Zinc in PDB 8ymz: Structure of ZBTB43 in Complex with Caca Containing B-Form Dna

Protein crystallography data

The structure of Structure of ZBTB43 in Complex with Caca Containing B-Form Dna, PDB code: 8ymz was solved by X.Li, Y.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.02 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.979, 67.535, 99.466, 90, 90, 90
R / Rfree (%) 26.9 / 29.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna (pdb code 8ymz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna, PDB code: 8ymz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8ymz

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Zinc binding site 1 out of 6 in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of ZBTB43 in Complex with Caca Containing B-Form Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:136.0
occ:1.00
 SG E:CYS430 2.4 106.5 1.0
CB E:CYS433 2.5 120.5 1.0
SG E:CYS450 2.8 146.9 1.0
SG E:CYS433 2.8 114.0 1.0
N E:CYS433 3.2 125.3 1.0
CD2 E:HIS446 3.3 118.3 1.0
CB E:CYS450 3.4 145.2 1.0
CA E:CYS433 3.4 125.6 1.0
NE2 E:HIS446 3.5 115.0 1.0
CG1 E:ILE432 3.7 129.7 1.0
CB E:CYS430 3.8 113.9 1.0
CD1 E:ILE432 4.3 131.3 1.0
C E:ILE432 4.4 123.6 1.0
C E:CYS433 4.5 125.8 1.0
O E:HIS446 4.6 132.6 1.0
CG E:HIS446 4.7 122.4 1.0
CA E:CYS450 4.7 146.3 1.0
N E:ILE432 4.7 117.4 1.0
CB E:ILE432 4.7 126.4 1.0
CE1 E:HIS446 4.8 127.5 1.0
CA E:ILE432 4.8 123.5 1.0
C E:CYS450 4.9 148.8 1.0
N E:ALA434 5.0 124.7 1.0

Zinc binding site 2 out of 6 in 8ymz

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Zinc binding site 2 out of 6 in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of ZBTB43 in Complex with Caca Containing B-Form Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:87.0
occ:1.00
 NE2 E:HIS418 2.0 60.9 1.0
NE2 E:HIS422 2.1 94.3 1.0
CD2 E:HIS422 2.3 92.0 1.0
SG E:CYS405 2.3 67.9 1.0
SG E:CYS402 2.3 84.2 1.0
CD2 E:HIS418 2.9 59.9 1.0
CB E:CYS402 3.1 79.2 1.0
CE1 E:HIS418 3.1 63.8 1.0
CE1 E:HIS422 3.4 92.0 1.0
CB E:CYS405 3.5 89.3 1.0
CG E:HIS422 3.6 91.7 1.0
N E:CYS405 3.8 93.8 1.0
CE E:MET419 4.0 67.2 1.0
CG E:HIS418 4.0 60.0 1.0
ND1 E:HIS422 4.1 97.3 1.0
ND1 E:HIS418 4.1 60.2 1.0
CA E:CYS405 4.3 83.1 1.0
CA E:CYS402 4.5 65.8 1.0
CB E:VAL404 4.6 99.4 1.0
CB E:HIS422 4.8 81.1 1.0
N E:GLY406 4.8 80.2 1.0
C E:VAL404 4.9 96.3 1.0

Zinc binding site 3 out of 6 in 8ymz

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Zinc binding site 3 out of 6 in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of ZBTB43 in Complex with Caca Containing B-Form Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn503

b:67.6
occ:1.00
 CE1 E:HIS390 1.8 64.5 1.0
ND1 E:HIS390 2.1 65.9 1.0
SG E:CYS375 2.2 51.7 1.0
NE2 E:HIS394 2.4 58.0 1.0
CD2 E:HIS394 2.8 65.4 1.0
SG E:CYS377 3.0 60.6 1.0
NE2 E:HIS390 3.1 74.3 1.0
CB E:CYS377 3.2 68.0 1.0
CG E:HIS390 3.4 59.0 1.0
N E:CYS377 3.4 53.8 1.0
CB E:CYS375 3.4 67.2 1.0
CE1 E:HIS394 3.5 62.5 1.0
N E:GLN376 3.6 60.2 1.0
C E:GLN376 3.8 53.6 1.0
CD2 E:HIS390 3.8 54.9 1.0
CG E:HIS394 3.9 51.8 1.0
CA E:CYS377 3.9 56.1 1.0
CA E:GLN376 4.1 47.6 1.0
C E:CYS375 4.2 59.8 1.0
ND1 E:HIS394 4.2 59.9 1.0
SD E:MET391 4.3 49.4 1.0
CA E:CYS375 4.4 65.9 1.0
O E:GLN376 4.4 67.8 1.0
CB E:HIS390 4.5 52.2 1.0
CB E:GLN376 4.5 47.1 1.0
O E:HIS390 4.7 63.2 1.0
C E:HIS390 4.7 50.9 1.0
CE2 E:PHE381 5.0 56.4 1.0
N E:MET391 5.0 46.9 1.0

