Zinc in PDB 8sss: Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER

Protein crystallography data

The structure of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER, PDB code: 8sss was solved by J.R.Horton, J.Yang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.18 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.013, 41.147, 135.661, 90, 105.18, 90
R / Rfree (%) 19.9 / 23.1

Other elements in 8sss:

The structure of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER (pdb code 8sss). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER, PDB code: 8sss:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 8sss

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Zinc binding site 1 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:129.2
occ:1.00
 NE2 A:HIS284 2.0 110.2 1.0
NE2 A:HIS288 2.0 112.8 1.0
SG A:CYS268 2.3 124.8 1.0
SG A:CYS271 2.3 121.3 1.0
CE1 A:HIS288 2.6 108.0 1.0
CE1 A:HIS284 3.0 107.3 1.0
CD2 A:HIS284 3.0 104.4 1.0
CD2 A:HIS288 3.3 110.9 1.0
CB A:CYS268 3.4 124.2 1.0
CB A:CYS271 3.5 127.5 1.0
N A:CYS271 3.6 125.6 1.0
ND1 A:HIS288 3.8 103.1 1.0
ND1 A:HIS284 4.1 104.7 1.0
CG A:HIS284 4.1 101.3 1.0
CA A:CYS271 4.1 125.0 1.0
CB A:LEU270 4.2 122.8 1.0
CG A:HIS288 4.2 108.0 1.0
CB A:TYR273 4.4 107.8 1.0
C A:LEU270 4.5 125.3 1.0
CA A:LEU270 4.7 126.7 1.0
N A:LEU270 4.8 128.3 1.0
CA A:CYS268 4.8 126.3 1.0
C A:CYS271 4.8 126.7 1.0
SD A:MET285 4.9 128.1 1.0
O A:HIS284 4.9 108.8 1.0

Zinc binding site 2 out of 14 in 8sss

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Zinc binding site 2 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:67.1
occ:1.00
 NE2 A:HIS316 2.0 58.2 1.0
NE2 A:HIS312 2.0 71.9 1.0
SG A:CYS299 2.3 57.9 1.0
SG A:CYS296 2.4 73.5 1.0
CD2 A:HIS312 2.8 62.2 1.0
CD2 A:HIS316 3.0 68.8 1.0
CE1 A:HIS316 3.1 67.1 1.0
CE1 A:HIS312 3.2 57.8 1.0
CB A:CYS296 3.3 83.0 1.0
CB A:CYS299 3.4 76.8 1.0
N A:CYS299 3.7 75.6 1.0
CG A:HIS312 4.0 70.8 1.0
CA A:CYS299 4.1 67.8 1.0
CG A:HIS316 4.1 66.0 1.0
ND1 A:HIS316 4.1 71.7 1.0
ND1 A:HIS312 4.2 59.3 1.0
CB A:LEU298 4.4 73.9 1.0
C A:LEU298 4.6 86.9 1.0
C A:CYS299 4.7 84.1 1.0
CA A:CYS296 4.8 83.3 1.0
CA A:LEU298 4.9 82.4 1.0
N A:LEU298 4.9 73.1 1.0
O A:CYS299 4.9 86.5 1.0

Zinc binding site 3 out of 14 in 8sss

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Zinc binding site 3 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:70.2
occ:1.00
 NE2 A:HIS340 2.0 57.0 1.0
NE2 A:HIS345 2.0 87.6 1.0
SG A:CYS327 2.3 74.6 1.0
SG A:CYS324 2.3 74.8 1.0
CD2 A:HIS340 2.9 52.6 1.0
CE1 A:HIS345 3.0 68.6 1.0
CD2 A:HIS345 3.0 83.5 1.0
CE1 A:HIS340 3.1 56.0 1.0
CB A:CYS324 3.2 76.3 1.0
CB A:CYS327 3.6 75.5 1.0
N A:CYS327 3.9 80.8 1.0
ND1 A:HIS345 4.0 73.8 1.0
CG A:HIS340 4.1 55.6 1.0
CG A:HIS345 4.1 75.0 1.0
ND1 A:HIS340 4.1 55.9 1.0
CA A:CYS327 4.3 84.3 1.0
C A:ASP326 4.5 83.9 1.0
CB A:ASP326 4.7 82.2 1.0
CA A:CYS324 4.7 75.8 1.0
C A:CYS327 4.8 90.1 1.0
CB A:MET329 4.8 73.2 1.0
N A:ASP326 4.9 79.3 1.0
CA A:ASP326 4.9 85.2 1.0
CB A:LYS344 4.9 53.9 1.0
O A:CYS327 4.9 88.3 1.0

