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Zinc in PDB 5k5l: Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure

Protein crystallography data

The structure of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure, PDB code: 5k5l was solved by H.Hashimoto, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.73 / 3.13
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 126.792, 52.397, 69.135, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure (pdb code 5k5l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure, PDB code: 5k5l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5k5l

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Zinc binding site 1 out of 7 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:92.5
occ:1.00
NE2 E:HIS460 2.0 82.1 1.0
NE2 E:HIS455 2.0 84.2 1.0
SG E:CYS442 2.3 77.8 1.0
SG E:CYS439 2.3 77.2 1.0
CD2 E:HIS460 2.6 82.3 1.0
CD2 E:HIS455 2.7 85.3 1.0
CB E:CYS439 3.2 78.1 1.0
CE1 E:HIS455 3.2 86.0 1.0
CE1 E:HIS460 3.3 79.3 1.0
CG E:HIS460 3.8 79.2 1.0
CB E:CYS442 3.9 79.5 1.0
CG E:HIS455 3.9 87.8 1.0
ND1 E:HIS460 4.1 77.5 1.0
ND1 E:HIS455 4.2 88.0 1.0
N E:CYS442 4.3 72.1 1.0
CB E:THR444 4.6 83.2 1.0
OG1 E:THR444 4.6 85.5 1.0
CA E:CYS442 4.7 77.1 1.0
CA E:CYS439 4.7 75.9 1.0
C E:HIS441 4.8 81.5 1.0
CB E:GLN459 4.9 79.8 1.0
CB E:HIS441 4.9 80.3 1.0

Zinc binding site 2 out of 7 in 5k5l

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Zinc binding site 2 out of 7 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:66.0
occ:1.00
NE2 E:HIS485 2.0 49.4 1.0
NE2 E:HIS489 2.1 47.8 1.0
SG E:CYS472 2.3 44.9 1.0
SG E:CYS469 2.4 46.8 1.0
CD2 E:HIS485 2.9 52.4 1.0
CE1 E:HIS489 3.0 47.5 1.0
CD2 E:HIS489 3.0 50.2 1.0
CE1 E:HIS485 3.0 44.9 1.0
CB E:CYS469 3.3 47.3 1.0
CB E:CYS472 3.5 44.9 1.0
N E:CYS472 3.8 47.0 1.0
ND1 E:HIS489 4.0 49.2 1.0
CG E:HIS489 4.1 51.1 1.0
CG E:HIS485 4.1 49.7 1.0
ND1 E:HIS485 4.1 45.5 1.0
CA E:CYS472 4.2 46.1 1.0
C E:TYR471 4.5 46.6 1.0
CB E:ALA474 4.6 47.4 1.0
CB E:TYR471 4.7 47.7 1.0
C E:CYS472 4.7 47.0 1.0
CA E:CYS469 4.8 49.2 1.0
N E:TYR471 4.8 49.0 1.0
O E:CYS472 4.9 48.3 1.0
CA E:TYR471 4.9 48.0 1.0

Zinc binding site 3 out of 7 in 5k5l

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Zinc binding site 3 out of 7 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:89.3
occ:1.00
NE2 F:HIS460 2.0 79.3 1.0
NE2 F:HIS455 2.1 76.1 1.0
SG F:CYS442 2.3 85.7 1.0
SG F:CYS439 2.3 88.7 1.0
CD2 F:HIS460 2.7 80.1 1.0
CD2 F:HIS455 2.9 78.7 1.0
CE1 F:HIS455 3.2 74.2 1.0
CE1 F:HIS460 3.2 75.8 1.0
CB F:CYS439 3.4 100.0 1.0
CB F:CYS442 3.5 83.3 1.0
N F:CYS442 3.8 89.2 1.0
CG F:HIS460 4.0 77.4 1.0
CG F:HIS455 4.1 78.8 1.0
ND1 F:HIS460 4.2 74.6 1.0
ND1 F:HIS455 4.2 75.9 1.0
CA F:CYS442 4.2 89.5 1.0
OG1 F:THR444 4.4 97.0 1.0
CD2 F:LEU456 4.4 80.0 1.0
CB F:HIS441 4.4 85.1 1.0
C F:HIS441 4.4 89.3 1.0
N F:HIS441 4.7 93.4 1.0
CA F:HIS441 4.7 88.7 1.0
CA F:CYS439 4.8 0.9 1.0
C F:CYS442 4.8 96.2 1.0

Zinc binding site 4 out of 7 in 5k5l

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Zinc binding site 4 out of 7 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:0.0
occ:1.00
NE2 F:HIS489 2.0 98.3 1.0
NE2 F:HIS485 2.0 86.5 1.0
SG F:CYS472 2.3 0.1 1.0
SG F:CYS469 2.3 78.9 1.0
CD2 F:HIS485 2.5 86.2 1.0
CD2 F:HIS489 2.7 0.0 1.0
CB F:CYS469 3.1 77.7 1.0
CE1 F:HIS489 3.1 94.9 1.0
CE1 F:HIS485 3.2 84.6 1.0
CG F:HIS485 3.7 83.6 1.0
CB F:CYS472 3.8 90.8 1.0
CG F:HIS489 3.9 0.3 1.0
ND1 F:HIS485 4.0 85.0 1.0
ND1 F:HIS489 4.1 96.5 1.0
N F:CYS472 4.2 89.3 1.0
CB F:ALA474 4.5 84.8 1.0
CA F:CYS472 4.5 83.4 1.0
CA F:CYS469 4.6 81.6 1.0
O F:HIS485 4.8 88.3 1.0
C F:HIS485 5.0 85.6 1.0
CA F:GLN486 5.0 86.2 1.0

