Zinc in PDB 7n5v: ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)

The structure of ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20), PDB code: 7n5v 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)	43.47 / 3.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.292, 60.067, 133.729, 90, 98.5, 90
R / Rfree (%)	26 / 31.4

The binding sites of Zinc atom in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20) (pdb code 7n5v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20), PDB code: 7n5v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:197.5 occ:1.00 NE2 A:HIS428 2.0 177.5 1.0 NE2 A:HIS432 2.0 206.4 1.0 SG A:CYS415 2.3 157.1 1.0 SG A:CYS412 2.3 230.1 1.0 CD2 A:HIS428 2.6 168.0 1.0 CE1 A:HIS432 2.8 204.4 1.0 CD2 A:HIS432 3.0 222.9 1.0 CE1 A:HIS428 3.1 180.3 1.0 CB A:CYS415 3.5 174.0 1.0 CB A:CYS412 3.6 192.5 1.0 CG A:HIS428 3.7 165.2 1.0 N A:CYS415 3.8 180.2 1.0 ND1 A:HIS432 3.9 212.2 1.0 ND1 A:HIS428 3.9 174.2 1.0 CG A:HIS432 4.0 219.8 1.0 CA A:CYS415 4.2 173.7 1.0 O A:HIS428 4.5 192.6 1.0 CB A:ILE414 4.5 200.9 1.0 SD A:MET429 4.7 250.3 1.0 N A:ILE414 4.8 192.8 1.0 C A:ILE414 4.8 189.8 1.0 C A:HIS428 4.9 162.9 1.0 CA A:ILE414 5.0 192.3 1.0 CA A:CYS412 5.0 193.9 1.0

Zinc binding site 2 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:142.9 occ:1.00 NE2 A:HIS404 2.0 90.9 1.0 NE2 A:HIS400 2.0 89.9 1.0 SG A:CYS384 2.2 132.9 1.0 SG A:CYS387 2.3 82.2 1.0 CD2 A:HIS400 2.5 89.2 1.0 CD2 A:HIS404 2.9 91.5 1.0 CE1 A:HIS404 3.0 140.4 1.0 CE1 A:HIS400 3.2 121.6 1.0 CB A:CYS387 3.5 84.6 1.0 CB A:CYS384 3.5 116.4 1.0 CG A:HIS400 3.7 89.7 1.0 N A:CYS387 3.8 84.9 1.0 CG A:HIS404 4.0 120.1 1.0 ND1 A:HIS404 4.0 144.9 1.0 ND1 A:HIS400 4.0 129.8 1.0 O A:HIS400 4.1 95.6 1.0 CB A:ILE386 4.3 90.5 1.0 CA A:CYS387 4.3 104.4 1.0 C A:ILE386 4.7 94.8 1.0 CD1 A:ILE401 4.7 87.3 1.0 C A:HIS400 4.8 89.7 1.0 CA A:CYS384 4.8 111.7 1.0 N A:ILE386 4.8 129.9 1.0 CA A:ILE386 4.8 112.8 1.0 CG2 A:ILE386 4.9 108.4 1.0

Zinc binding site 3 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:174.8 occ:1.00 NE2 B:HIS428 2.0 152.2 1.0 NE2 B:HIS432 2.0 168.3 1.0 SG B:CYS412 2.3 165.5 1.0 SG B:CYS415 2.3 226.3 1.0 CE1 B:HIS432 2.6 151.0 1.0 CB B:CYS415 2.7 138.2 1.0 CE1 B:HIS428 2.9 133.2 1.0 CD2 B:HIS428 2.9 132.7 1.0 CD2 B:HIS432 3.0 147.6 1.0 N B:CYS415 3.5 159.3 1.0 ND1 B:HIS432 3.7 128.9 1.0 CA B:CYS415 3.7 150.4 1.0 CB B:CYS412 3.7 159.1 1.0 CG B:HIS432 3.9 147.4 1.0 ND1 B:HIS428 3.9 141.0 1.0 CG B:HIS428 4.0 125.7 1.0 SD B:MET429 4.7 147.5 1.0 C B:ILE414 4.8 176.0 1.0 O B:HIS428 4.8 142.6 1.0 C B:CYS415 4.8 146.6 1.0 N B:ILE414 4.9 176.8 1.0 CA B:CYS412 5.0 165.8 1.0