Zinc binding site 4 out of 14 in 8sss

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Zinc binding site 4 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:42.9
occ:1.00
 NE2 A:HIS373 2.0 46.3 1.0
NE2 A:HIS369 2.0 47.4 1.0
SG A:CYS356 2.3 41.2 1.0
SG A:CYS353 2.3 42.6 1.0
CD2 A:HIS373 2.7 42.2 1.0
CD2 A:HIS369 2.9 38.2 1.0
CE1 A:HIS369 3.1 44.7 1.0
CE1 A:HIS373 3.2 42.7 1.0
CB A:CYS353 3.2 39.6 1.0
CB A:CYS356 3.4 42.8 1.0
N A:CYS356 3.7 43.0 1.0
CG A:HIS373 3.9 46.7 1.0
CG A:HIS369 4.1 43.5 1.0
ND1 A:HIS373 4.1 43.2 1.0
CA A:CYS356 4.1 43.4 1.0
ND1 A:HIS369 4.2 41.8 1.0
C A:MET355 4.3 43.7 1.0
CB A:MET355 4.4 46.8 1.0
CB A:TYR358 4.4 39.7 1.0
C A:CYS356 4.7 48.0 1.0
CA A:MET355 4.7 47.9 1.0
CA A:CYS353 4.7 40.0 1.0
N A:MET355 4.7 42.9 1.0
CE A:MET355 4.8 50.0 1.0
O A:CYS356 5.0 47.4 1.0

Zinc binding site 5 out of 14 in 8sss

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Zinc binding site 5 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:57.9
occ:1.00
 NE2 A:HIS397 2.1 51.7 1.0
NE2 A:HIS401 2.1 69.1 1.0
SG A:CYS384 2.3 56.3 1.0
SG A:CYS381 2.3 66.5 1.0
CD2 A:HIS401 3.0 66.7 1.0
CE1 A:HIS397 3.0 50.2 1.0
CD2 A:HIS397 3.0 50.7 1.0
CE1 A:HIS401 3.1 68.1 1.0
CB A:CYS381 3.5 60.5 1.0
CB A:CYS384 3.5 61.2 1.0
N A:CYS384 3.7 72.1 1.0
ND1 A:HIS397 4.1 49.9 1.0
CG A:HIS401 4.1 69.9 1.0
CA A:CYS384 4.1 72.1 1.0
CG A:HIS397 4.1 50.8 1.0
ND1 A:HIS401 4.2 71.6 1.0
CB A:LEU383 4.3 70.8 1.0
C A:LEU383 4.4 74.6 1.0
CE A:MET398 4.4 56.8 1.0
CB A:TYR386 4.5 57.0 1.0
C A:CYS384 4.7 73.7 1.0
CA A:LEU383 4.7 68.1 1.0
N A:LEU383 4.7 74.0 1.0
CA A:CYS381 4.9 59.6 1.0
O A:CYS384 4.9 67.9 1.0
OG1 A:THR400 4.9 59.1 1.0

Zinc binding site 6 out of 14 in 8sss

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Zinc binding site 6 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:57.2
occ:1.00
 NE2 A:HIS430 2.0 61.6 1.0
NE2 A:HIS425 2.0 60.2 1.0
SG A:CYS412 2.3 66.1 1.0
SG A:CYS409 2.4 60.3 1.0
CD2 A:HIS425 2.9 48.4 1.0
CD2 A:HIS430 3.0 59.0 1.0
CE1 A:HIS430 3.0 60.9 1.0
CE1 A:HIS425 3.1 61.6 1.0
CB A:CYS412 3.2 59.1 1.0
CB A:CYS409 3.3 65.2 1.0
N A:CYS412 3.5 67.4 1.0
CA A:CYS412 3.9 68.2 1.0
CG A:HIS425 4.1 54.6 1.0
ND1 A:HIS430 4.1 56.8 1.0
CG A:HIS430 4.1 59.1 1.0
ND1 A:HIS425 4.2 52.0 1.0
CB A:ILE411 4.4 66.2 1.0
C A:CYS412 4.6 67.5 1.0
C A:ILE411 4.6 73.9 1.0
N A:HIS413 4.8 71.4 1.0
CA A:CYS409 4.8 63.4 1.0
CB A:ALA414 4.9 63.2 1.0
CA A:ILE411 4.9 67.1 1.0
N A:ILE411 4.9 68.8 1.0
CG2 A:ILE411 5.0 65.6 1.0
N A:ALA414 5.0 59.9 1.0

Zinc binding site 7 out of 14 in 8sss

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Zinc binding site 7 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:68.8
occ:1.00
 NE2 A:HIS460 2.0 78.3 1.0
NE2 A:HIS455 2.0 73.4 1.0
SG A:CYS442 2.3 74.5 1.0
SG A:CYS439 2.3 72.3 1.0
CD2 A:HIS455 2.8 57.4 1.0
CD2 A:HIS460 3.0 77.6 1.0
CE1 A:HIS460 3.0 79.2 1.0
CE1 A:HIS455 3.2 64.0 1.0
CB A:CYS439 3.3 64.9 1.0
CB A:CYS442 3.5 69.4 1.0
N A:CYS442 3.9 67.7 1.0
CG A:HIS455 4.0 68.2 1.0
ND1 A:HIS460 4.1 73.9 1.0
CG A:HIS460 4.1 81.8 1.0
ND1 A:HIS455 4.2 61.6 1.0
CA A:CYS442 4.2 70.8 1.0
OG1 A:THR444 4.3 77.0 1.0
C A:HIS441 4.5 78.8 1.0
O A:CYS442 4.6 80.7 1.0
CB A:THR444 4.6 70.8 1.0
C A:CYS442 4.7 77.7 1.0
CA A:CYS439 4.8 66.5 1.0
CB A:HIS441 4.8 79.6 1.0
N A:HIS441 4.9 77.8 1.0
CA A:HIS441 5.0 78.2 1.0

