Zinc in PDB 3vek: Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form

The structure of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form, PDB code: 3vek 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)	48.68 / 2.63
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.195, 62.415, 66.046, 72.39, 74.57, 73.63
R / Rfree (%)	23.5 / 27.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form (pdb code 3vek). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form, PDB code: 3vek:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 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, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:59.6 occ:1.00 OP1 A:DT6 2.3 60.8 1.0 NE2 C:HIS289 2.3 64.4 1.0 OP2 A:DT6 2.7 56.7 1.0 P A:DT6 2.8 59.1 1.0 CE1 C:HIS289 3.2 62.9 1.0 CD2 C:HIS289 3.3 65.5 1.0 O3' A:DC5 3.7 53.6 1.0 C3' A:DC5 3.9 53.1 1.0 O5' A:DT6 4.2 51.3 1.0 ND1 C:HIS289 4.3 62.2 1.0 CG C:HIS289 4.4 64.0 1.0 CE2 C:TYR285 4.7 52.6 1.0 OH C:TYR285 4.8 57.5 1.0 C2' A:DC5 5.0 51.0 1.0

Zinc binding site 2 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 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, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:92.3 occ:1.00 N7 A:DG15 2.3 65.0 1.0 C8 A:DG15 3.1 67.3 1.0 C5 A:DG15 3.4 60.3 1.0 O6 A:DG15 3.9 56.0 1.0 C6 A:DG15 4.0 57.1 1.0 N9 A:DG15 4.3 66.5 1.0 C4 A:DG15 4.5 61.7 1.0 C6 A:DT14 4.5 54.8 1.0 O6 A:DG16 4.6 72.0 1.0 C5 A:DT14 4.6 53.4 1.0 C7 A:DT14 4.7 53.0 1.0 C2' A:DT14 4.8 62.3 1.0

Zinc binding site 3 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 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, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:62.5 occ:1.00 N7 B:DG38 2.5 48.2 1.0 C8 B:DG38 3.4 49.0 1.0 C5 B:DG38 3.6 45.2 1.0 O6 B:DG38 3.7 45.1 1.0 C6 B:DG38 4.0 44.4 1.0 C8 B:DA37 4.4 50.4 1.0 N7 B:DA37 4.5 49.7 1.0 OP2 B:DA37 4.5 53.8 1.0 N9 B:DG38 4.6 46.6 1.0 C4 B:DG38 4.7 44.9 1.0 N6 B:DA39 4.9 51.2 1.0

Zinc binding site 4 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:53.0 occ:1.00 SG C:CYS207 2.1 48.3 1.0 SG C:CYS228 2.1 53.4 1.0 SG C:CYS225 2.2 48.1 1.0 SG C:CYS204 2.5 53.1 1.0 CB C:CYS228 3.2 48.1 1.0 CB C:CYS207 3.3 52.4 1.0 CB C:CYS204 3.5 51.0 1.0 CB C:CYS225 3.6 47.6 1.0 N C:CYS207 3.8 52.2 1.0 N C:CYS225 4.0 46.5 1.0 CA C:CYS207 4.1 53.4 1.0 NH1 C:ARG239 4.2 52.0 1.0 N C:CYS228 4.3 47.9 1.0 CA C:CYS225 4.3 46.5 1.0 CA C:CYS228 4.4 48.5 1.0 CB C:ASN206 4.5 51.3 1.0 CB C:ALA209 4.7 49.2 1.0 N C:GLY208 4.8 52.0 1.0 C C:CYS207 4.8 54.4 1.0 C C:ASN206 4.8 54.4 1.0 ND2 C:ASN206 4.9 50.6 1.0 CA C:CYS204 4.9 51.2 1.0 O C:CYS225 4.9 46.7 1.0 C C:CYS225 5.0 46.6 1.0 N C:ALA209 5.0 50.2 1.0

Zinc binding site 5 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:42.3 occ:1.00 SG C:CYS261 2.3 67.9 1.0 SG C:CYS282 2.4 42.7 1.0 SG C:CYS279 2.5 41.5 1.0 SG C:CYS258 2.5 66.2 1.0 CB C:CYS279 3.0 42.5 1.0 CB C:CYS258 3.2 70.4 1.0 CB C:CYS282 3.2 42.7 1.0 N C:CYS279 3.5 44.7 1.0 CB C:CYS261 3.7 69.3 1.0 CG2 C:THR263 3.8 65.3 1.0 CA C:CYS279 3.8 41.3 1.0 N C:CYS261 4.1 73.0 1.0 N C:CYS282 4.3 38.4 1.0 CA C:CYS282 4.3 40.5 1.0 CA C:CYS261 4.4 73.6 1.0 NH1 C:ARG293 4.4 52.7 1.0 C C:CYS279 4.6 37.6 1.0 CA C:CYS258 4.6 73.7 1.0 C C:VAL278 4.6 46.3 1.0 O C:CYS279 4.8 36.2 1.0 CB C:THR263 4.8 68.9 1.0 C C:CYS261 4.9 76.2 1.0 CA C:VAL278 5.0 50.2 1.0

