 3.8 47.3 1.0
CA A:CYS443 4.0 46.0 1.0
N A:CYS460 4.2 42.7 1.0
CA A:CYS457 4.2 46.3 1.0
CA A:CYS460 4.2 43.7 1.0
NH1 A:ARG489 4.4 46.3 1.0
CB A:ASP445 4.4 50.7 1.0
OG A:SER459 4.5 45.1 1.0
CB A:VAL442 4.5 46.1 1.0
C A:CYS443 4.6 51.4 1.0
C A:VAL442 4.7 41.7 1.0
CA A:CYS440 4.7 52.4 1.0
N A:ASP445 4.8 51.6 1.0
N A:SER444 4.8 53.9 1.0
C A:CYS457 4.9 48.6 1.0
NH2 A:ARG496 4.9 36.9 1.0
CD A:ARG489 4.9 45.4 1.0
C A:THR456 4.9 53.7 1.0
N A:VAL442 4.9 50.0 1.0
O A:CYS457 5.0 48.8 1.0
CA A:VAL442 5.0 42.0 1.0

Zinc binding site 2 out of 4 in 3g9i

Go back to Zinc Binding Sites List in 3g9i
Zinc binding site 2 out of 4 in the Gr Dna Binding Domain: Pal Complex-35


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 Complex-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn527

b:28.4
occ:1.00
SG A:CYS476 2.2 25.3 1.0
SG A:CYS482 2.3 27.7 1.0
SG A:CYS495 2.4 27.3 1.0
SG A:CYS492 2.4 27.3 1.0
CB A:CYS482 3.2 25.8 1.0
CB A:CYS476 3.3 23.4 1.0
CB A:CYS492 3.3 23.9 1.0
CB A:CYS495 3.4 23.4 1.0
N A:CYS482 3.9 31.7 1.0
CA A:CYS476 4.0 20.7 1.0
O A:HOH528 4.0 27.9 1.0
N A:CYS495 4.2 27.2 1.0
CA A:CYS482 4.2 29.4 1.0
O A:HOH9 4.2 31.4 1.0
CA A:CYS495 4.3 33.0 1.0
O A:HOH18 4.6 35.4 1.0
CA A:ASN480 4.6 24.9 1.0
N A:ASP481 4.6 21.5 1.0
O A:HOH8 4.6 29.2 1.0
N A:ALA477 4.6 21.8 1.0
N A:ASN480 4.7 24.9 1.0
CA A:CYS492 4.7 23.1 1.0
C A:CYS476 4.8 24.6 1.0
N A:GLY478 4.8 27.3 1.0
C A:ASN480 4.8 28.8 1.0

Zinc binding site 3 out of 4 in 3g9i

Go back to Zinc Binding Sites List in 3g9i
Zinc binding site 3 out of 4 in the Gr Dna Binding Domain: Pal Complex-35


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 Complex-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn526

b:31.6
occ:1.00
SG B:CYS460 2.3 28.3 1.0
SG B:CYS443 2.3 31.6 1.0
SG B:CYS457 2.3 32.6 1.0
SG B:CYS440 2.4 28.9 1.0
CB B:CYS460 3.2 29.2 1.0
CB B:CYS443 3.3 25.2 1.0
CB B:CYS440 3.3 41.8 1.0
CB B:CYS457 3.5 33.6 1.0
N B:CYS443 3.7 30.5 1.0
N B:CYS457 3.9 30.1 1.0
CA B:CYS443 4.0 30.8 1.0
N B:CYS460 4.2 26.1 1.0
CA B:CYS460 4.2 24.6 1.0
CA B:CYS457 4.3 33.0 1.0
NH1 B:ARG489 4.3 36.4 1.0
CB B:VAL442 4.4 23.1 1.0
OG B:SER459 4.5 31.6 1.0
CB B:ASP445 4.6 48.5 1.0
C B:CYS443 4.7 37.9 1.0
C B:VAL442 4.7 32.2 1.0
CA B:CYS440 4.8 34.0 1.0
N B:SER444 4.8 36.3 1.0
N B:ASP445 4.8 48.4 1.0
C B:CYS457 4.8 34.0 1.0
NH2 B:ARG496 4.8 27.6 1.0
O B:CYS457 4.9 30.8 1.0
CD B:ARG489 4.9 27.4 1.0
CB B:THR456 4.9 31.3 1.0
CA B:VAL442 5.0 28.7 1.0
C B:THR456 5.0 40.5 1.0

Zinc binding site 4 out of 4 in 3g9i

Go back to Zinc Binding Sites List in 3g9i
Zinc binding site 4 out of 4 in the Gr Dna Binding Domain: Pal Complex-35


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 Complex-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn527

b:26.4
occ:1.00
SG B:CYS482 2.2 24.2 1.0
SG B:CYS476 2.3 26.4 1.0
SG B:CYS495 2.3 25.4 1.0
SG B:CYS492 2.4 24.6 1.0
CB B:CYS482 3.1 25.9 1.0
CB B:CYS492 3.3 20.2 1.0
CB B:CYS476 3.3 26.5 1.0
CB B:CYS495 3.4 20.6 1.0
O A:HOH1 3.9 23.2 1.0
N B:CYS482 3.9 26.4 1.0
CA B:CYS476 4.0 27.3 1.0
CA B:CYS482 4.2 19.0 1.0
N B:CYS495 4.2 20.9 1.0
CA B:CYS495 4.4 23.0 1.0
O B:HOH34 4.4 49.6 1.0
CA B:ASN480 4.4 34.7 1.0
N B:ASN480 4.5 32.5 1.0
O A:HOH8 4.6 29.2 1.0
N B:ASP481 4.6 27.2 1.0
O B:HOH5 4.7 23.4 1.0
N B:ALA477 4.7 28.4 1.0
CA B:CYS492 4.7 22.2 1.0
C B:CYS476 4.8 32.4 1.0
N B:GLY478 4.8 29.2 1.0
C B:ASN480 4.8 35.9 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 10:14:28 2020
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