Zinc in PDB 5l2l: NAB2 Zn Fingers 5-7 Bound to A11G Rna
Protein crystallography data
The structure of NAB2 Zn Fingers 5-7 Bound to A11G Rna, PDB code: 5l2l
was solved by
M.Stewart,
S.Aibara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.09 /
1.55
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.669,
85.035,
64.956,
90.00,
99.07,
90.00
|
R / Rfree (%)
|
13.1 /
15.2
|
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Zinc atom in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
(pdb code 5l2l). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the
NAB2 Zn Fingers 5-7 Bound to A11G Rna, PDB code: 5l2l:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 1 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:17.5
occ:1.00
|
NE2
|
A:HIS430
|
2.1
|
17.5
|
1.0
|
SG
|
A:CYS415
|
2.3
|
18.4
|
1.0
|
SG
|
A:CYS426
|
2.4
|
19.1
|
1.0
|
SG
|
A:CYS421
|
2.4
|
18.0
|
1.0
|
HB2
|
A:CYS421
|
3.0
|
21.6
|
1.0
|
HB2
|
A:CYS415
|
3.0
|
20.9
|
1.0
|
CE1
|
A:HIS430
|
3.1
|
16.9
|
1.0
|
CD2
|
A:HIS430
|
3.1
|
19.0
|
1.0
|
CB
|
A:CYS421
|
3.2
|
18.0
|
1.0
|
CB
|
A:CYS426
|
3.2
|
19.8
|
1.0
|
CB
|
A:CYS415
|
3.2
|
17.4
|
1.0
|
HE1
|
A:HIS430
|
3.3
|
20.2
|
1.0
|
HD2
|
A:HIS430
|
3.3
|
22.8
|
1.0
|
HB3
|
A:CYS426
|
3.3
|
23.8
|
1.0
|
HB2
|
A:CYS426
|
3.3
|
23.8
|
1.0
|
HB3
|
A:CYS421
|
3.4
|
21.6
|
1.0
|
HB3
|
A:CYS415
|
3.6
|
20.9
|
1.0
|
HB2
|
A:TYR428
|
4.0
|
23.7
|
1.0
|
O
|
G:HOH127
|
4.0
|
42.0
|
1.0
|
H2
|
G:A3
|
4.1
|
29.9
|
1.0
|
HD2
|
A:PHE417
|
4.1
|
22.1
|
1.0
|
O
|
A:HOH676
|
4.2
|
30.6
|
1.0
|
ND1
|
A:HIS430
|
4.2
|
18.6
|
1.0
|
CG
|
A:HIS430
|
4.2
|
16.8
|
1.0
|
H61
|
C:A4
|
4.3
|
23.1
|
1.0
|
HB3
|
A:ASN423
|
4.3
|
26.1
|
1.0
|
HB2
|
A:PHE417
|
4.3
|
21.1
|
1.0
|
H
|
A:TYR428
|
4.5
|
22.9
|
1.0
|
CA
|
A:CYS415
|
4.6
|
15.1
|
1.0
|
HD2
|
A:TYR428
|
4.6
|
26.5
|
1.0
|
HA
|
A:CYS415
|
4.6
|
18.1
|
1.0
|
CA
|
A:CYS421
|
4.6
|
18.5
|
1.0
|
CA
|
A:CYS426
|
4.7
|
20.6
|
1.0
|
C2
|
G:A3
|
4.7
|
24.9
|
1.0
|
H
|
A:PHE417
|
4.7
|
20.5
|
1.0
|
HA
|
A:CYS421
|
4.8
|
22.2
|
1.0
|
HA
|
A:CYS426
|
4.9
|
24.7
|
1.0
|
HD1
|
A:HIS430
|
4.9
|
22.4
|
1.0
|
N6
|
C:A4
|
5.0
|
19.3
|
1.0
|
CB
|
A:TYR428
|
5.0
|
19.7
|
1.0
|
H
|
A:ASN423
