Zinc in PDB 4k7s: Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
Enzymatic activity of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
All present enzymatic activity of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub:
6.3.2.19;
Protein crystallography data
The structure of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7s
was solved by
S.Fermani,
G.Falini,
M.Calvaresi,
A.Bottoni,
F.Arnesano,
G.Natile,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.36 /
1.76
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.840,
50.330,
94.030,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.9 /
27.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
(pdb code 4k7s). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub, PDB code: 4k7s:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 4k7s
Go back to
Zinc Binding Sites List in 4k7s
Zinc binding site 1 out
of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn101
b:13.2
occ:0.95
|
O
|
C:HOH223
|
2.0
|
16.7
|
1.0
|
OE1
|
A:GLU16
|
2.1
|
13.1
|
1.0
|
N
|
A:MET1
|
2.3
|
15.4
|
1.0
|
CA
|
A:MET1
|
2.9
|
13.0
|
1.0
|
CD
|
A:GLU16
|
3.0
|
10.9
|
1.0
|
OE2
|
A:GLU16
|
3.1
|
12.9
|
1.0
|
C
|
A:MET1
|
3.3
|
12.0
|
1.0
|
O
|
A:HOH297
|
3.7
|
23.4
|
1.0
|
O
|
A:MET1
|
3.8
|
12.5
|
1.0
|
N
|
A:GLN2
|
3.8
|
10.1
|
1.0
|
O
|
A:HOH306
|
3.9
|
29.6
|
1.0
|
O
|
A:VAL17
|
4.1
|
7.5
|
1.0
|
OD2
|
C:ASP32
|
4.2
|
11.5
|
1.0
|
CB
|
A:MET1
|
4.3
|
14.0
|
1.0
|
CG
|
A:GLU16
|
4.4
|
10.7
|
1.0
|
O
|
C:HOH271
|
4.8
|
28.7
|
1.0
|
CA
|
A:GLN2
|
4.8
|
7.9
|
1.0
|
|
Zinc binding site 2 out
of 6 in 4k7s
Go back to
Zinc Binding Sites List in 4k7s
Zinc binding site 2 out
of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn102
b:11.1
occ:1.00
|
O1
|
A:EDO103
|
1.8
|
21.9
|
1.0
|
O
|
A:HOH299
|
1.9
|
7.6
|
1.0
|
OD1
|
A:ASP21
|
2.0
|
11.3
|
1.0
|
C1
|
A:EDO103
|
2.5
|
21.2
|
1.0
|
CG
|
A:ASP21
|
2.7
|
6.1
|
1.0
|
OD2
|
A:ASP21
|
2.9
|
11.1
|
1.0
|
C2
|
A:EDO103
|
3.6
|
17.4
|
1.0
|
O2
|
A:EDO103
|
4.0
|
16.2
|
1.0
|
ND2
|
A:ASN25
|
4.0
|
4.0
|
1.0
|
O
|
A:HOH201
|
4.0
|
18.4
|
1.0
|
CB
|
A:ASP21
|
4.2
|
4.5
|
1.0
|
NZ
|
A:LYS29
|
4.3
|
10.8
|
1.0
|
O
|
C:ACT103
|
4.4
|
21.8
|
1.0
|
CE
|
A:LYS29
|
4.4
|
10.8
|
1.0
|
OE1
|
A:GLU18
|
4.4
|
22.0
|
1.0
|
CA
|
A:ASP21
|
4.7
|
3.6
|
1.0
|
CG
|
A:GLU18
|
4.8
|
11.1
|
1.0
|
CG
|
A:ASN25
|
4.8
|
2.0
|
1.0
|
N
|
A:GLU18
|
4.9
|
6.0
|
1.0
|
CB
|
A:GLU18
|
4.9
|
8.6
|
1.0
|
CB
|
A:ASN25
|
5.0
|
3.3
|
1.0
|
|
Zinc binding site 3 out
of 6 in 4k7s
Go back to
Zinc Binding Sites List in 4k7s
Zinc binding site 3 out
of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn101
b:11.7
occ:1.00
|
NE2
|
A:HIS68
|
2.0
|
5.1
|
1.0
|
NE2
|
B:HIS68
|
2.0
|
13.1
|
1.0
|
O
|
B:HOH203
|
2.1
|
15.8
|
1.0
|
O
|
A:HOH265
|
2.6
|
28.4
|
1.0
|
CD2
|
B:HIS68
|
3.0
|
11.3
|
1.0
|
CE1
|
A:HIS68
|
3.0
|
8.9
|
1.0
|
CD2
|
A:HIS68
|
3.0
|
6.8
|
1.0
|
CE1
|
B:HIS68
|
3.1
