Zinc in PDB 1m55: Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
Protein crystallography data
The structure of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein, PDB code: 1m55
was solved by
A.B.Hickman,
D.R.Ronning,
R.M.Kotin,
F.Dyda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.888,
73.455,
65.560,
90.00,
94.49,
90.00
|
R / Rfree (%)
|
17.8 /
19.6
|
Other elements in 1m55:
The structure of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
(pdb code 1m55). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein, PDB code: 1m55:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 1m55
Go back to
Zinc Binding Sites List in 1m55
Zinc binding site 1 out
of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn202
b:9.8
occ:1.00
|
NE2
|
A:HIS91
|
2.0
|
7.9
|
1.0
|
NE2
|
A:HIS89
|
2.1
|
7.6
|
1.0
|
OE1
|
A:GLU82
|
2.1
|
10.3
|
1.0
|
CD2
|
A:HIS91
|
3.0
|
7.9
|
1.0
|
CE1
|
A:HIS89
|
3.0
|
7.8
|
1.0
|
CE1
|
A:HIS91
|
3.1
|
7.8
|
1.0
|
CD2
|
A:HIS89
|
3.1
|
7.7
|
1.0
|
CD
|
A:GLU82
|
3.1
|
10.9
|
1.0
|
OE2
|
A:GLU82
|
3.7
|
10.7
|
1.0
|
NZ
|
A:LYS157
|
3.9
|
11.7
|
1.0
|
CB
|
A:GLU82
|
4.1
|
7.8
|
1.0
|
CG
|
A:GLU82
|
4.1
|
9.1
|
1.0
|
CG
|
A:HIS91
|
4.1
|
7.8
|
1.0
|
ND1
|
A:HIS91
|
4.2
|
7.9
|
1.0
|
ND1
|
A:HIS89
|
4.2
|
7.8
|
1.0
|
CG
|
A:HIS89
|
4.2
|
7.4
|
1.0
|
OE2
|
A:GLU161
|
4.5
|
19.7
|
1.0
|
|
Zinc binding site 2 out
of 6 in 1m55
Go back to
Zinc Binding Sites List in 1m55
Zinc binding site 2 out
of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn205
b:27.5
occ:1.00
|
OE2
|
A:GLU95
|
2.2
|
15.2
|
1.0
|
OE1
|
A:GLN73
|
2.3
|
22.5
|
1.0
|
O
|
A:HOH1011
|
2.4
|
22.1
|
1.0
|
O
|
A:HOH1211
|
2.4
|
30.0
|
1.0
|
CD
|
A:GLU95
|
3.0
|
23.6
|
1.0
|
OE1
|
A:GLU95
|
3.1
|
30.1
|
1.0
|
CD
|
A:GLN73
|
3.4
|
21.6
|
1.0
|
NE2
|
A:GLN73
|
3.9
|
23.8
|
1.0
|
CG
|
A:LYS76
|
4.2
|
15.2
|
1.0
|
CG
|
A:GLU95
|
4.3
|
17.5
|
1.0
|
N
|
A:LYS76
|
4.4
|
9.1
|
1.0
|
O
|
A:GLU74
|
4.5
|
10.2
|
1.0
|
O
|
B:HOH2153
|
4.5
|
30.5
|
1.0
|
CA
|
A:SER75
|
4.6
|
9.5
|
1.0
|
CG
|
A:GLN73
|
4.7
|
16.0
|
1.0
|
CB
|
A:LYS76
|
4.9
|
12.0
|
1.0
|
CB
|
A:SER97
|
5.0
|
21.6
|
1.0
|
C
|
A:SER75
|
5.0
|
9.8
|
1.0
|
|
Zinc binding site 3 out
of 6 in 1m55
Go back to
Zinc Binding Sites List in 1m55
Zinc binding site 3 out
of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:9.3
occ:1.00
|
NE2
|
B:HIS91
|
2.0
|
8.4
|
1.0
|
NE2
|
B:HIS89
|
2.0
|
7.4
|
1.0
|
OE1
|
B:GLU82
|
2.1
|
10.1
|
1.0
|
CD2
|
B:HIS91
|
2.9
|
8.2
|
1.0
|
CE1
|
B:HIS89
|
3.0
|
7.9
|
1.0
|
CE1
|
B:HIS91
|
3.1
|
8.4
|
1.0
|
CD
|
B:GLU82
|
3.1
|
11.3
|
1.0
|
CD2
|
B:HIS89
|
3.1
|
7.4
|