|
5.0
|
23.8
|
1.0
|
|
Zinc binding site 2 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 2 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:17.6
occ:1.00
|
NE2
|
A:HIS452
|
2.1
|
17.2
|
1.0
|
SG
|
A:CYS443
|
2.4
|
18.4
|
1.0
|
SG
|
A:CYS448
|
2.4
|
17.5
|
1.0
|
SG
|
A:CYS437
|
2.4
|
19.1
|
1.0
|
CE1
|
A:HIS452
|
3.0
|
17.0
|
1.0
|
HB2
|
A:CYS437
|
3.0
|
21.4
|
1.0
|
HB2
|
A:CYS443
|
3.1
|
23.5
|
1.0
|
CB
|
A:CYS443
|
3.1
|
19.6
|
1.0
|
HB3
|
A:CYS443
|
3.1
|
23.5
|
1.0
|
HE1
|
A:HIS452
|
3.2
|
20.4
|
1.0
|
CD2
|
A:HIS452
|
3.2
|
18.3
|
1.0
|
HB3
|
A:CYS448
|
3.3
|
22.2
|
1.0
|
CB
|
A:CYS437
|
3.3
|
17.8
|
1.0
|
CB
|
A:CYS448
|
3.3
|
18.5
|
1.0
|
HD2
|
A:HIS452
|
3.4
|
22.0
|
1.0
|
HB2
|
A:CYS448
|
3.4
|
22.2
|
1.0
|
HB3
|
A:CYS437
|
3.6
|
21.4
|
1.0
|
HH12
|
A:ARG429
|
3.7
|
21.5
|
1.0
|
O
|
D:HOH137
|
3.8
|
36.0
|
1.0
|
HB2
|
A:PHE450
|
3.8
|
22.0
|
1.0
|
H61
|
D:A11
|
4.2
|
24.2
|
1.0
|
ND1
|
A:HIS452
|
4.2
|
17.0
|
1.0
|
NH1
|
A:ARG429
|
4.2
|
17.9
|
1.0
|
CG
|
A:HIS452
|
4.3
|
17.2
|
1.0
|
O
|
A:HOH611
|
4.3
|
49.5
|
1.0
|
HH11
|
A:ARG429
|
4.4
|
21.5
|
1.0
|
HB3
|
A:ARG445
|
4.4
|
22.9
|
1.0
|
HB2
|
A:GLU439
|
4.5
|
30.3
|
1.0
|
H
|
A:PHE450
|
4.5
|
19.8
|
1.0
|
CA
|
A:CYS443
|
4.6
|
18.5
|
1.0
|
CA
|
A:CYS437
|
4.7
|
17.7
|
1.0
|
HD2
|
A:PHE450
|
4.7
|
21.9
|
1.0
|
HA
|
A:CYS437
|
4.7
|
21.2
|
1.0
|
CA
|
A:CYS448
|
4.8
|
17.0
|
1.0
|
HH22
|
A:ARG429
|
4.8
|
23.9
|
1.0
|
CB
|
A:PHE450
|
4.8
|
18.3
|
1.0
|
N6
|
D:A11
|
4.8
|
20.1
|
1.0
|
O
|
A:PHE450
|
4.8
|
18.5
|
1.0
|
H62
|
D:A11
|
4.8
|
24.2
|
1.0
|
H
|
A:ARG445
|
4.9
|
23.3
|
1.0
|
H
|
A:GLU439
|
4.9
|
25.4
|
1.0
|
HA
|
A:CYS443
|
4.9
|
22.2
|
1.0
|
CZ
|
A:ARG429
|
4.9
|
17.9
|
1.0
|
HD1
|
A:HIS452
|
4.9
|
20.4
|
1.0
|
|
Zinc binding site 3 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 3 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:17.7
occ:1.00
|
NE2
|
A:HIS473
|
2.1
|
17.9
|
1.0
|
SG
|
A:CYS464
|
2.4
|
17.7
|
1.0
|
SG
|
A:CYS458
|
2.4
|
17.3
|
1.0
|
SG
|
A:CYS469
|
2.4
|
18.3
|
1.0
|
CE1
|
A:HIS473
|
3.0
|
19.1
|
1.0
|
HB3
|
A:CYS469
|
3.1
|
22.5
|
1.0
|
CD2
|
A:HIS473
|
3.1
|
19.8
|
1.0
|
HB2
|
A:CYS464
|
3.2
|
20.9
|
1.0
|
HE1
