Zinc in PDB 1ubd: Co-Crystal Structure of Human YY1 Zinc Finger Domain Bound to the Adeno-Associated Virus P5 Initiator Element
Protein crystallography data
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
|
Zinc Binding Sites:
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 1ubd
Go back to
Zinc Binding Sites List in 1ubd
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 1ubd
Go back to
Zinc Binding Sites List in 1ubd
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 1ubd
Go back to
Zinc Binding Sites List in 1ubd
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 1ubd
Go back to
Zinc Binding Sites List in 1ubd
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
|
|
Reference:
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
Page generated: Wed Oct 16 19:29:18 2024
|