Zinc binding site 4 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:128.7 occ:1.00 NE2 B:HIS404 2.0 132.4 1.0 NE2 B:HIS400 2.0 90.2 1.0 SG B:CYS387 2.3 88.0 1.0 SG B:CYS384 2.3 138.1 1.0 CD2 B:HIS404 2.6 121.2 1.0 CD2 B:HIS400 2.8 106.7 1.0 CE1 B:HIS400 2.9 115.6 1.0 CE1 B:HIS404 3.1 146.7 1.0 CB B:CYS387 3.2 107.1 1.0 CB B:CYS384 3.4 122.6 1.0 N B:CYS387 3.7 112.7 1.0 CG B:HIS404 3.7 120.9 1.0 CG B:HIS400 3.8 96.3 1.0 ND1 B:HIS400 3.9 114.7 1.0 ND1 B:HIS404 3.9 137.5 1.0 O B:HIS400 4.0 119.3 1.0 CA B:CYS387 4.1 108.3 1.0 CB B:ILE386 4.4 107.9 1.0 CA B:CYS384 4.8 96.0 1.0 C B:ILE386 4.8 117.4 1.0 C B:HIS400 4.9 100.1 1.0 CG2 B:ILE386 4.9 143.6 1.0 C B:CYS387 5.0 111.3 1.0 CA B:ILE386 5.0 119.5 1.0 N B:ILE386 5.0 135.3 1.0

Zinc binding site 5 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:126.0 occ:1.00 NE2 B:HIS456 2.0 81.1 1.0 NE2 B:HIS460 2.0 163.3 1.0 SG B:CYS440 2.2 97.8 1.0 CD2 B:HIS460 2.2 150.5 1.0 SG B:CYS443 2.3 82.8 1.0 CE1 B:HIS456 2.9 81.5 1.0 N B:CYS443 3.1 96.2 1.0 CD2 B:HIS456 3.1 85.3 1.0 CE1 B:HIS460 3.2 162.7 1.0 CB B:CYS443 3.3 93.4 1.0 CB B:GLN442 3.4 126.2 1.0 CG B:HIS460 3.4 110.1 1.0 CB B:CYS440 3.5 110.8 1.0 CA B:CYS443 3.7 112.7 1.0 ND1 B:HIS460 3.9 98.7 1.0 C B:GLN442 4.0 111.3 1.0 ND1 B:HIS456 4.0 89.2 1.0 CG B:GLN442 4.1 111.3 1.0 CA B:GLN442 4.1 120.1 1.0 CG B:HIS456 4.1 112.3 1.0 N B:GLN442 4.3 116.5 1.0 C B:CYS443 4.6 116.6 1.0 N B:GLY444 4.6 110.3 1.0 CB B:HIS460 4.6 119.4 1.0 SD B:MET457 4.7 103.5 1.0 CA B:CYS440 4.9 97.5 1.0

Zinc binding site 6 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:132.3 occ:1.00 NE2 B:HIS484 2.0 130.1 1.0 SG B:CYS468 2.3 125.0 1.0 SG B:CYS471 2.3 142.2 1.0 SG B:CYS490 2.3 100.8 1.0 CD2 B:HIS484 2.6 142.8 1.0 OG B:SER470 2.9 134.2 1.0 CB B:CYS471 2.9 97.4 1.0 CE1 B:HIS484 3.2 126.6 1.0 CB B:CYS490 3.2 111.7 1.0 N B:CYS471 3.4 126.3 1.0 CB B:CYS468 3.5 135.2 1.0 CA B:CYS471 3.8 97.5 1.0 CG B:HIS484 3.9 112.3 1.0 ND1 B:HIS484 4.2 129.2 1.0 CB B:SER470 4.2 139.4 1.0 C B:SER470 4.4 106.4 1.0 CD1 B:LEU485 4.5 99.1 1.0 C B:CYS471 4.7 102.6 1.0 CA B:SER470 4.7 127.6 1.0 CA B:CYS490 4.7 156.3 1.0 N B:SER470 4.8 139.6 1.0 CA B:CYS468 4.8 123.4 1.0 C B:CYS468 5.0 132.8 1.0

