Zinc in PDB 8e3d: ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)

Protein crystallography data

The structure of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11), PDB code: 8e3d was solved by J.R.Horton, R.Ren, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.15 / 2.62
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 196.181, 196.181, 54.964, 90, 90, 120
R / Rfree (%) 20.6 / 23.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) (pdb code 8e3d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11), PDB code: 8e3d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 8e3d

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Zinc binding site 1 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:59.5
occ:1.00
 NE2 A:HIS432 2.0 58.4 1.0
NE2 A:HIS428 2.0 49.8 1.0
SG A:CYS415 2.3 52.1 1.0
SG A:CYS412 2.3 50.5 1.0
CD2 A:HIS432 2.7 52.4 1.0
CD2 A:HIS428 2.9 40.0 1.0
CE1 A:HIS428 3.1 54.9 1.0
CE1 A:HIS432 3.2 57.6 1.0
CB A:CYS412 3.3 50.1 1.0
CB A:CYS415 3.3 53.8 1.0
N A:CYS415 3.7 50.3 1.0
CG A:HIS432 3.9 60.6 1.0
CA A:CYS415 4.1 58.8 1.0
CG A:HIS428 4.1 40.0 1.0
ND1 A:HIS432 4.1 59.7 1.0
ND1 A:HIS428 4.2 56.3 1.0
CB A:ILE414 4.5 58.8 1.0
CA A:CYS412 4.7 45.6 1.0
C A:CYS415 4.8 59.8 1.0
C A:ILE414 4.8 54.3 1.0

Zinc binding site 2 out of 12 in 8e3d

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Zinc binding site 2 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:46.1
occ:1.00
 NE2 A:HIS400 2.0 49.5 1.0
NE2 A:HIS404 2.0 59.6 1.0
SG A:CYS387 2.2 43.9 1.0
SG A:CYS384 2.3 51.3 1.0
CE1 A:HIS400 2.9 53.4 1.0
CD2 A:HIS400 3.0 39.0 1.0
CD2 A:HIS404 3.0 56.3 1.0
CE1 A:HIS404 3.0 50.2 1.0
CB A:CYS384 3.0 43.6 1.0
CB A:CYS387 3.5 51.9 1.0
N A:CYS387 3.8 56.3 1.0
ND1 A:HIS400 4.0 42.8 1.0
CG A:HIS400 4.0 44.7 1.0
ND1 A:HIS404 4.1 59.0 1.0
CG A:HIS404 4.1 54.6 1.0
CA A:CYS387 4.2 48.9 1.0
CA A:CYS384 4.5 54.4 1.0
CB A:ILE386 4.6 61.5 1.0
O A:HIS400 4.8 55.2 1.0
C A:CYS387 4.8 55.5 1.0
CB A:LYS389 4.9 59.4 1.0
C A:ILE386 4.9 66.8 1.0
N A:GLU388 5.0 62.0 1.0
N A:ILE386 5.0 55.0 1.0

Zinc binding site 3 out of 12 in 8e3d

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Zinc binding site 3 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:59.1
occ:1.00
 NE2 A:HIS456 2.0 63.3 1.0
NE2 A:HIS460 2.0 76.2 1.0
SG A:CYS440 2.2 48.5 1.0
SG A:CYS443 2.3 60.3 1.0
CD2 A:HIS460 2.8 64.0 1.0
CE1 A:HIS456 2.9 53.5 1.0
CE1 A:HIS460 3.0 70.8 1.0
CD2 A:HIS456 3.0 42.0 1.0
CB A:CYS440 3.3 52.0 1.0
CB A:CYS443 3.4 53.7 1.0
N A:CYS443 3.8 66.1 1.0
CG A:HIS460 3.9 67.0 1.0
ND1 A:HIS460 4.0 67.6 1.0
ND1 A:HIS456 4.0 47.1 1.0
CG A:HIS456 4.1 49.1 1.0
CA A:CYS443 4.2 73.9 1.0
SD A:MET457 4.6 76.1 1.0
CB A:ALA445 4.6 57.8 1.0
CB A:GLN442 4.7 81.7 1.0
CA A:CYS440 4.7 52.8 1.0
C A:GLN442 4.8 77.8 1.0
C A:CYS443 4.8 75.4 1.0
N A:GLY444 4.9 71.4 1.0
N A:ALA445 5.0 68.8 1.0

