Atomistry » Zinc » PDB 3ujz-3v2j » 3uk3
Atomistry »
  Zinc »
    PDB 3ujz-3v2j »
      3uk3 »

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

Protein crystallography data

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

Other elements in 3uk3:

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

Chlorine (Cl) 1 atom

Zinc Binding Sites:

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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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 3uk3

Go back to Zinc Binding Sites List in 3uk3
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

Reference:

M.S.Vandevenne, D.A.Jacques, J.M.Guss, J.P.Mackay. Rediscovering Dna Recognition By Classical Zinc Fingers. To Be Published.
Page generated: Sat Oct 26 17:24:23 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy