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Zinc in PDB 4is1: Crystal Structure of ZNF217 Bound to Dna

Protein crystallography data

The structure of Crystal Structure of ZNF217 Bound to Dna, PDB code: 4is1 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 (%) 23.7 / 26.2

Other elements in 4is1:

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 4is1). 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: 4is1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4is1

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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:Zn101

b:71.7
occ:1.00
O B:HOH210 2.0 54.9 1.0
N7 B:DG12 2.5 49.5 1.0
C8 B:DG12 3.4 47.8 1.0
C5 B:DG12 3.5 44.1 1.0
O6 B:DG12 3.7 57.1 1.0
C6 B:DG12 4.0 46.2 1.0
O4 A:DT10 4.3 37.3 1.0
C6 B:DC11 4.5 50.0 1.0
N9 B:DG12 4.6 47.2 1.0
C4 B:DG12 4.7 45.6 1.0
C5 B:DC11 4.7 45.3 1.0
C2' B:DC11 4.7 51.8 1.0
N6 B:DA13 5.0 37.8 1.0

Zinc binding site 2 out of 8 in 4is1

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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:Zn102

b:83.9
occ:1.00
OP2 B:DT17 2.0 33.9 1.0
O D:HOH718 2.3 50.9 1.0
O B:HOH211 2.4 84.5 1.0
O D:HOH714 3.0 61.3 1.0
P B:DT17 3.4 34.7 1.0
O5' B:DT17 3.6 35.1 1.0
OP1 B:DT17 4.3 35.3 1.0
CD D:ARG481 4.4 38.3 1.0
C2' B:DC16 4.5 29.8 1.0
O3' B:DC16 4.5 33.1 1.0
C3' B:DC16 4.5 30.2 1.0
CD1 D:PHE480 4.7 34.0 1.0
CB D:ARG481 4.7 41.2 1.0
N D:ARG481 4.9 44.0 1.0
CG D:ARG481 4.9 40.1 1.0
C2' B:DT17 4.9 37.4 1.0

Zinc binding site 3 out of 8 in 4is1

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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:Zn601

b:78.1
occ:1.00
SG C:CYS504 1.9 74.5 1.0
NE2 C:HIS517 2.0 56.9 1.0
SG C:CYS501 2.3 61.6 1.0
NE2 C:HIS522 2.4 68.6 1.0
CE1 C:HIS517 3.0 58.1 1.0
CB C:CYS504 3.0 79.8 1.0
CD2 C:HIS517 3.0 55.5 1.0
CE1 C:HIS522 3.1 71.2 1.0
CB C:CYS501 3.3 60.9 1.0
N C:CYS504 3.4 75.0 1.0
CD2 C:HIS522 3.5 68.9 1.0
CA C:CYS504 3.6 78.9 1.0
CB C:TYR506 3.8 57.8 1.0
C C:CYS504 4.1 74.5 1.0
ND1 C:HIS517 4.1 54.9 1.0
O C:CYS504 4.1 67.8 1.0
CG C:HIS517 4.2 53.8 1.0
C C:PHE503 4.2 79.2 1.0
ND1 C:HIS522 4.3 73.3 1.0
CG C:HIS522 4.5 73.5 1.0
N C:TYR506 4.6 63.0 1.0
CG C:TYR506 4.7 53.9 1.0
CB C:PHE503 4.7 77.4 1.0
CA C:CYS501 4.7 61.5 1.0
CA C:TYR506 4.9 60.2 1.0
O C:PHE503 4.9 78.4 1.0
CA C:PHE503 4.9 79.1 1.0
N C:PHE503 5.0 75.2 1.0

Zinc binding site 4 out of 8 in 4is1

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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:Zn602

b:57.8
occ:1.00
NE2 C:HIS489 2.0 48.7 1.0
NE2 C:HIS493 2.2 65.5 1.0
SG C:CYS476 2.3 59.8 1.0
SG C:CYS473 2.4 52.6 1.0
CD2 C:HIS489 2.8 48.4 1.0
CD2 C:HIS493 2.9 64.5 1.0
CE1 C:HIS489 3.2 47.5 1.0
CB C:CYS476 3.3 65.6 1.0
CB C:CYS473 3.3 54.7 1.0
CE1 C:HIS493 3.4 68.2 1.0
N C:CYS476 3.8 69.1 1.0
CG C:HIS489 4.1 46.7 1.0
CG C:HIS493 4.1 65.8 1.0
CA C:CYS476 4.1 70.3 1.0
ND1 C:HIS489 4.2 46.4 1.0
CB C:TYR475 4.2 73.8 1.0
ND1 C:HIS493 4.3 65.2 1.0
C C:TYR475 4.7 72.2 1.0
CA C:CYS473 4.8 58.8 1.0
CG2 C:THR492 4.8 60.6 1.0
CZ C:PHE480 4.8 40.7 1.0
CE2 C:PHE480 4.8 41.9 1.0
CA C:TYR475 4.9 72.3 1.0
C C:CYS476 4.9 71.0 1.0
N C:TYR475 4.9 69.7 1.0