Zinc binding site 4 out of 6 in 8ymz

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Zinc binding site 4 out of 6 in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of ZBTB43 in Complex with Caca Containing B-Form Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:73.8
occ:1.00
 NE2 F:HIS394 1.9 64.4 1.0
ND1 F:HIS390 2.4 63.3 1.0
SG F:CYS375 2.4 63.8 1.0
SG F:CYS377 2.7 70.7 1.0
CE1 F:HIS394 2.7 72.2 1.0
CE1 F:HIS390 2.8 64.5 1.0
CD2 F:HIS394 3.0 63.5 1.0
CB F:CYS377 3.0 75.1 1.0
N F:CYS377 3.4 92.1 1.0
CB F:CYS375 3.5 85.3 1.0
CG F:HIS390 3.6 58.9 1.0
N F:GLN376 3.8 79.2 1.0
ND1 F:HIS394 3.8 65.7 1.0
CA F:CYS377 3.8 88.6 1.0
C F:GLN376 3.9 89.7 1.0
CG F:HIS394 4.0 64.3 1.0
NE2 F:HIS390 4.1 62.8 1.0
C F:CYS375 4.3 81.9 1.0
CB F:HIS390 4.3 63.7 1.0
CA F:GLN376 4.3 88.3 1.0
CD2 F:HIS390 4.5 60.9 1.0
CA F:CYS375 4.5 90.3 1.0
O F:GLN376 4.6 80.9 1.0
O F:HIS390 4.8 65.4 1.0
CB F:GLN376 4.9 76.2 1.0
C F:HIS390 4.9 62.2 1.0

Zinc binding site 5 out of 6 in 8ymz

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Zinc binding site 5 out of 6 in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of ZBTB43 in Complex with Caca Containing B-Form Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:73.3
occ:1.00
 NE2 F:HIS418 2.0 52.6 1.0
NE2 F:HIS422 2.1 75.6 1.0
SG F:CYS405 2.2 79.9 1.0
SG F:CYS402 2.3 74.5 1.0
CD2 F:HIS418 2.7 52.4 1.0
CB F:CYS402 2.8 76.6 1.0
CD2 F:HIS422 2.9 65.6 1.0
CE1 F:HIS418 3.2 58.3 1.0
CB F:CYS405 3.2 87.1 1.0
CE1 F:HIS422 3.3 73.7 1.0
N F:CYS405 3.6 73.8 1.0
CA F:CYS405 4.0 84.5 1.0
CG F:HIS418 4.0 60.5 1.0
CG F:HIS422 4.1 64.4 1.0
ND1 F:HIS418 4.1 56.5 1.0
ND1 F:HIS422 4.3 65.2 1.0
CA F:CYS402 4.3 76.2 1.0
N F:GLY406 4.3 95.1 1.0
C F:CYS405 4.7 94.2 1.0
CB F:VAL404 4.7 76.0 1.0
C F:VAL404 4.8 79.6 1.0
N F:LYS407 4.9 79.7 1.0
C F:CYS402 4.9 76.8 1.0

Zinc binding site 6 out of 6 in 8ymz

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Zinc binding site 6 out of 6 in the Structure of ZBTB43 in Complex with Caca Containing B-Form Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of ZBTB43 in Complex with Caca Containing B-Form Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn503

b:145.8
occ:1.00
 SG F:CYS430 2.3 130.3 1.0
CB F:CYS433 2.5 144.5 1.0
SG F:CYS433 2.6 179.4 1.0
SG F:CYS450 2.6 157.2 1.0
N F:CYS433 3.4 153.3 1.0
NE2 F:HIS446 3.4 133.7 1.0
CA F:CYS433 3.5 154.8 1.0
CG1 F:ILE432 3.7 162.8 1.0
CD2 F:HIS446 3.8 139.1 1.0
CB F:CYS430 3.8 139.3 1.0
CE1 F:HIS446 3.8 134.9 1.0
CB F:CYS450 4.1 153.3 1.0
CD1 F:ILE432 4.3 162.8 1.0
ND1 F:HIS446 4.5 122.8 1.0
CG F:HIS446 4.5 131.7 1.0
C F:ILE432 4.5 150.1 1.0
O F:HIS446 4.6 144.4 1.0
N F:ILE432 4.6 145.7 1.0
C F:CYS433 4.7 150.3 1.0
CB F:ILE432 4.8 159.2 1.0
CA F:ILE432 4.9 153.5 1.0

Reference:

Y.Yang, S.Zhang, L.Xu, Y.Pan, Y.Xuan, Y.Kai, X.Chen. Structural Insights Into the Recognition of Purine-Pyrimidine Dinucleotide Repeats By Zinc Finger Protein ZBTB43. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 39344089
DOI: 10.1111/FEBS.17286
Page generated: Thu Oct 31 14:06:22 2024

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