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Zinc in PDB 6ml6: ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification)

Protein crystallography data

The structure of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification), PDB code: 6ml6 was solved by J.R.Horton, X.Cheng, R.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.04 / 1.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.163, 68.244, 49.259, 90.00, 92.90, 90.00
R / Rfree (%) 20.2 / 22.2

Zinc Binding Sites:

The binding sites of Zinc atom in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification) (pdb code 6ml6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification), PDB code: 6ml6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6ml6

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Zinc binding site 1 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:28.3
occ:1.00
NE2 A:HIS399 2.0 35.2 1.0
NE2 A:HIS395 2.0 30.1 1.0
SG A:CYS382 2.3 29.9 1.0
SG A:CYS379 2.3 26.2 1.0
CD2 A:HIS399 3.0 32.5 1.0
CE1 A:HIS395 3.0 26.7 1.0
CD2 A:HIS395 3.0 26.0 1.0
CE1 A:HIS399 3.0 34.3 1.0
CB A:CYS379 3.2 25.4 1.0
CB A:CYS382 3.4 31.2 1.0
N A:CYS382 3.6 32.0 1.0
ND1 A:HIS395 4.1 28.0 1.0
CA A:CYS382 4.1 31.5 1.0
ND1 A:HIS399 4.1 37.2 1.0
CG A:HIS399 4.1 37.8 1.0
CG A:HIS395 4.2 26.4 1.0
CB A:GLN381 4.3 37.4 1.0
C A:GLN381 4.6 36.1 1.0
CA A:CYS379 4.7 24.2 1.0
CG2 A:VAL398 4.7 30.3 1.0
C A:CYS382 4.8 34.5 1.0
N A:GLY383 4.8 31.9 1.0
CA A:GLN381 4.8 34.8 1.0
N A:GLN381 4.9 32.2 1.0

Zinc binding site 2 out of 5 in 6ml6

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Zinc binding site 2 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:20.0
occ:1.00
NE2 A:HIS423 2.0 17.7 1.0
NE2 A:HIS427 2.0 22.0 1.0
SG A:CYS410 2.3 20.9 1.0
SG A:CYS407 2.3 18.5 1.0
CD2 A:HIS423 3.0 18.4 1.0
CD2 A:HIS427 3.0 18.8 1.0
CE1 A:HIS423 3.0 16.8 1.0
CE1 A:HIS427 3.0 24.4 1.0
CB A:CYS407 3.2 15.3 1.0
CB A:CYS410 3.4 22.5 1.0
N A:CYS410 3.6 21.8 1.0
CA A:CYS410 4.0 23.1 1.0
ND1 A:HIS423 4.1 16.7 1.0
CG A:HIS423 4.1 16.1 1.0
ND1 A:HIS427 4.1 24.4 1.0
CG A:HIS427 4.1 20.1 1.0
CB A:HIS409 4.3 26.9 1.0
NH2 A:ARG412 4.4 55.6 1.0
C A:HIS409 4.6 25.4 1.0
CA A:CYS407 4.6 14.9 1.0
C A:CYS410 4.7 24.8 1.0
N A:HIS411 4.8 21.8 1.0
N A:HIS409 4.8 23.8 1.0
CA A:HIS409 4.8 23.1 1.0
CZ A:ARG412 4.9 52.6 1.0

Zinc binding site 3 out of 5 in 6ml6

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Zinc binding site 3 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:15.0
occ:1.00
NE2 A:HIS451 2.0 11.6 1.0
NE2 A:HIS455 2.0 18.6 1.0
SG A:CYS435 2.3 14.3 1.0
SG A:CYS438 2.3 15.2 1.0
CD2 A:HIS455 3.0 19.0 1.0
CD2 A:HIS451 3.0 11.6 1.0
CE1 A:HIS451 3.0 11.8 1.0
CE1 A:HIS455 3.1 21.5 1.0
CB A:CYS435 3.1 13.8 1.0
CB A:CYS438 3.3 17.6 1.0
N A:CYS438 3.7 16.3 1.0
CA A:CYS438 4.1 17.9 1.0
ND1 A:HIS451 4.1 11.8 1.0
CG A:HIS455 4.1 18.8 1.0
CG A:HIS451 4.2 11.2 1.0
ND1 A:HIS455 4.2 20.8 1.0
O A:HOH808 4.2 24.3 1.0
CB A:ILE437 4.4 18.7 1.0
CA A:CYS435 4.6 14.6 1.0
C A:ILE437 4.6 19.4 1.0
C A:CYS438 4.8 16.3 1.0
N A:GLY439 4.8 14.4 1.0
CA A:ILE437 4.9 18.5 1.0
N A:ILE437 4.9 17.3 1.0
CG2 A:ILE437 4.9 17.6 1.0
C A:CYS435 5.0 14.0 1.0