Zinc binding site 4 out of 12 in 8e3d

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Zinc binding site 4 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:63.9
occ:1.00
 NE2 A:HIS484 2.0 58.3 1.0
SG A:CYS471 2.2 64.0 1.0
SG A:CYS468 2.3 66.4 1.0
SG A:CYS490 2.3 84.7 1.0
CB A:CYS471 2.8 69.5 1.0
CD2 A:HIS484 2.8 51.1 1.0
CE1 A:HIS484 3.2 57.7 1.0
CB A:CYS468 3.2 57.7 1.0
CB A:CYS490 3.5 87.8 1.0
N A:CYS471 3.6 71.8 1.0
CA A:CYS471 3.7 60.4 1.0
CG A:HIS484 4.0 56.5 1.0
ND1 A:HIS484 4.2 65.3 1.0
CD2 A:LEU485 4.3 56.8 1.0
C A:SER470 4.4 74.9 1.0
C A:CYS471 4.5 71.3 1.0
CA A:CYS468 4.6 47.0 1.0
CA A:CYS490 4.7 115.6 1.0
CB A:SER470 4.7 57.8 1.0
N A:SER470 4.8 68.9 1.0
CA A:SER470 4.9 55.5 1.0
O A:CYS471 5.0 105.3 1.0

Zinc binding site 5 out of 12 in 8e3d

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Zinc binding site 5 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:60.3
occ:1.00
 NE2 B:HIS432 2.0 61.3 1.0
NE2 B:HIS428 2.0 47.1 1.0
SG B:CYS415 2.3 51.4 1.0
SG B:CYS412 2.3 64.3 1.0
CD2 B:HIS432 2.8 59.9 1.0
CD2 B:HIS428 2.9 51.9 1.0
CE1 B:HIS428 3.1 62.2 1.0
CE1 B:HIS432 3.1 67.0 1.0
CB B:CYS412 3.2 47.6 1.0
CB B:CYS415 3.5 55.4 1.0
N B:CYS415 3.7 56.4 1.0
CG B:HIS432 4.0 64.2 1.0
CA B:CYS415 4.1 49.4 1.0
CG B:HIS428 4.1 51.5 1.0
ND1 B:HIS428 4.1 59.0 1.0
ND1 B:HIS432 4.1 67.9 1.0
CG1 B:VAL417 4.4 64.1 1.0
CB B:ILE414 4.4 63.9 1.0
SD B:MET429 4.6 54.6 1.0
CA B:CYS412 4.6 45.0 1.0
C B:ILE414 4.7 63.3 1.0
C B:CYS415 4.8 58.0 1.0
N B:ILE414 4.9 59.7 1.0
CA B:ILE414 4.9 60.4 1.0
N B:LYS416 4.9 56.8 1.0

Zinc binding site 6 out of 12 in 8e3d

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Zinc binding site 6 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:59.8
occ:1.00
 NE2 B:HIS404 2.0 47.6 1.0
NE2 B:HIS400 2.0 57.1 1.0
SG B:CYS384 2.2 62.8 1.0
SG B:CYS387 2.3 60.0 1.0
CD2 B:HIS404 2.6 46.2 1.0
CD2 B:HIS400 2.7 43.0 1.0
CE1 B:HIS400 3.1 66.0 1.0
CB B:CYS384 3.2 62.1 1.0
CE1 B:HIS404 3.2 66.1 1.0
CB B:CYS387 3.5 57.2 1.0
N B:CYS387 3.8 54.4 1.0
CG B:HIS404 3.9 48.6 1.0
CG B:HIS400 3.9 55.7 1.0
ND1 B:HIS400 4.0 48.8 1.0
ND1 B:HIS404 4.1 58.6 1.0
CA B:CYS387 4.2 62.7 1.0
CB B:ILE386 4.5 64.0 1.0
CA B:CYS384 4.6 70.0 1.0
C B:CYS387 4.8 71.9 1.0
C B:ILE386 4.8 62.8 1.0
CB B:LYS389 5.0 53.7 1.0
O B:HIS400 5.0 59.0 1.0
N B:ILE386 5.0 63.8 1.0
N B:GLU388 5.0 71.8 1.0

Zinc binding site 7 out of 12 in 8e3d

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Zinc binding site 7 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:57.8
occ:1.00
 NE2 B:HIS456 2.0 60.9 1.0
NE2 B:HIS460 2.0 86.7 1.0
SG B:CYS443 2.2 61.1 1.0
SG B:CYS440 2.3 68.7 1.0
CD2 B:HIS456 2.9 59.4 1.0
CE1 B:HIS460 2.9 64.4 1.0
CD2 B:HIS460 3.0 75.0 1.0
CE1 B:HIS456 3.0 64.2 1.0
CB B:CYS440 3.2 58.3 1.0
CB B:CYS443 3.2 50.9 1.0
N B:CYS443 3.6 67.2 1.0
CA B:CYS443 3.9 62.0 1.0
ND1 B:HIS460 4.0 61.9 1.0
CG B:HIS460 4.0 67.8 1.0
CG B:HIS456 4.1 55.7 1.0
ND1 B:HIS456 4.1 65.9 1.0
CB B:GLN442 4.4 67.9 1.0
SD B:MET457 4.5 96.5 1.0
C B:GLN442 4.6 65.3 1.0
C B:CYS443 4.6 67.2 1.0
CA B:CYS440 4.6 61.9 1.0
N B:GLY444 4.7 59.3 1.0
CG1 B:VAL459 4.8 58.4 1.0
N B:GLN442 4.9 67.5 1.0
CA B:GLN442 4.9 65.6 1.0
CB B:ALA445 4.9 54.9 1.0
N B:ALA445 5.0 60.5 1.0

