Zinc in PDB 6ml4: BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3)

Protein crystallography data

The structure of BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3), PDB code: 6ml4 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 / 1.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.277, 68.807, 48.434, 90.00, 92.40, 90.00
R / Rfree (%) 19.1 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3) (pdb code 6ml4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3), PDB code: 6ml4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6ml4

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Zinc binding site 1 out of 5 in the BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:28.5
occ:1.00
NE2 A:HIS399 2.0 37.0 1.0
NE2 A:HIS395 2.0 31.7 1.0
SG A:CYS382 2.3 31.2 1.0
SG A:CYS379 2.3 28.5 1.0
CD2 A:HIS399 2.9 35.3 1.0
CE1 A:HIS395 3.0 29.8 1.0
CD2 A:HIS395 3.1 27.9 1.0
CE1 A:HIS399 3.1 37.5 1.0
CB A:CYS379 3.3 25.8 1.0
CB A:CYS382 3.4 33.4 1.0
N A:CYS382 3.7 32.6 1.0
ND1 A:HIS395 4.1 29.9 1.0
CG A:HIS399 4.1 36.0 1.0
CA A:CYS382 4.1 32.3 1.0
ND1 A:HIS399 4.1 38.9 1.0
CG A:HIS395 4.2 28.2 1.0
CB A:GLN381 4.4 35.4 1.0
O A:HOH750 4.4 45.5 1.0
C A:GLN381 4.6 35.5 1.0
CA A:CYS379 4.7 24.5 1.0
C A:CYS382 4.8 31.6 1.0
N A:GLY383 4.9 29.7 1.0
CA A:GLN381 4.9 34.2 1.0
N A:GLN381 4.9 32.3 1.0
CG2 A:VAL398 5.0 30.2 1.0

Zinc binding site 2 out of 5 in 6ml4

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Zinc binding site 2 out of 5 in the BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:17.3
occ:1.00
NE2 A:HIS423 2.0 16.6 1.0
NE2 A:HIS427 2.0 19.3 1.0
SG A:CYS410 2.3 20.2 1.0
SG A:CYS407 2.3 15.3 1.0
CD2 A:HIS427 2.9 17.9 1.0
CD2 A:HIS423 2.9 17.2 1.0
CE1 A:HIS423 3.0 18.6 1.0
CE1 A:HIS427 3.1 20.8 1.0
CB A:CYS407 3.2 15.4 1.0
CB A:CYS410 3.4 20.7 1.0
N A:CYS410 3.6 19.1 1.0
CA A:CYS410 4.0 20.6 1.0
CG A:HIS423 4.1 14.0 1.0
ND1 A:HIS423 4.1 15.3 1.0
CG A:HIS427 4.1 18.1 1.0
ND1 A:HIS427 4.2 21.1 1.0
CB A:HIS409 4.2 19.2 0.5
CB A:HIS409 4.2 19.3 0.5
C A:HIS409 4.6 20.8 1.0
CA A:CYS407 4.6 16.3 1.0
CA A:HIS409 4.7 19.1 0.5
C A:CYS410 4.8 23.2 1.0
CA A:HIS409 4.8 19.1 0.5
N A:HIS409 4.8 16.3 1.0
N A:HIS411 4.8 20.2 1.0
NH2 A:ARG412 4.8 38.3 1.0
CG A:HIS409 4.9 22.6 0.5
O A:HOH775 4.9 29.5 1.0
ND1 A:HIS409 5.0 25.4 0.5
OG1 A:THR426 5.0 19.0 1.0