Zinc binding site 8 out of 14 in 8sss

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Zinc binding site 8 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:129.8
occ:1.00
 NE2 D:HIS284 2.0 118.5 1.0
NE2 D:HIS288 2.0 111.2 1.0
SG D:CYS268 2.3 130.3 1.0
SG D:CYS271 2.3 110.5 1.0
CD2 D:HIS284 2.6 111.9 1.0
CD2 D:HIS288 2.9 107.1 1.0
CE1 D:HIS288 3.0 108.0 1.0
CE1 D:HIS284 3.2 114.0 1.0
CB D:CYS271 3.4 120.5 1.0
CB D:CYS268 3.5 131.2 1.0
N D:CYS271 3.5 123.7 1.0
CG D:HIS284 3.8 110.5 1.0
CA D:CYS271 4.0 125.6 1.0
CB D:LEU270 4.0 119.9 1.0
CG D:HIS288 4.1 103.9 1.0
ND1 D:HIS288 4.1 100.9 1.0
ND1 D:HIS284 4.1 108.9 1.0
C D:LEU270 4.3 123.4 1.0
CB D:TYR273 4.4 116.5 1.0
CA D:LEU270 4.6 128.6 1.0
C D:CYS271 4.6 132.0 1.0
N D:LEU270 4.7 130.7 1.0
SD D:MET285 4.8 119.7 1.0
O D:HIS284 4.8 104.7 1.0
CA D:CYS268 4.9 134.3 1.0

Zinc binding site 9 out of 14 in 8sss

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Zinc binding site 9 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:70.9
occ:1.00
 NE2 D:HIS312 2.0 68.5 1.0
NE2 D:HIS316 2.0 72.5 1.0
SG D:CYS299 2.3 57.0 1.0
SG D:CYS296 2.3 81.7 1.0
CD2 D:HIS312 2.8 65.0 1.0
CD2 D:HIS316 2.8 72.3 1.0
CE1 D:HIS312 3.1 60.6 1.0
CE1 D:HIS316 3.1 70.0 1.0
CB D:CYS296 3.3 79.1 1.0
N D:CYS299 3.7 78.4 1.0
CB D:CYS299 3.7 72.3 1.0
CG D:HIS312 4.0 65.3 1.0
CG D:HIS316 4.0 73.0 1.0
ND1 D:HIS312 4.1 56.4 1.0
ND1 D:HIS316 4.1 68.1 1.0
CB D:LEU298 4.2 73.2 1.0
CA D:CYS299 4.2 85.7 1.0
C D:LEU298 4.6 84.2 1.0
CA D:CYS296 4.7 74.5 1.0
CA D:LEU298 4.7 85.2 1.0
N D:LEU298 4.7 84.9 1.0
C D:CYS299 4.8 90.6 1.0
O D:CYS299 4.8 82.4 1.0
CG D:LEU298 5.0 78.2 1.0

Zinc binding site 10 out of 14 in 8sss

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Zinc binding site 10 out of 14 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:82.2
occ:1.00
 NE2 D:HIS345 2.0 98.9 1.0
NE2 D:HIS340 2.0 70.3 1.0
SG D:CYS327 2.3 72.3 1.0
SG D:CYS324 2.3 86.7 1.0
CD2 D:HIS345 2.9 91.7 1.0
CD2 D:HIS340 3.0 69.6 1.0
CE1 D:HIS345 3.1 91.8 1.0
CE1 D:HIS340 3.1 73.4 1.0
CB D:CYS324 3.4 90.9 1.0
CB D:CYS327 3.5 91.8 1.0
N D:CYS327 3.7 97.0 1.0
CG D:HIS345 4.1 91.4 1.0
ND1 D:HIS345 4.1 91.0 1.0
CG D:HIS340 4.1 67.7 1.0
ND1 D:HIS340 4.1 63.9 1.0
CA D:CYS327 4.2 90.5 1.0
CB D:ASP326 4.4 101.2 1.0
C D:ASP326 4.6 95.5 1.0
CA D:CYS324 4.8 93.1 1.0
C D:CYS327 4.8 93.2 1.0
CA D:ASP326 4.9 102.2 1.0
N D:ASP326 4.9 105.2 1.0

Reference:

J.Yang, J.R.Horton, B.Liu, V.G.Corces, R.M.Blumenthal, X.Zhang, X.Cheng. Structures of Ctcf-Dna Complexes Including All 11 Zinc Fingers. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37439339
DOI: 10.1093/NAR/GKAD594
Page generated: Thu Oct 31 11:08:41 2024

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