Zinc binding site 6 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:90.8 occ:1.00 ND1 C:HIS222 2.3 59.6 1.0 OD2 C:ASP218 2.5 62.3 1.0 CE1 C:HIS222 3.2 63.8 1.0 CG C:HIS222 3.3 58.0 1.0 CG C:ASP218 3.3 60.9 1.0 CB C:THR220 3.5 69.3 1.0 OD1 C:ASP218 3.5 63.1 1.0 OG1 C:THR220 3.5 69.5 1.0 CB C:HIS222 3.6 54.8 1.0 CG2 C:THR220 4.3 72.9 1.0 NE2 C:HIS222 4.3 63.6 1.0 CD2 C:HIS222 4.4 59.7 1.0 N C:HIS222 4.5 56.9 1.0 CA C:HIS222 4.6 54.3 1.0 CB C:ASP218 4.6 58.7 1.0 CA C:THR220 4.7 69.9 1.0 N C:THR220 4.9 68.7 1.0

Zinc binding site 7 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:59.1 occ:1.00 NE2 F:HIS289 2.2 64.5 1.0 OP1 D:DT6 2.5 62.3 1.0 OP2 D:DT6 2.6 58.1 1.0 P D:DT6 2.9 60.1 1.0 CE1 F:HIS289 3.1 63.4 1.0 CD2 F:HIS289 3.2 65.4 1.0 O3' D:DC5 3.7 55.5 1.0 C3' D:DC5 3.9 54.7 1.0 ND1 F:HIS289 4.3 62.4 1.0 O5' D:DT6 4.3 53.4 1.0 CG F:HIS289 4.3 64.4 1.0 OH F:TYR285 4.6 57.4 1.0 CE2 F:TYR285 4.6 53.1 1.0 C2' D:DC5 4.9 51.9 1.0 CZ F:TYR285 4.9 55.9 1.0

Zinc binding site 8 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:93.6 occ:1.00 N7 D:DG15 2.2 64.3 1.0 C8 D:DG15 3.1 66.2 1.0 C5 D:DG15 3.3 59.3 1.0 O6 D:DG15 3.7 54.4 1.0 C6 D:DG15 3.9 56.0 1.0 N9 D:DG15 4.3 65.3 1.0 O6 D:DG16 4.4 70.5 1.0 C4 D:DG15 4.4 60.6 1.0 C6 D:DT14 4.7 53.5 1.0 C5 D:DT14 4.7 51.9 1.0 C7 D:DT14 4.9 51.4 1.0 C2' D:DT14 4.9 61.1 1.0

Zinc binding site 9 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn101 b:69.7 occ:1.00 N7 E:DG38 2.4 50.9 1.0 C8 E:DG38 3.2 51.9 1.0 C5 E:DG38 3.5 47.5 1.0 O6 E:DG38 3.8 47.9 1.0 C6 E:DG38 4.0 46.7 1.0 C8 E:DA37 4.3 52.4 1.0 N7 E:DA37 4.4 51.3 1.0 N9 E:DG38 4.5 49.4 1.0 OP2 E:DA37 4.5 55.3 1.0 C4 E:DG38 4.6 47.1 1.0 N6 E:DA39 4.7 53.9 1.0

Zinc binding site 10 out of 14 in the Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Both Zn Fingers of GATA1 Bound to Palindromic Dna Recognition Site, P1 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:51.6 occ:1.00 SG F:CYS228 2.1 50.5 1.0 SG F:CYS207 2.1 47.4 1.0 SG F:CYS204 2.3 49.6 1.0 SG F:CYS225 2.3 45.2 1.0 CB F:CYS228 3.2 45.2 1.0 CB F:CYS207 3.4 50.6 1.0 CB F:CYS204 3.4 48.4 1.0 CB F:CYS225 3.6 45.6 1.0 N F:CYS207 3.7 49.9 1.0 N F:CYS225 4.0 43.9 1.0 CA F:CYS207 4.1 51.4 1.0 NH1 F:ARG239 4.3 50.5 1.0 N F:CYS228 4.4 45.2 1.0 CA F:CYS228 4.4 45.6 1.0 CA F:CYS225 4.4 44.1 1.0 CB F:ASN206 4.4 49.1 1.0 CB F:ALA209 4.7 47.9 1.0 N F:GLY208 4.8 49.7 1.0 C F:ASN206 4.8 52.2 1.0 CA F:CYS204 4.9 48.6 1.0 C F:CYS207 4.9 52.2 1.0 O F:CYS225 4.9 42.9 1.0 ND2 F:ASN206 5.0 49.4 1.0 N F:ALA209 5.0 48.6 1.0 C F:CYS225 5.0 44.0 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.