Zinc binding site 5 out of 7 in 5k5l

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Zinc binding site 5 out of 7 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:54.7
occ:1.00
NE2 G:HIS460 2.0 47.4 1.0
NE2 G:HIS455 2.1 43.9 1.0
SG G:CYS442 2.3 56.5 1.0
SG G:CYS439 2.3 48.2 1.0
CD2 G:HIS460 3.0 48.1 1.0
CD2 G:HIS455 3.0 44.6 1.0
CE1 G:HIS455 3.0 46.0 1.0
CE1 G:HIS460 3.1 47.4 1.0
CB G:CYS439 3.5 48.9 1.0
CB G:CYS442 3.6 54.1 1.0
N G:CYS442 4.0 50.6 1.0
CG G:HIS455 4.1 47.6 1.0
ND1 G:HIS455 4.1 48.6 1.0
CG G:HIS460 4.1 49.1 1.0
ND1 G:HIS460 4.1 48.6 1.0
CA G:CYS442 4.3 51.4 1.0
CB G:HIS441 4.4 46.3 1.0
C G:HIS441 4.4 43.5 1.0
OG1 G:THR444 4.6 54.8 1.0
CB G:THR444 4.7 55.5 1.0
N G:HIS441 4.7 42.0 1.0
CA G:HIS441 4.7 43.4 1.0
CA G:CYS439 4.9 46.9 1.0
C G:CYS442 4.9 51.3 1.0
CB G:GLN459 5.0 49.1 1.0

Zinc binding site 6 out of 7 in 5k5l

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Zinc binding site 6 out of 7 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn502

b:0.8
occ:1.00
NE2 G:HIS489 2.0 88.2 1.0
NE2 G:HIS485 2.1 88.7 1.0
CE1 G:HIS489 2.2 91.9 1.0
SG G:CYS472 2.3 97.5 1.0
SG G:CYS469 2.4 91.1 1.0
CD2 G:HIS485 2.9 83.6 1.0
CE1 G:HIS485 3.1 89.2 1.0
CD2 G:HIS489 3.3 86.2 1.0
CB G:CYS469 3.3 90.4 1.0
CB G:CYS472 3.4 0.1 1.0
ND1 G:HIS489 3.4 92.1 1.0
N G:CYS472 3.8 0.2 1.0
CG G:HIS489 3.9 88.6 1.0
CG G:HIS485 4.0 81.1 1.0
ND1 G:HIS485 4.1 84.6 1.0
CA G:CYS472 4.2 0.8 1.0
CB G:TYR471 4.5 97.8 1.0
C G:TYR471 4.8 0.0 1.0
CA G:CYS469 4.8 89.0 1.0
CD2 G:TYR471 4.8 90.5 1.0
O G:HIS485 4.9 81.4 1.0
C G:CYS472 4.9 0.2 1.0
CA G:TYR471 5.0 99.4 1.0

Zinc binding site 7 out of 7 in 5k5l

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Zinc binding site 7 out of 7 in the Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Homo Sapiens Ccctc-Binding Factor (Ctcf) ZNF6-8 and H19 Sequence Dna Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn503

b:84.5
occ:1.00
NE2 G:HIS430 2.0 77.9 1.0
NE2 G:HIS425 2.0 88.6 1.0
SG G:CYS409 2.3 72.7 1.0
SG G:CYS412 2.3 75.6 1.0
CD2 G:HIS430 2.8 76.4 1.0
CD2 G:HIS425 2.9 87.2 1.0
CB G:CYS412 3.0 88.0 1.0
CE1 G:HIS425 3.1 93.7 1.0
CE1 G:HIS430 3.2 77.9 1.0
N G:CYS412 3.7 81.6 1.0
CB G:CYS409 3.8 84.4 1.0
CA G:CYS412 3.9 85.8 1.0
CG G:HIS430 4.0 75.5 1.0
CG G:HIS425 4.1 91.9 1.0
ND1 G:HIS425 4.1 94.9 1.0
ND1 G:HIS430 4.2 76.3 1.0
CB G:ILE411 4.7 68.6 1.0
O G:CYS409 4.8 96.5 1.0
C G:ILE411 4.8 82.9 1.0

Reference:

H.Hashimoto, D.Wang, J.R.Horton, X.Zhang, V.G.Corces, X.Cheng. Structural Basis For the Versatile and Methylation-Dependent Binding of Ctcf to Dna. Mol. Cell V. 66 711 2017.
ISSN: ISSN 1097-4164
PubMed: 28529057
DOI: 10.1016/J.MOLCEL.2017.05.004
Page generated: Wed Dec 16 06:26:20 2020

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