Zinc in PDB 1ubd: Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element

The structure of Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element, PDB code: 1ubd was solved by H.B.Houbaviy, A.Usheva, T.Shenk, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.000, 65.700, 117.100, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 33

The binding sites of Zinc atom in the Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element (pdb code 1ubd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element, PDB code: 1ubd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:34.8 occ:1.00 NE2 C:HIS316 2.0 32.9 1.0 NE2 C:HIS320 2.0 27.6 1.0 SG C:CYS303 2.3 36.8 1.0 SG C:CYS298 2.3 38.9 1.0 CD2 C:HIS316 2.9 31.1 1.0 CE1 C:HIS320 3.0 28.5 1.0 CD2 C:HIS320 3.0 27.0 1.0 CE1 C:HIS316 3.1 26.8 1.0 CB C:CYS298 3.1 43.8 1.0 CB C:CYS303 3.1 36.2 1.0 CB C:HIS300 4.0 46.3 1.0 CG C:HIS316 4.1 30.1 1.0 ND1 C:HIS320 4.1 29.0 1.0 ND1 C:HIS316 4.2 28.6 1.0 CG C:HIS320 4.2 24.9 1.0 CA C:CYS298 4.6 46.5 1.0 CA C:CYS303 4.6 42.0 1.0 CG C:HIS300 4.8 40.8 1.0 CD1 C:LEU317 4.8 39.0 1.0 CB C:LYS305 4.8 46.3 1.0 O C:HIS316 4.9 22.5 1.0 CD C:LYS305 4.9 40.2 1.0 C C:CYS298 5.0 45.8 1.0

Zinc binding site 2 out of 4 in the Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:27.1 occ:1.00 NE2 C:HIS347 2.0 16.0 1.0 NE2 C:HIS343 2.0 11.6 1.0 SG C:CYS327 2.3 17.6 1.0 SG C:CYS330 2.3 17.6 1.0 CE1 C:HIS347 3.0 20.5 1.0 CD2 C:HIS347 3.0 8.0 1.0 CD2 C:HIS343 3.0 9.2 1.0 CE1 C:HIS343 3.1 3.1 1.0 CB C:CYS327 3.3 12.7 1.0 CB C:CYS330 3.4 15.7 1.0 N C:CYS330 3.6 20.9 1.0 CA C:CYS330 4.1 20.4 1.0 ND1 C:HIS347 4.1 16.7 1.0 CG C:HIS347 4.1 17.1 1.0 CB C:GLU329 4.2 21.6 1.0 CG C:HIS343 4.2 6.2 1.0 ND1 C:HIS343 4.2 2.0 1.0 C C:GLU329 4.5 18.0 1.0 NE2 C:GLN344 4.6 19.0 1.0 CA C:GLU329 4.7 19.9 1.0 CA C:CYS327 4.7 11.1 1.0 C C:CYS330 4.8 19.3 1.0 N C:GLY331 4.8 18.9 1.0 N C:GLU329 4.8 20.5 1.0 CB C:LYS332 5.0 8.9 1.0

Zinc binding site 3 out of 4 in the Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:42.8 occ:1.00 NE2 C:HIS377 2.0 41.1 1.0 NE2 C:HIS373 2.0 36.6 1.0 SG C:CYS360 2.3 41.8 1.0 SG C:CYS355 2.3 26.9 1.0 CE1 C:HIS373 2.9 26.9 1.0 CE1 C:HIS377 3.0 43.9 1.0 CD2 C:HIS377 3.0 42.8 1.0 CD2 C:HIS373 3.1 37.2 1.0 CB C:CYS355 3.2 31.9 1.0 CB C:CYS360 3.2 45.8 1.0 ND1 C:HIS373 4.1 33.4 1.0 ND1 C:HIS377 4.1 51.5 1.0 CG C:HIS377 4.1 49.8 1.0 CG C:HIS373 4.2 36.0 1.0 CB C:PHE357 4.3 44.5 1.0 CA C:CYS355 4.6 36.5 1.0 CA C:CYS360 4.6 45.8 1.0 CA C:VAL374 4.8 43.8 1.0 CB C:LYS362 4.8 30.5 1.0 N C:GLY361 4.9 43.2 1.0 CG C:PHE357 4.9 40.1 1.0

Zinc binding site 4 out of 4 in the Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn504 b:56.0 occ:1.00 NE2 C:HIS403 2.0 52.9 1.0 NE2 C:HIS407 2.0 62.0 1.0 SG C:CYS385 2.3 60.1 1.0 SG C:CYS390 2.4 59.4 1.0 CE1 C:HIS403 2.9 51.6 1.0 CD2 C:HIS407 3.0 62.6 1.0 CE1 C:HIS407 3.1 63.2 1.0 CD2 C:HIS403 3.1 51.8 1.0 CB C:CYS390 3.3 54.0 1.0 CB C:CYS385 3.3 56.1 1.0 ND1 C:HIS403 4.1 52.9 1.0 CG C:HIS403 4.2 52.9 1.0 ND1 C:HIS407 4.2 62.2 1.0 CG C:HIS407 4.2 61.6 1.0 CB C:PHE387 4.4 49.4 1.0 CD1 C:PHE387 4.4 57.0 1.0 CG C:PHE387 4.6 54.2 1.0 CA C:CYS390 4.6 53.1 1.0 CB C:LYS392 4.7 41.2 1.0 O C:CYS390 4.7 51.3 1.0 CA C:CYS385 4.7 52.2 1.0 C C:CYS390 4.8 50.5 1.0 CD C:LYS392 4.8 46.5 1.0

H.B.Houbaviy, A.Usheva, T.Shenk, S.K.Burley. Cocrystal Structure of YY1 Bound to the Adeno-Associated Virus P5 Initiator. Proc.Natl.Acad.Sci.Usa V. 93 13577 1996.
ISSN: ISSN 0027-8424
PubMed: 8942976
DOI: 10.1073/PNAS.93.24.13577