Zinc in PDB 3uk3: Crystal Structure of ZNF217 Bound to Dna

The structure of Crystal Structure of ZNF217 Bound to Dna, PDB code: 3uk3 was solved by M.S.Vandevenne, D.A.Jacques, J.M.Guss, J.P.Mackay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.670, 40.980, 52.040, 90.00, 97.21, 90.00
R / Rfree (%)	22.4 / 25.6

The structure of Crystal Structure of ZNF217 Bound to Dna also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of ZNF217 Bound to Dna (pdb code 3uk3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of ZNF217 Bound to Dna, PDB code: 3uk3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn21 b:76.9 occ:1.00 O B:HOH51 2.5 30.6 1.0 N7 B:DG12 2.5 48.4 1.0 C8 B:DG12 3.4 46.3 1.0 C5 B:DG12 3.6 42.4 1.0 O6 B:DG12 3.9 48.3 1.0 C6 B:DG12 4.1 45.6 1.0 O4 A:DT10 4.3 35.7 1.0 C6 B:DC11 4.5 50.9 1.0 N9 B:DG12 4.6 46.5 1.0 C4 B:DG12 4.7 44.1 1.0 C2' B:DC11 4.7 59.1 1.0 C5 B:DC11 4.8 45.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn22 b:72.6 occ:1.00 OP2 B:DT17 2.2 33.4 1.0 O D:HOH50 2.3 13.9 1.0 O B:HOH53 2.6 17.0 1.0 O D:HOH44 3.2 24.3 1.0 P B:DT17 3.5 36.0 1.0 O5' B:DT17 3.7 35.4 1.0 CD D:ARG481 4.3 36.1 1.0 OP1 B:DT17 4.4 38.9 1.0 C2' B:DC16 4.6 30.1 1.0 CB D:ARG481 4.6 40.5 1.0 O3' B:DC16 4.7 32.9 1.0 CG D:ARG481 4.7 38.6 1.0 N D:ARG481 4.7 39.7 1.0 C3' B:DC16 4.8 30.4 1.0 CD1 D:PHE480 4.8 34.0 1.0 C2' B:DT17 4.8 40.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn967 b:67.4 occ:1.00 NE2 C:HIS517 2.1 51.5 1.0 SG C:CYS504 2.1 73.9 1.0 NE2 C:HIS522 2.2 69.3 1.0 SG C:CYS501 2.4 64.2 1.0 CE1 C:HIS522 3.0 74.6 1.0 CD2 C:HIS517 3.1 54.1 1.0 CE1 C:HIS517 3.1 57.3 1.0 CD2 C:HIS522 3.2 70.7 1.0 CB C:CYS504 3.3 75.6 1.0 CB C:CYS501 3.3 62.3 1.0 N C:CYS504 3.6 75.6 1.0 CA C:CYS504 3.9 76.3 1.0 CB C:TYR506 4.1 57.1 1.0 ND1 C:HIS522 4.2 76.3 1.0 ND1 C:HIS517 4.2 51.2 1.0 CG C:HIS517 4.2 52.8 1.0 CG C:HIS522 4.3 75.3 1.0 C C:PHE503 4.4 79.7 1.0 C C:CYS504 4.4 73.2 1.0 CB C:PHE503 4.5 79.6 1.0 O C:CYS504 4.5 70.8 1.0 CA C:CYS501 4.8 62.4 1.0 CA C:PHE503 4.8 79.9 1.0 N C:TYR506 4.9 62.1 1.0 N C:PHE503 4.9 76.6 1.0 CG C:TYR506 4.9 52.8 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn968 b:58.1 occ:1.00 NE2 C:HIS489 2.0 49.8 1.0 NE2 C:HIS493 2.1 59.3 1.0 SG C:CYS476 2.2 62.5 1.0 SG C:CYS473 2.5 48.1 1.0 CD2 C:HIS489 2.9 48.3 1.0 CD2 C:HIS493 2.9 61.5 1.0 CE1 C:HIS489 3.1 50.0 1.0 CE1 C:HIS493 3.2 63.4 1.0 CB C:CYS476 3.4 67.4 1.0 CB C:CYS473 3.4 53.8 1.0 N C:CYS476 3.8 70.0 1.0 CG C:HIS489 4.1 47.3 1.0 CG C:HIS493 4.1 61.7 1.0 