|
A:HIS473
|
3.2
|
22.9
|
1.0
|
CB
|
A:CYS469
|
3.2
|
18.7
|
1.0
|
CB
|
A:CYS464
|
3.2
|
17.4
|
1.0
|
HB2
|
A:CYS458
|
3.2
|
22.1
|
1.0
|
HB3
|
A:CYS464
|
3.3
|
20.9
|
1.0
|
HD2
|
A:HIS473
|
3.3
|
23.8
|
1.0
|
HB2
|
A:CYS469
|
3.3
|
22.5
|
1.0
|
CB
|
A:CYS458
|
3.4
|
18.4
|
1.0
|
HB3
|
A:CYS458
|
3.7
|
22.1
|
1.0
|
HB2
|
A:PHE471
|
3.8
|
22.4
|
1.0
|
HB2
|
A:PHE460
|
4.0
|
21.7
|
1.0
|
O
|
A:HOH683
|
4.0
|
22.8
|
1.0
|
HD2
|
A:PHE460
|
4.1
|
20.9
|
1.0
|
ND1
|
A:HIS473
|
4.2
|
19.9
|
1.0
|
CG
|
A:HIS473
|
4.3
|
20.5
|
1.0
|
HH21
|
A:ARG477
|
4.4
|
25.0
|
1.0
|
NH2
|
A:ARG477
|
4.5
|
20.9
|
1.0
|
HB3
|
A:ASN466
|
4.5
|
21.7
|
1.0
|
H2
|
C:A5
|
4.5
|
20.0
|
1.0
|
H
|
A:PHE460
|
4.6
|
20.0
|
1.0
|
H61
|
C:A6
|
4.6
|
23.4
|
1.0
|
HH22
|
A:ARG477
|
4.6
|
25.0
|
1.0
|
HD2
|
A:PHE471
|
4.7
|
23.2
|
1.0
|
H
|
A:PHE471
|
4.7
|
20.3
|
1.0
|
CA
|
A:CYS464
|
4.7
|
18.6
|
1.0
|
CA
|
A:CYS469
|
4.7
|
17.4
|
1.0
|
CA
|
A:CYS458
|
4.7
|
17.8
|
1.0
|
HA
|
A:CYS458
|
4.8
|
21.3
|
1.0
|
CZ
|
A:ARG477
|
4.8
|
21.2
|
1.0
|
CB
|
A:PHE471
|
4.8
|
18.7
|
1.0
|
H62
|
C:A6
|
4.8
|
23.4
|
1.0
|
CB
|
A:PHE460
|
4.9
|
18.1
|
1.0
|
HD1
|
A:HIS473
|
4.9
|
23.9
|
1.0
|
HA
|
A:CYS464
|
4.9
|
22.4
|
1.0
|
N6
|
C:A6
|
5.0
|
19.5
|
1.0
|
|
Zinc binding site 4 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 4 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn504
b:33.4
occ:0.47
|
O
|
A:HOH614
|
2.0
|
50.4
|
1.0
|
O
|
A:HOH621
|
2.1
|
44.8
|
1.0
|
OE1
|
A:GLU413
|
2.1
|
32.6
|
1.0
|
O
|
G:HOH138
|
2.2
|
57.9
|
1.0
|
O
|
A:HOH680
|
2.4
|
54.6
|
1.0
|
N7
|
G:A3
|
2.6
|
29.8
|
1.0
|
H62
|
G:A3
|
3.0
|
31.6
|
1.0
|
CD
|
A:GLU413
|
3.1
|
33.2
|
1.0
|
OE2
|
A:GLU413
|
3.4
|
34.2
|
1.0
|
C8
|
G:A3
|
3.5
|
29.4
|
1.0
|
H8
|
G:A3
|
3.6
|
35.3
|
1.0
|
C5
|
G:A3
|
3.6
|
27.6
|
1.0
|
N6
|
G:A3
|
3.7
|
26.4
|
1.0
|
OH
|
A:TYR428
|
4.0
|
32.8
|
1.0
|
C6
|
G:A3
|
4.1
|
26.3
|
1.0
|
HH
|
A:TYR428
|
4.2
|
39.3
|
1.0
|
CZ
|
A:TYR428
|
4.4
|
29.6
|
1.0
|
H61
|
G:A3
|
4.5
|
31.6
|
1.0
|
CG
|
A:GLU413
|
4.5
|
29.2
|
1.0
|
HG2
|
A:GLU413
|
4.5
|
35.0
|
1.0
|
HE1
|
A:TYR428
|
4.7
|
32.4
|
1.0
|
CE1
|
A:TYR428
|
4.7
|
27.0
|
1.0
|
N9
|
G:A3
|
4.8
|
30.1
|
1.0
|
C4
|
G:A3
|