Zinc binding site 5 out of 8 in 4is1

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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:Zn603

b:0.7
occ:1.00
NE2 C:HIS521 2.3 80.1 1.0
CD2 C:HIS521 3.1 76.5 1.0
CE1 C:HIS521 3.3 71.9 1.0
OP1 A:DA13 3.7 57.9 1.0
CG C:HIS521 4.3 73.8 1.0
ND1 C:HIS521 4.4 69.2 1.0
OP2 A:DA13 4.5 58.8 1.0
P A:DA13 4.6 61.9 1.0

Zinc binding site 6 out of 8 in 4is1

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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:Zn601

b:70.6
occ:1.00
NE2 D:HIS522 2.0 73.3 1.0
SG D:CYS501 2.1 74.6 1.0
SG D:CYS504 2.3 74.3 1.0
NE2 D:HIS517 2.5 64.6 1.0
CD2 D:HIS522 2.8 72.3 1.0
CE1 D:HIS522 3.1 77.2 1.0
CD2 D:HIS517 3.2 61.0 1.0
CB D:CYS501 3.4 66.5 1.0
CB D:CYS504 3.4 75.4 1.0
CE1 D:HIS517 3.5 65.1 1.0
N D:CYS504 3.7 76.2 1.0
CG D:HIS522 4.0 74.5 1.0
ND1 D:HIS522 4.1 78.4 1.0
CA D:CYS504 4.1 75.9 1.0
CB D:PHE503 4.2 80.2 1.0
C D:PHE503 4.2 82.1 1.0
CB D:TYR506 4.4 67.2 1.0
CG D:HIS517 4.4 58.6 1.0
ND1 D:HIS517 4.5 61.2 1.0
CA D:PHE503 4.6 82.2 1.0
N D:PHE503 4.7 80.9 1.0
CA D:CYS501 4.8 67.5 1.0
C D:CYS504 4.8 74.2 1.0
O D:PHE503 4.9 87.8 1.0
ND1 D:HIS521 4.9 74.6 0.5

Zinc binding site 7 out of 8 in 4is1

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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:Zn602

b:35.2
occ:1.00
NE2 D:HIS493 2.1 38.2 1.0
NE2 D:HIS489 2.1 31.9 1.0
SG D:CYS476 2.2 35.2 1.0
SG D:CYS473 2.2 36.1 1.0
CD2 D:HIS493 2.9 36.2 1.0
CD2 D:HIS489 3.0 31.0 1.0
CB D:CYS473 3.1 37.2 1.0
CE1 D:HIS489 3.2 29.8 1.0
CE1 D:HIS493 3.2 40.2 1.0
CB D:CYS476 3.4 37.3 1.0
N D:CYS476 3.7 38.6 1.0
CA D:CYS476 4.1 38.2 1.0
CG D:HIS493 4.1 37.9 1.0
CG D:HIS489 4.1 29.1 1.0
ND1 D:HIS489 4.2 29.3 1.0
ND1 D:HIS493 4.2 39.1 1.0
CB D:TYR475 4.4 38.9 1.0
CA D:CYS473 4.6 39.3 1.0
C D:TYR475 4.8 39.5 1.0
C D:CYS476 4.8 39.5 1.0
N D:GLY477 4.9 38.6 1.0
CA D:TYR475 4.9 39.4 1.0
N D:TYR475 5.0 38.4 1.0

Zinc binding site 8 out of 8 in 4is1

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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:Zn603

b:0.6
occ:1.00
CE1 D:HIS521 2.9 75.5 0.5
ND1 D:HIS521 3.1 74.6 0.5
O D:HIS521 3.2 79.9 1.0
NE2 D:HIS521 3.8 74.3 0.5
CG D:HIS521 4.1 72.4 0.5
ND1 D:HIS522 4.2 78.4 1.0
CD2 D:HIS521 4.4 72.4 0.5
CE1 D:HIS522 4.4 77.2 1.0
C D:HIS521 4.4 76.2 1.0

Reference:

M.Vandevenne, D.A.Jacques, C.Artuz, C.D.Nguyen, A.H.Kwan, D.J.Segal, J.M.Matthews, M.Crossley, J.M.Guss, J.P.Mackay. New Insights Into Dna Recognition By Zinc Fingers Revealed By Structural Analysis of the Oncoprotein ZNF217. J.Biol.Chem. V. 288 10616 2013.
ISSN: ESSN 1083-351X
PubMed: 23436653
DOI: 10.1074/JBC.M112.441451
Page generated: Wed Dec 16 05:24:31 2020

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