ND1 C:HIS489 4.1 49.6 1.0 CA C:CYS476 4.2 70.8 1.0 ND1 C:HIS493 4.2 62.7 1.0 CB C:TYR475 4.3 71.5 1.0 CG2 C:THR492 4.6 57.5 1.0 C C:TYR475 4.7 73.7 1.0 CZ C:PHE480 4.8 37.5 1.0 CE2 C:PHE480 4.8 41.0 1.0 CA C:CYS473 4.8 57.0 1.0 CA C:TYR475 4.9 73.1 1.0 C C:CYS476 4.9 70.5 1.0 N C:TYR475 5.0 70.6 1.0 CD C:LYS478 5.0 59.2 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1 b:0.1 occ:1.00 NE2 C:HIS521 2.1 77.7 1.0 CD2 C:HIS521 3.0 78.3 1.0 CE1 C:HIS521 3.1 72.1 1.0 OP1 A:DA13 3.6 59.8 1.0 CG C:HIS521 4.2 75.4 1.0 ND1 C:HIS521 4.2 68.9 1.0 OP2 A:DA13 4.4 64.1 1.0 P A:DA13 4.5 61.0 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn967 b:71.7 occ:1.00 NE2 D:HIS522 2.0 69.4 1.0 SG D:CYS501 2.2 74.1 1.0 SG D:CYS504 2.3 79.5 1.0 NE2 D:HIS517 2.4 63.8 1.0 CD2 D:HIS522 2.8 70.9 1.0 CD2 D:HIS517 3.1 62.3 1.0 CE1 D:HIS522 3.1 75.8 1.0 CB D:CYS504 3.4 80.8 1.0 CB D:CYS501 3.5 68.1 1.0 CE1 D:HIS517 3.5 66.4 1.0 N D:CYS504 3.7 81.8 1.0 CG D:HIS522 4.0 75.8 1.0 CA D:CYS504 4.1 82.2 1.0 ND1 D:HIS522 4.1 78.3 1.0 CB D:PHE503 4.3 85.7 1.0 CG D:HIS517 4.3 59.1 1.0 C D:PHE503 4.3 86.5 1.0 CB D:TYR506 4.4 65.7 1.0 ND1 D:HIS517 4.5 61.5 1.0 CA D:PHE503 4.7 86.6 1.0 C D:CYS504 4.7 79.0 1.0 N D:PHE503 4.8 83.6 1.0 ND1 D:HIS521 4.8 77.4 0.5 CA D:CYS501 4.8 68.8 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn968 b:32.2 occ:1.00 NE2 D:HIS493 2.0 33.2 1.0 NE2 D:HIS489 2.0 31.8 1.0 SG D:CYS476 2.2 35.2 1.0 SG D:CYS473 2.2 32.9 1.0 CD2 D:HIS489 2.9 31.1 1.0 CD2 D:HIS493 2.9 32.0 1.0 CB D:CYS473 3.1 34.1 1.0 CE1 D:HIS493 3.1 36.4 1.0 CE1 D:HIS489 3.1 31.7 1.0 CB D:CYS476 3.3 34.5 1.0 N D:CYS476 3.7 38.1 1.0 CA D:CYS476 4.1 38.4 1.0 CG D:HIS489 4.1 29.5 1.0 CG D:HIS493 4.1 33.0 1.0 ND1 D:HIS493 4.2 34.3 1.0 ND1 D:HIS489 4.2 28.9 1.0 CB D:TYR475 4.4 39.6 1.0 CA D:CYS473 4.6 36.1 1.0 C D:CYS476 4.7 38.8 1.0 C D:TYR475 4.8 40.7 1.0 N D:GLY477 4.9 40.5 1.0 CA D:TYR475 5.0 40.7 1.0 N D:TYR475 5.0 38.8 1.0 CE2 D:PHE480 5.0 38.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of ZNF217 Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of ZNF217 Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:93.3 occ:1.00 O D:HIS521 3.2 83.3 1.0 CE1 D:HIS521 3.3 74.8 0.5 ND1 D:HIS521 3.6 77.4 0.5 NE2 D:HIS521 4.1 72.5 0.5 ND1 D:HIS522 4.4 78.3 1.0 CG D:HIS521 4.4 73.9 0.5 C D:HIS521 4.5 80.2 1.0 CE1 D:HIS522 4.7 75.8 1.0 CD2 D:HIS521 4.7 72.0 0.5

M.S.Vandevenne, D.A.Jacques, J.M.Guss, J.P.Mackay. Rediscovering Dna Recognition By Classical Zinc Fingers. To Be Published.