4.8
|
27.6
|
1.0
|
HG3
|
A:GLU413
|
4.9
|
35.0
|
1.0
|
OP2
|
G:A3
|
4.9
|
59.0
|
1.0
|
CE2
|
A:TYR428
|
5.0
|
25.5
|
1.0
|
|
Zinc binding site 5 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 5 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:17.0
occ:1.00
|
NE2
|
B:HIS430
|
2.1
|
16.3
|
1.0
|
SG
|
B:CYS426
|
2.3
|
18.8
|
1.0
|
SG
|
B:CYS415
|
2.3
|
17.8
|
1.0
|
SG
|
B:CYS421
|
2.3
|
17.1
|
1.0
|
HB2
|
B:CYS421
|
3.0
|
20.5
|
1.0
|
HB2
|
B:CYS415
|
3.1
|
20.9
|
1.0
|
CE1
|
B:HIS430
|
3.1
|
17.0
|
1.0
|
CD2
|
B:HIS430
|
3.1
|
15.7
|
1.0
|
CB
|
B:CYS421
|
3.2
|
17.1
|
1.0
|
CB
|
B:CYS426
|
3.2
|
20.7
|
1.0
|
HB2
|
B:CYS426
|
3.2
|
24.8
|
1.0
|
HE1
|
B:HIS430
|
3.3
|
20.4
|
1.0
|
HB3
|
B:CYS426
|
3.3
|
24.8
|
1.0
|
HD2
|
B:HIS430
|
3.3
|
18.8
|
1.0
|
CB
|
B:CYS415
|
3.3
|
17.5
|
1.0
|
HB3
|
B:CYS421
|
3.3
|
20.5
|
1.0
|
HB3
|
B:CYS415
|
3.7
|
20.9
|
1.0
|
O
|
H:HOH119
|
3.9
|
29.2
|
1.0
|
H2
|
H:A3
|
4.0
|
27.9
|
1.0
|
HB2
|
B:TYR428
|
4.1
|
22.2
|
1.0
|
O
|
B:HOH685
|
4.2
|
38.0
|
1.0
|
ND1
|
B:HIS430
|
4.2
|
18.8
|
1.0
|
CG
|
B:HIS430
|
4.2
|
16.8
|
1.0
|
HB3
|
B:ASN423
|
4.2
|
24.4
|
1.0
|
HD2
|
B:PHE417
|
4.3
|
22.7
|
1.0
|
HB2
|
B:PHE417
|
4.3
|
21.0
|
1.0
|
H61
|
D:A4
|
4.4
|
21.7
|
1.0
|
H
|
B:TYR428
|
4.5
|
22.1
|
1.0
|
CA
|
B:CYS421
|
4.6
|
17.1
|
1.0
|
CA
|
B:CYS415
|
4.6
|
17.3
|
1.0
|
C2
|
H:A3
|
4.6
|
23.2
|
1.0
|
HA
|
B:CYS415
|
4.7
|
20.7
|
1.0
|
HD2
|
B:TYR428
|
4.7
|
26.8
|
1.0
|
CA
|
B:CYS426
|
4.7
|
20.1
|
1.0
|
H
|
B:PHE417
|
4.7
|
19.2
|
1.0
|
HA
|
B:CYS421
|
4.8
|
20.5
|
1.0
|
HA
|
B:CYS426
|
4.9
|
24.1
|
1.0
|
HD1
|
B:HIS430
|
4.9
|
22.6
|
1.0
|
H
|
B:ASN423
|
5.0
|
23.0
|
1.0
|
|
Zinc binding site 6 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 6 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn502
b:19.1
occ:1.00
|
NE2
|
B:HIS452
|
2.1
|
18.1
|
1.0
|
SG
|
B:CYS443
|
2.4
|
19.8
|
1.0
|
SG
|
B:CYS437
|
2.4
|
20.1
|
1.0
|
SG
|
B:CYS448
|
2.4
|
18.2
|
1.0
|
CE1
|
B:HIS452
|
3.0
|
17.8
|
1.0
|
HB2
|
B:CYS443
|
3.1
|
25.1
|
1.0
|
HB2
|
B:CYS437
|
3.1
|
22.4
|
1.0
|
CB
|
B:CYS443
|
3.1
|
21.0
|
1.0
|
CD2
|
B:HIS452
|
3.2
|
18.5
|
1.0
|
HE1
|
B:HIS452
|
3.2
|
21.3
|
1.0
|
HB3
|
B:CYS443