Zinc binding site 7 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn601 b:174.2 occ:1.00 NE2 F:HIS432 2.0 183.9 1.0 NE2 F:HIS428 2.0 170.3 1.0 SG F:CYS412 2.2 172.7 1.0 SG F:CYS415 2.3 189.0 1.0 CD2 F:HIS428 2.6 148.8 1.0 CD2 F:HIS432 2.7 159.6 1.0 CE1 F:HIS428 3.1 165.4 1.0 CE1 F:HIS432 3.2 199.6 1.0 CB F:CYS412 3.4 171.2 1.0 CB F:CYS415 3.5 173.3 1.0 N F:CYS415 3.7 172.1 1.0 CG F:HIS428 3.8 143.0 1.0 CG F:HIS432 3.9 169.0 1.0 ND1 F:HIS428 4.0 164.4 1.0 ND1 F:HIS432 4.1 203.5 1.0 CA F:CYS415 4.2 185.0 1.0 CB F:ILE414 4.4 168.8 1.0 SD F:MET429 4.7 205.5 1.0 O F:HIS428 4.8 152.6 1.0 C F:ILE414 4.8 164.7 1.0 CA F:CYS412 4.8 139.6 1.0 N F:ILE414 4.8 131.1 1.0 CA F:ILE414 4.9 152.3 1.0 C F:CYS415 5.0 175.5 1.0

Zinc binding site 8 out of 8 in the ZBTB7A Zinc Finger Domain Bound to Dna Duplex Containing Ggaccc (Oligo 20)


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 Ggaccc (Oligo 20) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn602 b:112.4 occ:1.00 NE2 F:HIS400 2.0 95.1 1.0 NE2 F:HIS404 2.0 101.5 1.0 SG F:CYS384 2.2 155.3 1.0 SG F:CYS387 2.3 185.5 1.0 CB F:CYS387 2.3 107.0 1.0 CE1 F:HIS400 2.7 95.0 1.0 CE1 F:HIS404 2.8 114.5 1.0 CD2 F:HIS404 3.2 111.1 1.0 CD2 F:HIS400 3.2 95.4 1.0 N F:CYS387 3.2 101.8 1.0 CB F:CYS384 3.3 142.6 1.0 CA F:CYS387 3.3 90.1 1.0 ND1 F:HIS400 3.9 107.7 1.0 ND1 F:HIS404 4.0 99.2 1.0 CG F:HIS400 4.2 95.5 1.0 CG F:HIS404 4.2 94.3 1.0 C F:CYS387 4.2 102.1 1.0 C F:ILE386 4.3 111.7 1.0 CB F:ILE386 4.5 100.0 1.0 CB F:LYS389 4.6 110.6 1.0 N F:GLU388 4.7 103.3 1.0 CA F:CYS384 4.7 99.5 1.0 CA F:ILE386 4.8 114.5 1.0 N F:ILE386 4.8 115.9 1.0 N F:LYS389 4.9 110.9 1.0 CG2 F:ILE386 4.9 93.2 1.0 O F:CYS387 4.9 116.3 1.0

R.Ren, J.R.Horton, Q.Chen, J.Yang, B.Liu, B.Crossley, R.M.Blumenthal, X.Zhang, X.Cheng. Structural Basis For ZBTB7A Recognition of Dna, and the Effects of ZBTB7A Somatic Mutations in Human Acute Myeloid Leukemia To Be Published.