Zinc binding site 8 out of 12 in 8e3d

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Zinc binding site 8 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn605

b:81.2
occ:1.00
 NE2 B:HIS484 2.0 71.1 1.0
SG B:CYS471 2.3 108.6 1.0
SG B:CYS490 2.3 137.6 1.0
SG B:CYS468 2.3 86.4 1.0
CD2 B:HIS484 2.9 70.4 1.0
CE1 B:HIS484 3.1 74.9 1.0
CB B:CYS468 3.3 79.6 1.0
CB B:CYS471 3.4 96.5 1.0
N B:CYS471 3.7 101.5 1.0
CB B:CYS490 3.9 161.2 1.0
CG B:HIS484 4.1 69.2 1.0
CA B:CYS471 4.1 93.7 1.0
ND1 B:HIS484 4.2 74.9 1.0
CB B:SER470 4.5 124.8 1.0
CA B:CYS468 4.7 66.9 1.0
CD2 B:LEU485 4.8 85.4 1.0
C B:SER470 4.8 119.6 1.0
C B:CYS471 4.8 94.4 1.0
N B:CYS490 4.9 186.1 1.0
N B:SER470 5.0 112.4 1.0

Zinc binding site 9 out of 12 in 8e3d

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Zinc binding site 9 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn601

b:189.8
occ:1.00
 NE2 F:HIS428 2.0 166.0 1.0
NE2 F:HIS432 2.0 201.8 1.0
CD2 F:HIS432 2.0 202.5 1.0
SG F:CYS415 2.3 163.7 1.0
SG F:CYS412 2.3 162.8 1.0
CD2 F:HIS428 2.6 160.1 1.0
CE1 F:HIS428 3.2 164.8 1.0
CE1 F:HIS432 3.4 205.7 1.0
CG F:HIS432 3.4 206.8 1.0
CB F:CYS412 3.5 162.8 1.0
CB F:CYS415 3.6 171.5 1.0
CE F:MET429 3.6 167.8 1.0
N F:CYS415 3.9 172.0 1.0
CG F:HIS428 3.9 158.0 1.0
ND1 F:HIS432 4.0 208.9 1.0
ND1 F:HIS428 4.1 157.2 1.0
CA F:CYS415 4.3 168.7 1.0
CB F:ILE414 4.3 177.7 1.0
CB F:HIS432 4.6 203.0 1.0
C F:ILE414 4.8 179.8 1.0
CA F:CYS412 4.9 156.7 1.0
CG2 F:ILE414 4.9 176.3 1.0
CA F:ILE414 5.0 179.8 1.0
O F:HIS428 5.0 156.6 1.0

Zinc binding site 10 out of 12 in 8e3d

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Zinc binding site 10 out of 12 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Cast Sequence (#11) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn602

b:69.8
occ:1.00
 NE2 F:HIS400 2.0 81.0 1.0
NE2 F:HIS404 2.0 61.4 1.0
SG F:CYS387 2.3 76.4 1.0
SG F:CYS384 2.3 75.9 1.0
CD2 F:HIS404 2.7 76.9 1.0
CE1 F:HIS400 2.9 85.5 1.0
CD2 F:HIS400 3.0 82.0 1.0
CE1 F:HIS404 3.1 72.3 1.0
CB F:CYS384 3.1 81.6 1.0
CB F:CYS387 3.3 66.2 1.0
N F:CYS387 3.7 62.7 1.0
CG F:HIS404 3.8 70.2 1.0
ND1 F:HIS404 4.0 74.5 1.0
ND1 F:HIS400 4.0 83.9 1.0
CA F:CYS387 4.0 70.0 1.0
CG F:HIS400 4.1 84.8 1.0
CB F:ILE386 4.6 58.0 1.0
CA F:CYS384 4.6 89.2 1.0
C F:CYS387 4.8 75.5 1.0
C F:ILE386 4.8 74.8 1.0
O F:HIS400 5.0 83.2 1.0
N F:ILE386 5.0 70.2 1.0

Reference:

R.Ren, J.R.Horton, Q.Chen, J.Yang, B.Liu, Y.Huang, R.M.Blumenthal, X.Zhang, X.Cheng. Structural Basis For Transcription Factor ZBTB7A Recognition of Dna and Effects of ZBTB7A Somatic Mutations That Occur in Human Acute Myeloid Leukemia. J.Biol.Chem. 02885 2023.
ISSN: ESSN 1083-351X
PubMed: 36626981
DOI: 10.1016/J.JBC.2023.102885
Page generated: Wed Oct 30 19:26:31 2024

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