|
3.2
|
25.1
|
1.0
|
HB3
|
B:CYS448
|
3.2
|
23.4
|
1.0
|
CB
|
B:CYS448
|
3.3
|
19.5
|
1.0
|
CB
|
B:CYS437
|
3.3
|
18.6
|
1.0
|
HD2
|
B:HIS452
|
3.4
|
22.2
|
1.0
|
HB2
|
B:CYS448
|
3.4
|
23.4
|
1.0
|
HB3
|
B:CYS437
|
3.6
|
22.4
|
1.0
|
HH12
|
B:ARG429
|
3.7
|
25.3
|
1.0
|
O
|
C:HOH152
|
3.8
|
45.5
|
1.0
|
HB2
|
B:PHE450
|
3.9
|
21.6
|
1.0
|
HB2
|
B:GLU439
|
3.9
|
33.9
|
1.0
|
O
|
C:HOH141
|
4.0
|
30.8
|
1.0
|
NH1
|
B:ARG429
|
4.1
|
21.1
|
1.0
|
ND1
|
B:HIS452
|
4.2
|
18.5
|
1.0
|
H61
|
C:A11
|
4.2
|
25.1
|
1.0
|
CG
|
B:HIS452
|
4.3
|
19.2
|
1.0
|
HH11
|
B:ARG429
|
4.3
|
25.3
|
1.0
|
H
|
B:PHE450
|
4.4
|
20.2
|
1.0
|
HB3
|
B:ARG445
|
4.5
|
24.2
|
1.0
|
CA
|
B:CYS443
|
4.6
|
21.2
|
1.0
|
HH22
|
B:ARG429
|
4.7
|
24.7
|
1.0
|
CA
|
B:CYS437
|
4.7
|
18.8
|
1.0
|
CA
|
B:CYS448
|
4.7
|
18.4
|
1.0
|
H
|
B:GLU439
|
4.7
|
28.9
|
1.0
|
HA
|
B:CYS437
|
4.8
|
22.6
|
1.0
|
HD2
|
B:PHE450
|
4.8
|
22.1
|
1.0
|
N6
|
C:A11
|
4.8
|
20.9
|
1.0
|
O
|
B:PHE450
|
4.8
|
19.2
|
1.0
|
CB
|
B:PHE450
|
4.8
|
18.0
|
1.0
|
CB
|
B:GLU439
|
4.9
|
28.3
|
1.0
|
HA
|
B:CYS443
|
4.9
|
25.5
|
1.0
|
H62
|
C:A11
|
4.9
|
25.1
|
1.0
|
CZ
|
B:ARG429
|
4.9
|
19.1
|
1.0
|
H
|
B:ARG445
|
4.9
|
25.1
|
1.0
|
HD1
|
B:HIS452
|
4.9
|
22.2
|
1.0
|
|
Zinc binding site 7 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 7 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:20.8
occ:1.00
|
NE2
|
B:HIS473
|
2.1
|
21.4
|
1.0
|
SG
|
B:CYS458
|
2.4
|
20.8
|
1.0
|
SG
|
B:CYS469
|
2.4
|
19.9
|
1.0
|
SG
|
B:CYS464
|
2.4
|
21.5
|
1.0
|
CE1
|
B:HIS473
|
3.0
|
23.3
|
1.0
|
CD2
|
B:HIS473
|
3.1
|
23.3
|
1.0
|
HB2
|
B:CYS464
|
3.1
|
27.6
|
1.0
|
HB2
|
B:CYS458
|
3.1
|
27.0
|
1.0
|
HE1
|
B:HIS473
|
3.2
|
28.0
|
1.0
|
CB
|
B:CYS464
|
3.2
|
23.0
|
1.0
|
HB3
|
B:CYS464
|
3.2
|
27.6
|
1.0
|
HB3
|
B:CYS469
|
3.2
|
24.3
|
1.0
|
CB
|
B:CYS469
|
3.3
|
20.2
|
1.0
|
CB
|
B:CYS458
|
3.3
|
22.5
|
1.0
|
HD2
|
B:HIS473
|
3.3
|
28.0
|
1.0
|
HB2
|
B:CYS469
|
3.4
|
24.3
|
1.0
|
HB3
|
B:CYS458
|
3.6
|
27.0
|
1.0
|
HB2
|
B:PHE471
|
3.7
|
24.6
|
1.0
|
HB2
|
B:PHE460
|
4.0
|
27.9
|
1.0
|
O
|
D:HOH134
|
4.0
|
21.1
|
1.0
|
HD2
|
B:PHE460
|
4.1
|
29.0
|
1.0
|
ND1
|
B:HIS473
|
4.2
|
23.9
|
1.0
|
HH11
|
B:ARG477