Zinc binding site 3 out of 5 in 6ml4

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Zinc binding site 3 out of 5 in the BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:14.4
occ:1.00
NE2 A:HIS455 2.0 15.7 1.0
NE2 A:HIS451 2.0 12.5 1.0
SG A:CYS438 2.3 14.0 1.0
SG A:CYS435 2.3 12.9 1.0
CD2 A:HIS455 2.9 13.9 1.0
CD2 A:HIS451 3.0 11.7 1.0
CE1 A:HIS451 3.1 11.2 1.0
CE1 A:HIS455 3.1 16.9 1.0
CB A:CYS435 3.1 16.2 1.0
CB A:CYS438 3.3 15.8 1.0
N A:CYS438 3.6 14.4 1.0
CA A:CYS438 4.0 16.1 1.0
CG A:HIS455 4.1 15.0 1.0
ND1 A:HIS451 4.2 10.7 1.0
CG A:HIS451 4.2 11.0 1.0
ND1 A:HIS455 4.2 18.0 1.0
O E:HOH668 4.3 30.7 1.0
CB A:ILE437 4.4 16.9 1.0
CA A:CYS435 4.6 15.8 1.0
C A:ILE437 4.6 19.6 1.0
C A:CYS438 4.7 15.6 1.0
N A:GLY439 4.8 14.9 1.0
CA A:ILE437 4.8 18.1 1.0
N A:ILE437 4.9 17.6 1.0
CG2 A:ILE437 5.0 16.3 1.0
C A:CYS435 5.0 14.7 1.0

Zinc binding site 4 out of 5 in 6ml4

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Zinc binding site 4 out of 5 in the BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:13.7
occ:1.00
NE2 A:HIS479 2.0 13.7 1.0
NE2 A:HIS483 2.0 15.8 1.0
SG A:CYS466 2.3 14.9 1.0
SG A:CYS463 2.3 13.1 1.0
CE1 A:HIS479 3.0 14.2 1.0
CD2 A:HIS483 3.0 16.2 1.0
CD2 A:HIS479 3.0 13.1 1.0
CE1 A:HIS483 3.0 14.4 1.0
CB A:CYS463 3.1 13.9 1.0
CB A:CYS466 3.3 16.4 1.0
N A:CYS466 3.7 14.7 1.0
CA A:CYS466 4.0 15.8 1.0
ND1 A:HIS479 4.1 12.3 1.0
ND1 A:HIS483 4.1 15.7 1.0
CG A:HIS479 4.1 12.0 1.0
CG A:HIS483 4.2 14.4 1.0
CB A:ILE465 4.5 15.8 1.0
CA A:CYS463 4.6 12.9 1.0
C A:ILE465 4.7 16.2 1.0
C A:CYS466 4.7 15.4 1.0
N A:GLY467 4.8 14.4 1.0
CB A:LYS468 4.9 16.3 1.0
CA A:ILE465 4.9 15.5 1.0
N A:ILE465 4.9 14.4 1.0

Zinc binding site 5 out of 5 in 6ml4

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Zinc binding site 5 out of 5 in the BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of BTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:21.1
occ:1.00
NE2 A:HIS507 2.0 22.5 1.0
NE2 A:HIS511 2.0 29.0 1.0
SG A:CYS491 2.3 16.1 1.0
SG A:CYS494 2.3 22.8 1.0
CD2 A:HIS507 2.9 18.0 1.0
CD2 A:HIS511 2.9 27.3 1.0
CE1 A:HIS511 3.1 30.2 1.0
CE1 A:HIS507 3.1 21.6 1.0
CB A:CYS491 3.2 16.9 1.0
CB A:CYS494 3.4 23.8 1.0
N A:CYS494 3.7 20.0 1.0
CA A:CYS494 4.0 23.1 1.0
CG A:HIS507 4.1 19.2 1.0
CG A:HIS511 4.1 29.4 1.0
ND1 A:HIS507 4.1 21.8 1.0
ND1 A:HIS511 4.1 31.7 1.0
CB A:GLU493 4.4 22.6 1.0
C A:GLU493 4.6 23.2 1.0
CA A:CYS491 4.6 16.3 1.0
C A:CYS494 4.7 22.7 1.0
CB A:LEU496 4.7 24.9 1.0
N A:GLY495 4.8 19.4 1.0
CA A:GLU493 4.8 21.6 1.0
N A:GLU493 4.9 18.5 1.0
N A:LEU496 5.0 20.2 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 12:20:00 2020

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