|
13.2
|
1.0
|
CE
|
B:LYS6
|
3.1
|
24.8
|
1.0
|
NZ
|
B:LYS6
|
3.4
|
24.7
|
1.0
|
CD
|
B:LYS6
|
3.7
|
21.7
|
1.0
|
ND1
|
A:HIS68
|
4.1
|
6.9
|
1.0
|
CG
|
A:HIS68
|
4.1
|
6.0
|
1.0
|
CG
|
B:HIS68
|
4.1
|
8.6
|
1.0
|
ND1
|
B:HIS68
|
4.2
|
7.0
|
1.0
|
|
Zinc binding site 4 out
of 6 in 4k7s
Go back to
Zinc Binding Sites List in 4k7s
Zinc binding site 4 out
of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn102
b:17.0
occ:0.92
|
OE2
|
B:GLU16
|
2.0
|
21.2
|
1.0
|
N
|
B:MET1
|
2.0
|
12.8
|
1.0
|
O
|
B:HOH220
|
2.4
|
26.1
|
1.0
|
CA
|
B:MET1
|
2.7
|
13.2
|
1.0
|
CD
|
B:GLU16
|
2.9
|
16.8
|
1.0
|
C
|
B:MET1
|
3.0
|
13.0
|
1.0
|
OE1
|
B:GLU16
|
3.1
|
19.0
|
1.0
|
O
|
B:MET1
|
3.3
|
14.3
|
1.0
|
N
|
B:GLN2
|
3.8
|
10.0
|
1.0
|
O
|
B:HOH314
|
3.9
|
28.1
|
1.0
|
O
|
B:VAL17
|
3.9
|
5.0
|
1.0
|
O
|
B:HOH307
|
4.1
|
18.9
|
1.0
|
CB
|
B:MET1
|
4.1
|
15.1
|
1.0
|
O
|
B:HOH238
|
4.2
|
26.6
|
1.0
|
CG
|
B:GLU16
|
4.3
|
11.6
|
1.0
|
CA
|
B:GLN2
|
4.9
|
10.5
|
1.0
|
CG
|
B:MET1
|
4.9
|
15.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 4k7s
Go back to
Zinc Binding Sites List in 4k7s
Zinc binding site 5 out
of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn101
b:8.2
occ:1.00
|
OE1
|
C:GLU16
|
1.9
|
7.5
|
1.0
|
N
|
C:MET1
|
2.1
|
9.3
|
1.0
|
O
|
C:HOH204
|
2.2
|
8.8
|
1.0
|
CD
|
C:GLU16
|
2.7
|
6.3
|
1.0
|
OE2
|
C:GLU16
|
2.9
|
8.5
|
1.0
|
CA
|
C:MET1
|
3.0
|
9.6
|
1.0
|
C
|
C:MET1
|
3.4
|
9.1
|
1.0
|
O
|
C:HOH282
|
3.7
|
16.1
|
1.0
|
O
|
C:MET1
|
3.8
|
9.7
|
1.0
|
N
|
C:GLN2
|
4.0
|
9.2
|
1.0
|
O
|
C:HOH221
|
4.0
|
9.8
|
1.0
|
NZ
|
C:LYS63
|
4.1
|
8.3
|
0.5
|
O
|
C:VAL17
|
4.1
|
7.9
|
1.0
|
CG
|
C:GLU16
|
4.2
|
4.6
|
1.0
|
CB
|
C:MET1
|
4.4
|
9.7
|
1.0
|
O
|
C:HOH241
|
4.5
|
21.8
|
1.0
|
|
Zinc binding site 6 out
of 6 in 4k7s
Go back to
Zinc Binding Sites List in 4k7s
Zinc binding site 6 out
of 6 in the Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of ZN2-Hub (Human Ubiquitin) Adduct From A Solution 35 Mm Zinc Acetate/1.3 Mm Hub within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn102
b:10.7
occ:1.00
|
OXT
|
C:ACT103
|
2.0
|
19.6
|
1.0
|
OE1
|
C:GLU18
|
2.1
|
10.3
|
1.0
|
O2
|
A:EDO103
|
2.2
|
16.2
|
1.0
|
CD
|
C:GLU18
|
2.8
|
10.6
|
1.0
|
OE2
|
C:GLU18
|
2.8
|
7.2
|
1.0
|
C
|
C:ACT103
|
2.8
|
20.1
|
1.0
|
O
|
C:ACT103
|
2.9
|
21.8
|
1.0
|
C2
|
A:EDO103
|
3.1
|
17.4
|
1.0
|
O
|
A:HOH300
|
4.0
|
18.1
|
1.0
|
C1
|
A:EDO103
|
4.1
|
21.2
|
1.0
|
CH3
|
C:ACT103
|
4.2
|
19.9
|
1.0
|
CG
|
C:GLU18
|
4.2
|
6.3
|
1.0
|
O
|
C:HOH231
|
4.4
|
25.1
|
1.0
|
O
|
A:HOH268
|
4.6
|
23.1
|
1.0
|
CB
|
C:GLU18
|
5.0
|
7.8
|
1.0
|
|
Reference:
S.Fermani,
G.Falini,
M.Calvaresi,
A.Bottoni,
V.Calo,
V.Mangini,
F.Arnesano,
G.Natile.
Conformational Selection of Ubiquitin Quaternary Structures Driven By Zinc Ions. Chemistry V. 19 15480 2013.
ISSN: ISSN 0947-6539
PubMed: 24123543
DOI: 10.1002/CHEM.201302229
Page generated: Sun Oct 27 01:45:48 2024
|