1.0
|
OE2
|
B:GLU82
|
3.7
|
11.6
|
1.0
|
NZ
|
B:LYS157
|
3.9
|
10.2
|
1.0
|
CG
|
B:GLU82
|
4.1
|
8.9
|
1.0
|
CG
|
B:HIS91
|
4.1
|
7.9
|
1.0
|
CB
|
B:GLU82
|
4.1
|
6.7
|
1.0
|
ND1
|
B:HIS91
|
4.2
|
8.4
|
1.0
|
ND1
|
B:HIS89
|
4.2
|
7.7
|
1.0
|
CG
|
B:HIS89
|
4.2
|
7.2
|
1.0
|
OE2
|
B:GLU161
|
4.5
|
20.9
|
1.0
|
O
|
B:HOH1254
|
4.9
|
24.8
|
1.0
|
O
|
B:HOH1248
|
5.0
|
13.4
|
1.0
|
|
Zinc binding site 4 out
of 6 in 1m55
Go back to
Zinc Binding Sites List in 1m55
Zinc binding site 4 out
of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn203
b:25.8
occ:1.00
|
OE2
|
B:GLU16
|
2.1
|
22.3
|
1.0
|
O
|
B:HOH1376
|
2.4
|
25.2
|
1.0
|
CD
|
B:GLU16
|
2.8
|
22.0
|
1.0
|
OE1
|
B:GLU16
|
2.9
|
23.1
|
1.0
|
O
|
B:HOH2123
|
3.7
|
48.9
|
1.0
|
CG
|
B:GLU16
|
4.2
|
18.2
|
1.0
|
O
|
B:HOH2122
|
4.6
|
51.2
|
1.0
|
O
|
B:HOH1381
|
4.8
|
24.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 1m55
Go back to
Zinc Binding Sites List in 1m55
Zinc binding site 5 out
of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn204
b:20.8
occ:1.00
|
OE2
|
B:GLU95
|
2.2
|
11.7
|
1.0
|
O
|
B:HOH1058
|
2.2
|
16.7
|
1.0
|
O
|
B:HOH1059
|
2.2
|
21.1
|
1.0
|
OE1
|
B:GLN73
|
2.2
|
17.6
|
1.0
|
O
|
B:HOH1057
|
2.3
|
24.7
|
1.0
|
O
|
B:HOH1329
|
2.3
|
18.9
|
1.0
|
CD
|
B:GLU95
|
3.0
|
21.3
|
1.0
|
OE1
|
B:GLU95
|
3.2
|
24.4
|
1.0
|
CD
|
B:GLN73
|
3.3
|
16.4
|
1.0
|
NE2
|
B:GLN73
|
3.8
|
20.1
|
1.0
|
CG
|
B:LYS76
|
4.2
|
10.9
|
1.0
|
O
|
B:HOH1061
|
4.3
|
22.4
|
1.0
|
CG
|
B:GLU95
|
4.4
|
13.6
|
1.0
|
N
|
B:LYS76
|
4.4
|
7.8
|
1.0
|
O
|
B:GLU74
|
4.4
|
7.4
|
1.0
|
O
|
B:HOH1060
|
4.5
|
36.2
|
1.0
|
CG
|
B:GLN73
|
4.6
|
11.9
|
1.0
|
OG
|
B:SER97
|
4.6
|
27.3
|
1.0
|
CA
|
B:SER75
|
4.7
|
7.9
|
1.0
|
CB
|
B:SER97
|
4.8
|
16.6
|
1.0
|
CB
|
B:LYS76
|
4.9
|
8.3
|
1.0
|
|
Zinc binding site 6 out
of 6 in 1m55
Go back to
Zinc Binding Sites List in 1m55
Zinc binding site 6 out
of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn206
b:27.3
occ:1.00
|
OD1
|
B:ASP146
|
2.2
|
17.7
|
1.0
|
OD2
|
B:ASP146
|
2.3
|
25.8
|
1.0
|
CG
|
B:ASP146
|
2.6
|
18.6
|
1.0
|
O
|
B:HOH1088
|
3.7
|
46.2
|
1.0
|
CB
|
B:ASP146
|
4.1
|
17.2
|
1.0
|
CA
|
B:GLY148
|
4.3
|
10.4
|
1.0
|
N
|
B:GLY148
|
4.4
|
10.9
|
1.0
|
C
|
B:GLY148
|
4.9
|
10.9
|
1.0
|
CA
|
B:ASP146
|
5.0
|
14.8
|
1.0
|
|
Reference:
A.B.Hickman,
D.R.Ronning,
R.M.Kotin,
F.Dyda.
Structural Unity Among Viral Origin Binding Proteins: Crystal Structure of the Nuclease Domain of Adeno-Associated Virus Rep. Mol.Cell V. 10 327 2002.
ISSN: ISSN 1097-2765
PubMed: 12191478
DOI: 10.1016/S1097-2765(02)00592-0
Page generated: Sun Oct 13 05:20:16 2024
|