|
4.2
|
35.9
|
1.0
|
CG
|
B:HIS473
|
4.2
|
24.0
|
1.0
|
NH1
|
B:ARG477
|
4.3
|
29.9
|
1.0
|
H61
|
D:A6
|
4.5
|
26.6
|
1.0
|
H2
|
D:A5
|
4.6
|
24.5
|
1.0
|
HD2
|
B:PHE471
|
4.6
|
22.1
|
1.0
|
HB3
|
B:ASN466
|
4.6
|
23.1
|
1.0
|
HH12
|
B:ARG477
|
4.6
|
35.9
|
1.0
|
H
|
B:PHE471
|
4.6
|
23.4
|
1.0
|
H
|
B:PHE460
|
4.6
|
28.5
|
1.0
|
CA
|
B:CYS464
|
4.7
|
24.5
|
1.0
|
H62
|
D:A6
|
4.7
|
26.6
|
1.0
|
CA
|
B:CYS458
|
4.7
|
22.4
|
1.0
|
CB
|
B:PHE471
|
4.7
|
20.5
|
1.0
|
CZ
|
B:ARG477
|
4.7
|
31.0
|
1.0
|
HE
|
B:ARG477
|
4.7
|
35.9
|
1.0
|
HA
|
B:CYS458
|
4.7
|
26.9
|
1.0
|
CA
|
B:CYS469
|
4.8
|
19.0
|
1.0
|
NE
|
B:ARG477
|
4.9
|
29.9
|
1.0
|
N6
|
D:A6
|
4.9
|
22.2
|
1.0
|
CB
|
B:PHE460
|
4.9
|
23.3
|
1.0
|
HD1
|
B:HIS473
|
4.9
|
28.7
|
1.0
|
HA
|
B:CYS464
|
5.0
|
29.4
|
1.0
|
CD2
|
B:PHE460
|
5.0
|
24.1
|
1.0
|
|
Zinc binding site 8 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 8 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn501
b:17.7
occ:1.00
|
NE2
|
E:HIS430
|
2.1
|
18.2
|
1.0
|
SG
|
E:CYS421
|
2.3
|
17.9
|
1.0
|
SG
|
E:CYS415
|
2.3
|
17.8
|
1.0
|
SG
|
E:CYS426
|
2.4
|
19.5
|
1.0
|
HB2
|
E:CYS421
|
3.0
|
22.7
|
1.0
|
CD2
|
E:HIS430
|
3.1
|
18.0
|
1.0
|
CE1
|
E:HIS430
|
3.1
|
20.2
|
1.0
|
HB2
|
E:CYS415
|
3.1
|
21.1
|
1.0
|
CB
|
E:CYS421
|
3.2
|
18.9
|
1.0
|
HD2
|
E:HIS430
|
3.2
|
21.6
|
1.0
|
CB
|
E:CYS426
|
3.3
|
20.6
|
1.0
|
HE1
|
E:HIS430
|
3.3
|
24.3
|
1.0
|
HB2
|
E:CYS426
|
3.3
|
24.7
|
1.0
|
HB3
|
E:CYS426
|
3.3
|
24.7
|
1.0
|
CB
|
E:CYS415
|
3.3
|
17.6
|
1.0
|
HB3
|
E:CYS421
|
3.3
|
22.7
|
1.0
|
HB3
|
E:CYS415
|
3.7
|
21.1
|
1.0
|
HB2
|
E:TYR428
|
4.0
|
23.3
|
1.0
|
ND1
|
E:HIS430
|
4.2
|
20.6
|
1.0
|
CG
|
E:HIS430
|
4.2
|
19.3
|
1.0
|
O
|
E:HOH670
|
4.2
|
29.3
|
1.0
|
O
|
E:HOH658
|
4.2
|
43.5
|
1.0
|
HB3
|
E:ASN423
|
4.3
|
28.5
|
1.0
|
H2
|
D:A3
|
4.3
|
22.3
|
1.0
|
H61
|
H:A4
|
4.3
|
23.0
|
1.0
|
HD2
|
E:PHE417
|
4.3
|
22.5
|
1.0
|
HB2
|
E:PHE417
|
4.4
|
21.6
|
1.0
|
HD2
|
E:TYR428
|
4.5
|
26.2
|
1.0
|
H
|
E:TYR428
|
4.5
|
25.6
|
1.0
|
CA
|
E:CYS421
|
4.6
|
18.5
|
1.0
|
CA
|
E:CYS415
|
4.6
|
16.4
|
1.0
|
HA
|
E:CYS415
|
4.6
|
19.6
|
1.0
|
CA
|
E:CYS426
|
4.7
|
21.8
|
1.0
|
HA
|
E:CYS421
|
4.8
|
