Zinc in PDB 3vd6: Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form

The structure of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form, PDB code: 3vd6 was solved by D.A.Jacques, N.Ripin, L.E.Wilkinson-White, J.M.Guss, J.M.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.90 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.331, 37.401, 65.484, 90.00, 98.51, 90.00
R / Rfree (%)	21.8 / 24.7

The binding sites of Zinc atom in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form (pdb code 3vd6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form, PDB code: 3vd6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:44.9 occ:1.00 SG C:CYS204 2.2 42.3 1.0 SG C:CYS225 2.3 42.8 1.0 SG C:CYS207 2.3 50.4 1.0 SG C:CYS228 2.3 45.0 1.0 CB C:CYS228 3.2 42.2 1.0 CB C:CYS204 3.2 41.4 1.0 CB C:CYS207 3.2 49.8 1.0 CB C:CYS225 3.5 38.6 1.0 N C:CYS207 3.7 48.2 1.0 N C:CYS225 3.9 36.5 1.0 CA C:CYS207 4.0 50.7 1.0 CA C:CYS225 4.2 37.5 1.0 N C:CYS228 4.3 39.3 1.0 NH1 C:ARG239 4.3 61.0 1.0 CA C:CYS228 4.3 40.6 1.0 CB C:ALA209 4.5 47.9 1.0 CA C:CYS204 4.6 42.3 1.0 CB C:ASN206 4.7 44.5 1.0 C C:CYS207 4.7 52.2 1.0 N C:GLY208 4.7 51.5 1.0 N C:ALA209 4.8 50.1 1.0 C C:ASN206 4.9 48.5 1.0 C C:CYS225 4.9 36.2 1.0 O C:CYS225 4.9 36.3 1.0 ND2 C:ASN206 5.0 43.7 1.0

Zinc binding site 2 out of 3 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:47.5 occ:1.00 SG C:CYS261 2.2 54.5 1.0 SG C:CYS282 2.2 48.5 1.0 SG C:CYS279 2.3 43.0 1.0 SG C:CYS258 2.4 48.9 1.0 CB C:CYS282 3.2 46.1 1.0 CB C:CYS258 3.3 52.6 1.0 CB C:CYS261 3.3 56.4 1.0 CB C:CYS279 3.5 42.0 1.0 N C:CYS261 3.8 57.0 1.0 CG2 C:THR263 3.9 51.7 1.0 N C:CYS279 3.9 42.2 1.0 NH1 C:ARG293 4.0 54.0 1.0 CA C:CYS261 4.1 59.1 1.0 N C:CYS282 4.2 41.6 1.0 CA C:CYS279 4.2 40.6 1.0 CA C:CYS282 4.3 43.2 1.0 CB C:ASN260 4.7 54.1 1.0 C C:CYS261 4.7 61.9 1.0 CA C:CYS258 4.7 54.7 1.0 O C:CYS279 4.8 35.5 1.0 C C:CYS279 4.9 38.0 1.0 C C:ASN260 4.9 58.5 1.0 N C:GLN262 4.9 62.9 1.0 CB C:THR263 4.9 56.7 1.0

Zinc binding site 3 out of 3 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:72.9 occ:1.00 OD2 C:ASP218 1.8 56.0 1.0 ND1 C:HIS222 2.3 34.3 1.0 CG C:ASP218 2.9 49.1 1.0 CG C:HIS222 3.2 38.5 1.0 CE1 C:HIS222 3.3 44.8 1.0 OD1 C:ASP218 3.3 55.0 1.0 CB C:HIS222 3.4 42.7 1.0 CB C:ASP218 4.2 47.5 1.0 CD2 C:HIS222 4.4 41.0 1.0 NE2 C:HIS222 4.4 42.2 1.0 CB C:THR220 4.5 55.9 1.0 OG1 C:THR220 4.5 61.1 1.0 CA C:HIS222 4.7 42.3 1.0 CG2 C:VAL205 4.9 45.3 1.0 N C:HIS222 4.9 43.4 1.0

L.E.Wilkinson-White, N.Ripin, D.A.Jacques, J.M.Guss, J.M.Matthews. Dna Recognition By GATA1 Double Finger To Be Published.