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Zinc in PDB 3dfv: Adjacent Gata Dna Binding

Protein crystallography data

The structure of Adjacent Gata Dna Binding, PDB code: 3dfv was solved by D.L.Bates, G.K.Kim, L.Guo, L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.977, 35.756, 54.487, 90.00, 113.25, 90.00
R / Rfree (%) 27.6 / 28.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Adjacent Gata Dna Binding (pdb code 3dfv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Adjacent Gata Dna Binding, PDB code: 3dfv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3dfv

Go back to Zinc Binding Sites List in 3dfv
Zinc binding site 1 out of 2 in the Adjacent Gata Dna Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Adjacent Gata Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn30

b:28.2
occ:1.00
SG D:CYS341 2.3 24.5 1.0
SG D:CYS317 2.4 26.5 1.0
SG D:CYS320 2.4 34.1 1.0
SG D:CYS338 2.5 35.2 1.0
CB D:CYS320 2.5 35.5 1.0
CB D:CYS341 2.9 21.2 1.0
N D:CYS320 3.0 33.7 1.0
CA D:CYS320 3.3 35.4 1.0
CB D:CYS317 3.7 34.8 1.0
NH1 D:ARG352 3.7 15.1 1.0
CB D:CYS338 4.0 32.9 1.0
N D:CYS341 4.0 19.8 1.0
CA D:CYS341 4.0 19.4 1.0
O D:CYS338 4.1 31.0 1.0
C D:ASN319 4.2 33.5 1.0
N D:CYS338 4.3 35.0 1.0
C D:CYS320 4.3 36.0 1.0
CD D:ARG352 4.4 12.1 1.0
CB D:ASN319 4.4 31.4 1.0
CA D:CYS338 4.6 32.2 1.0
N D:GLN321 4.6 37.4 1.0
CA D:ASN319 4.7 33.1 1.0
C D:CYS338 4.8 30.4 1.0
N D:ASN319 4.8 34.0 1.0
CZ D:ARG352 4.9 14.2 1.0
OD1 D:ASN319 5.0 29.9 1.0

Zinc binding site 2 out of 2 in 3dfv

Go back to Zinc Binding Sites List in 3dfv
Zinc binding site 2 out of 2 in the Adjacent Gata Dna Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Adjacent Gata Dna Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn30

b:29.5
occ:1.00
SG C:CYS320 2.3 35.4 1.0
SG C:CYS317 2.3 27.5 1.0
CB C:CYS320 2.4 34.5 1.0
SG C:CYS338 2.4 34.1 1.0
SG C:CYS341 2.4 22.2 1.0
N C:CYS320 3.0 33.4 1.0
CB C:CYS341 3.1 19.5 1.0
CA C:CYS320 3.2 34.8 1.0
CB C:CYS317 3.6 34.9 1.0
NH1 C:ARG352 3.7 13.2 1.0
CB C:CYS338 3.9 31.8 1.0
C C:CYS320 4.1 35.9 1.0
N C:CYS341 4.1 20.6 1.0
CA C:CYS341 4.1 19.4 1.0
C C:ASN319 4.1 33.5 1.0
O C:CYS338 4.2 30.5 1.0
N C:GLN321 4.2 37.6 1.0
N C:CYS338 4.3 35.8 1.0
CD C:ARG352 4.5 15.2 1.0
CB C:ASN319 4.5 31.1 1.0
CA C:CYS338 4.6 31.2 1.0
CA C:ASN319 4.7 32.5 1.0
C C:CYS338 4.8 29.3 1.0
N C:ASN319 4.8 34.4 1.0
CZ C:ARG352 4.9 13.8 1.0
CA C:CYS317 5.0 37.0 1.0
O C:CYS320 5.0 36.3 1.0

Reference:

D.L.Bates, Y.Chen, G.Kim, L.Guo, L.Chen. Crystal Structures of Multiple Gata Zinc Fingers Bound to Dna Reveal New Insights Into Dna Recognition and Self-Association By Gata. J.Mol.Biol. V. 381 1292 2008.
ISSN: ISSN 0022-2836
PubMed: 18621058
DOI: 10.1016/J.JMB.2008.06.072
Page generated: Wed Dec 16 04:12:58 2020

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