22.2
|
1.0
|
H
|
E:PHE417
|
4.8
|
20.0
|
1.0
|
H
|
E:ASN423
|
4.9
|
26.6
|
1.0
|
HA
|
E:CYS426
|
4.9
|
26.2
|
1.0
|
CB
|
E:TYR428
|
4.9
|
19.4
|
1.0
|
C2
|
D:A3
|
4.9
|
18.6
|
1.0
|
HD1
|
E:HIS430
|
4.9
|
24.7
|
1.0
|
N6
|
H:A4
|
5.0
|
19.2
|
1.0
|
|
Zinc binding site 9 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 9 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn502
b:20.6
occ:1.00
|
NE2
|
E:HIS452
|
2.1
|
19.4
|
1.0
|
SG
|
E:CYS448
|
2.4
|
21.0
|
1.0
|
SG
|
E:CYS437
|
2.4
|
23.5
|
1.0
|
SG
|
E:CYS443
|
2.4
|
21.7
|
1.0
|
CE1
|
E:HIS452
|
3.0
|
18.5
|
1.0
|
HB2
|
E:CYS437
|
3.1
|
26.8
|
1.0
|
HE1
|
E:HIS452
|
3.1
|
22.2
|
1.0
|
HB2
|
E:CYS443
|
3.1
|
26.7
|
1.0
|
CB
|
E:CYS443
|
3.1
|
22.3
|
1.0
|
HB3
|
E:CYS443
|
3.1
|
26.7
|
1.0
|
CD2
|
E:HIS452
|
3.2
|
18.1
|
1.0
|
HB3
|
E:CYS448
|
3.3
|
26.5
|
1.0
|
CB
|
E:CYS437
|
3.3
|
22.3
|
1.0
|
CB
|
E:CYS448
|
3.3
|
22.1
|
1.0
|
HD2
|
E:HIS452
|
3.4
|
21.8
|
1.0
|
HB2
|
E:CYS448
|
3.5
|
26.5
|
1.0
|
HB3
|
E:CYS437
|
3.6
|
26.8
|
1.0
|
HH12
|
E:ARG429
|
3.7
|
26.3
|
1.0
|
HB2
|
E:PHE450
|
3.9
|
24.1
|
1.0
|
O
|
G:HOH135
|
3.9
|
33.7
|
1.0
|
HB2
|
E:GLU439
|
4.1
|
43.0
|
1.0
|
NH1
|
E:ARG429
|
4.1
|
21.9
|
1.0
|
ND1
|
E:HIS452
|
4.1
|
18.2
|
1.0
|
H61
|
G:A11
|
4.2
|
31.2
|
1.0
|
CG
|
E:HIS452
|
4.3
|
18.2
|
1.0
|
HH11
|
E:ARG429
|
4.3
|
26.3
|
1.0
|
HB3
|
E:ARG445
|
4.4
|
28.7
|
1.0
|
H
|
E:PHE450
|
4.5
|
21.2
|
1.0
|
CA
|
E:CYS443
|
4.6
|
22.5
|
1.0
|
CA
|
E:CYS437
|
4.6
|
23.0
|
1.0
|
HH22
|
E:ARG429
|
4.7
|
24.3
|
1.0
|
HA
|
E:CYS437
|
4.7
|
27.6
|
1.0
|
H
|
E:GLU439
|
4.8
|
37.0
|
1.0
|
N6
|
G:A11
|
4.8
|
26.0
|
1.0
|
CA
|
E:CYS448
|
4.8
|
21.7
|
1.0
|
O
|
E:HOH715
|
4.8
|
50.1
|
1.0
|
H62
|
G:A11
|
4.8
|
31.2
|
1.0
|
HD2
|
E:PHE450
|
4.8
|
26.2
|
1.0
|
CB
|
E:PHE450
|
4.8
|
20.1
|
1.0
|
O
|
E:PHE450
|
4.9
|
20.1
|
1.0
|
CZ
|
E:ARG429
|
4.9
|
19.9
|
1.0
|
H
|
E:ARG445
|
4.9
|
27.8
|
1.0
|
HD1
|
E:HIS452
|
4.9
|
21.9
|
1.0
|
HA
|
E:CYS443
|
4.9
|
27.0
|
1.0
|
|
Zinc binding site 10 out
of 14 in 5l2l
Go back to
Zinc Binding Sites List in 5l2l
Zinc binding site 10 out
