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Zinc in PDB 3g8x: Gr Dna Binding Domain:Gilz 16BP Complex-65

Protein crystallography data

The structure of Gr Dna Binding Domain:Gilz 16BP Complex-65, PDB code: 3g8x 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) 35.36 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.213, 37.914, 96.993, 90.00, 123.22, 90.00
R / Rfree (%) 21 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Gr Dna Binding Domain:Gilz 16BP Complex-65 (pdb code 3g8x). 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-65, PDB code: 3g8x:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3g8x

Go back to Zinc Binding Sites List in 3g8x
Zinc binding site 1 out of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65


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-65 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn526

b:54.6
occ:1.00
SG A:CYS457 2.2 59.5 1.0
SG A:CYS443 2.3 63.9 1.0
SG A:CYS460 2.3 55.2 1.0
SG A:CYS440 2.4 51.2 1.0
CB A:CYS443 3.0 55.2 1.0
CB A:CYS440 3.2 50.7 1.0
CB A:CYS460 3.2 41.4 1.0
N A:CYS443 3.7 58.2 1.0
CB A:CYS457 3.7 66.7 1.0
CA A:CYS443 3.9 60.6 1.0
N A:CYS457 4.0 53.6 1.0
OG A:SER459 4.0 70.2 1.0
N A:CYS460 4.2 41.6 1.0
CA A:CYS460 4.3 38.8 1.0
CA A:CYS457 4.3 63.4 1.0
CB A:VAL442 4.5 38.9 1.0
C A:CYS443 4.6 67.9 1.0
CA A:CYS440 4.6 63.3 1.0
NH2 A:ARG496 4.6 52.1 1.0
CB A:ASP445 4.7 76.5 1.0
NH1 A:ARG489 4.7 57.6 1.0
C A:VAL442 4.7 58.8 1.0
O A:CYS457 4.7 43.9 1.0
N A:SER444 4.7 62.6 1.0
N A:ASP445 4.8 63.4 1.0
C A:CYS457 4.8 61.2 1.0
O A:ASP445 4.9 84.1 1.0

Zinc binding site 2 out of 4 in 3g8x

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Zinc binding site 2 out of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65


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-65 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn527

b:37.1
occ:1.00
SG A:CYS476 2.2 37.0 1.0
SG A:CYS492 2.2 37.2 1.0
SG A:CYS482 2.2 36.8 1.0
SG A:CYS495 2.4 36.4 1.0
O1 A:EDO528 3.1 57.5 1.0
CB A:CYS482 3.2 47.4 1.0
CB A:CYS476 3.3 34.7 1.0
CB A:CYS492 3.4 33.9 1.0
CB A:CYS495 3.4 27.6 1.0
CA A:CYS476 3.9 37.2 1.0
N A:CYS482 4.0 43.3 1.0
N A:CYS495 4.1 32.8 1.0
CA A:CYS482 4.2 41.7 1.0
C1 A:EDO528 4.3 45.6 1.0
CA A:CYS495 4.3 33.5 1.0
CA A:ASN480 4.4 45.2 1.0
C2 A:EDO528 4.4 54.7 1.0
O A:HOH17 4.5 59.8 1.0
N A:ASN480 4.5 48.2 1.0
O A:HOH8 4.6 38.1 1.0
O2 A:EDO528 4.7 32.2 1.0
N A:ASP481 4.7 39.9 1.0
N A:ALA477 4.7 40.6 1.0
CA A:CYS492 4.7 37.8 1.0
C A:CYS476 4.8 48.0 1.0
N A:GLY478 4.8 40.4 1.0
C A:ASN480 4.8 43.3 1.0

Zinc binding site 3 out of 4 in 3g8x

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Zinc binding site 3 out of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65


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-65 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn526

b:96.2
occ:1.00
SG B:CYS460 2.3 67.8 1.0
SG B:CYS440 2.4 90.4 1.0
SG B:CYS457 2.5 86.7 1.0
SG B:CYS443 2.5 92.4 1.0
CB B:CYS440 3.2 0.6 1.0
CB B:CYS457 3.2 70.8 1.0
CB B:CYS443 3.3 89.0 1.0
CB B:CYS460 3.4 71.6 1.0
N B:CYS443 3.4 89.1 1.0
N B:CYS457 3.5 93.3 1.0
CA B:CYS443 3.8 89.0 1.0
CA B:CYS457 3.9 85.1 1.0
N B:SER444 4.1 0.8 1.0
C B:CYS443 4.2 98.7 1.0
CB B:VAL442 4.3 63.9 1.0
N B:ASP445 4.3 95.3 1.0
N B:CYS460 4.5 69.0 1.0
CB B:ASP445 4.5 84.3 1.0
CA B:CYS460 4.5 63.4 1.0
C B:THR456 4.6 90.6 1.0
C B:VAL442 4.6 80.8 1.0
CA B:CYS440 4.7 0.8 1.0
C B:CYS457 4.7 82.8 1.0
CB B:THR456 4.7 74.6 1.0
OG B:SER459 4.8 73.7 1.0
CA B:THR456 4.8 84.7 1.0
O B:CYS457 4.8 81.2 1.0
CA B:VAL442 4.9 72.2 1.0
N B:VAL442 4.9 73.8 1.0
CG1 B:VAL442 4.9 67.3 1.0
CA B:ASP445 5.0 98.8 1.0

Zinc binding site 4 out of 4 in 3g8x

Go back to Zinc Binding Sites List in 3g8x
Zinc binding site 4 out of 4 in the Gr Dna Binding Domain:Gilz 16BP Complex-65


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-65 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn527

b:40.1
occ:1.00
SG B:CYS476 2.2 36.4 1.0
SG B:CYS482 2.3 41.8 1.0
SG B:CYS492 2.4 38.4 1.0
SG B:CYS495 2.4 40.1 1.0
CB B:CYS482 3.1 44.8 1.0
CB B:CYS492 3.3 39.4 1.0
CB B:CYS476 3.3 27.6 1.0
CB B:CYS495 3.4 38.5 1.0
O B:HOH13 3.7 42.8 1.0
N B:CYS482 3.8 45.2 1.0
CA B:CYS476 3.9 40.7 1.0
O B:HOH4 4.1 48.4 1.0
CA B:CYS482 4.1 53.1 1.0
N B:CYS495 4.2 44.6 1.0
CA B:CYS495 4.4 44.5 1.0
CA B:ASN480 4.5 47.9 1.0
N B:ASN480 4.5 35.3 1.0
O2 A:EDO528 4.5 32.2 1.0
N B:ALA477 4.6 32.7 1.0
N B:ASP481 4.6 41.6 1.0
C B:CYS476 4.7 36.2 1.0
O B:HOH10 4.7 42.1 1.0
CA B:CYS492 4.7 38.2 1.0
N B:GLY478 4.7 43.1 1.0
C B:ASN480 4.8 46.7 1.0
C B:ASP481 5.0 46.3 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 10:14:08 2020
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