Zinc binding site 4 out of 5 in 6ml6

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Zinc binding site 4 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:15.8
occ:1.00
NE2 A:HIS483 2.0 17.0 1.0
NE2 A:HIS479 2.0 14.1 1.0
SG A:CYS466 2.3 14.1 1.0
SG A:CYS463 2.3 14.7 1.0
CD2 A:HIS479 3.0 16.9 1.0
CD2 A:HIS483 3.0 16.8 1.0
CE1 A:HIS483 3.0 16.1 1.0
CE1 A:HIS479 3.0 14.3 1.0
CB A:CYS463 3.1 14.4 1.0
CB A:CYS466 3.4 18.1 1.0
N A:CYS466 3.6 15.0 1.0
CA A:CYS466 4.1 17.0 1.0
ND1 A:HIS479 4.1 15.4 1.0
CG A:HIS479 4.1 12.2 1.0
ND1 A:HIS483 4.1 18.3 1.0
CG A:HIS483 4.2 17.2 1.0
CB A:ILE465 4.4 19.1 1.0
CA A:CYS463 4.6 16.1 1.0
C A:ILE465 4.7 17.5 1.0
C A:CYS466 4.7 17.9 1.0
N A:GLY467 4.8 18.2 1.0
CA A:ILE465 4.9 17.7 1.0
N A:ILE465 4.9 17.5 1.0
CB A:LYS468 4.9 15.3 1.0
CG2 A:ILE465 4.9 19.7 1.0
C A:CYS463 5.0 16.5 1.0

Zinc binding site 5 out of 5 in 6ml6

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Zinc binding site 5 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpa 5MC Modification) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:21.3
occ:1.00
NE2 A:HIS511 2.0 27.9 1.0
NE2 A:HIS507 2.0 20.9 1.0
SG A:CYS491 2.3 17.7 1.0
SG A:CYS494 2.3 23.2 1.0
CD2 A:HIS507 3.0 19.1 1.0
CD2 A:HIS511 3.0 25.0 1.0
CE1 A:HIS511 3.0 28.9 1.0
CE1 A:HIS507 3.1 22.3 1.0
CB A:CYS491 3.2 17.4 1.0
CB A:CYS494 3.4 26.0 1.0
N A:CYS494 3.7 23.4 1.0
CA A:CYS494 4.1 27.1 1.0
CG A:HIS507 4.1 18.4 1.0
ND1 A:HIS511 4.1 31.2 1.0
ND1 A:HIS507 4.1 20.7 1.0
CG A:HIS511 4.1 28.9 1.0
CB A:GLU493 4.3 25.2 1.0
O A:HOH878 4.5 37.2 1.0
C A:GLU493 4.6 25.9 1.0
CA A:CYS491 4.6 18.0 1.0
C A:CYS494 4.7 26.5 1.0
CB A:LEU496 4.7 22.4 1.0
N A:GLY495 4.8 20.3 1.0
CA A:GLU493 4.9 24.9 1.0
N A:GLU493 4.9 22.8 1.0
N A:LEU496 4.9 22.9 1.0

Reference:

R.Ren, S.Hardikar, J.R.Horton, Y.Lu, Y.Zeng, A.K.Singh, K.Lin, L.D.Coletta, J.Shen, C.S.Lin Kong, H.Hashimoto, X.Zhang, T.Chen, X.Cheng. Structural Basis of Specific Dna Binding By the Transcription Factor ZBTB24. Nucleic Acids Res. V. 47 8388 2019.
ISSN: ESSN 1362-4962
PubMed: 31226215
DOI: 10.1093/NAR/GKZ557
Page generated: Wed Dec 16 12:20:02 2020

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