of 14 in the NAB2 Zn Fingers 5-7 Bound to A11G Rna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of NAB2 Zn Fingers 5-7 Bound to A11G Rna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn503
b:16.4
occ:1.00
|
NE2
|
E:HIS473
|
2.1
|
16.3
|
1.0
|
SG
|
E:CYS458
|
2.3
|
16.8
|
1.0
|
SG
|
E:CYS469
|
2.4
|
16.5
|
1.0
|
SG
|
E:CYS464
|
2.4
|
17.5
|
1.0
|
CE1
|
E:HIS473
|
3.1
|
16.0
|
1.0
|
CD2
|
E:HIS473
|
3.1
|
16.6
|
1.0
|
HB2
|
E:CYS464
|
3.1
|
21.2
|
1.0
|
HB3
|
E:CYS469
|
3.2
|
19.5
|
1.0
|
HB2
|
E:CYS458
|
3.2
|
19.6
|
1.0
|
CB
|
E:CYS464
|
3.2
|
17.7
|
1.0
|
HE1
|
E:HIS473
|
3.2
|
19.2
|
1.0
|
HB3
|
E:CYS464
|
3.3
|
21.2
|
1.0
|
CB
|
E:CYS469
|
3.3
|
16.2
|
1.0
|
HD2
|
E:HIS473
|
3.3
|
19.9
|
1.0
|
CB
|
E:CYS458
|
3.4
|
16.3
|
1.0
|
HB2
|
E:CYS469
|
3.4
|
19.5
|
1.0
|
HB3
|
E:CYS458
|
3.7
|
19.6
|
1.0
|
HB2
|
E:PHE471
|
3.7
|
19.9
|
1.0
|
HB2
|
E:PHE460
|
3.9
|
23.2
|
1.0
|
O
|
H:HOH121
|
4.0
|
19.8
|
1.0
|
HD2
|
E:PHE460
|
4.1
|
27.4
|
1.0
|
ND1
|
E:HIS473
|
4.2
|
16.8
|
1.0
|
CG
|
E:HIS473
|
4.2
|
15.5
|
1.0
|
HH21
|
E:ARG477
|
4.2
|
27.6
|
1.0
|
NH2
|
E:ARG477
|
4.4
|
23.0
|
1.0
|
H61
|
H:A6
|
4.5
|
25.0
|
1.0
|
H2
|
H:A5
|
4.5
|
19.6
|
1.0
|
HB3
|
E:ASN466
|
4.6
|
21.6
|
1.0
|
H
|
E:PHE471
|
4.6
|
19.6
|
1.0
|
H
|
E:PHE460
|
4.6
|
19.3
|
1.0
|
H62
|
H:A6
|
4.6
|
25.0
|
1.0
|
HH22
|
E:ARG477
|
4.7
|
27.6
|
1.0
|
CA
|
E:CYS464
|
4.7
|
19.8
|
1.0
|
HD2
|
E:PHE471
|
4.7
|
20.1
|
1.0
|
CB
|
E:PHE471
|
4.7
|
16.6
|
1.0
|
CA
|
E:CYS458
|
4.7
|
14.7
|
1.0
|
CA
|
E:CYS469
|
4.7
|
16.1
|
1.0
|
HA
|
E:CYS458
|
4.8
|
17.6
|
1.0
|
CZ
|
E:ARG477
|
4.8
|
21.8
|
1.0
|
HE
|
E:ARG477
|
4.8
|
24.3
|
1.0
|
N6
|
H:A6
|
4.8
|
20.8
|
1.0
|
CB
|
E:PHE460
|
4.9
|
19.3
|
1.0
|
NE
|
E:ARG477
|
4.9
|
20.3
|
1.0
|
HA
|
E:CYS464
|
4.9
|
23.7
|
1.0
|
CD2
|
E:PHE460
|
5.0
|
22.9
|
1.0
|
HD1
|
E:HIS473
|
5.0
|
20.2
|
1.0
|
|
Reference:
S.Aibara,
J.M.Gordon,
A.S.Riesterer,
S.H.Mclaughlin,
M.Stewart.
Structural Basis For the Dimerization of NAB2 Generated By Rna Binding Provides Insight Into Its Contribution to Both Poly(A) Tail Length Determination and Transcript Compaction in Saccharomyces Cerevisiae. Nucleic Acids Res. V. 45 1529 2017.
ISSN: ESSN 1362-4962
PubMed: 28180315
DOI: 10.1093/NAR/GKW1224
Page generated: Sun Oct 27 20:44:42 2024
|