Zinc in PDB 6y75: BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)
Enzymatic activity of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)
All present enzymatic activity of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A):
2.4.2.31;
Protein crystallography data
The structure of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A), PDB code: 6y75
was solved by
A.Ilari,
V.Chiarini,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.57 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.821,
67.605,
82.445,
90,
114.58,
90
|
R / Rfree (%)
|
25.4 /
30.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)
(pdb code 6y75). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A), PDB code: 6y75:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6y75
Go back to
Zinc Binding Sites List in 6y75
Zinc binding site 1 out
of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:29.8
occ:1.00
|
NE2
|
A:HIS48
|
2.1
|
29.9
|
1.0
|
NE2
|
A:HIS125
|
2.1
|
24.5
|
1.0
|
N
|
A:ASN-4
|
2.2
|
35.8
|
1.0
|
O
|
A:ASN-4
|
2.2
|
31.4
|
1.0
|
C
|
A:ASN-4
|
3.0
|
33.2
|
1.0
|
CD2
|
A:HIS48
|
3.0
|
30.6
|
1.0
|
CE1
|
A:HIS48
|
3.1
|
30.6
|
1.0
|
CE1
|
A:HIS125
|
3.1
|
23.8
|
1.0
|
CD2
|
A:HIS125
|
3.1
|
23.7
|
1.0
|
CA
|
A:ASN-4
|
3.1
|
36.1
|
1.0
|
ND2
|
A:ASN-4
|
3.8
|
43.4
|
1.0
|
ND1
|
A:HIS48
|
4.1
|
32.2
|
1.0
|
CG
|
A:HIS48
|
4.2
|
30.9
|
1.0
|
ND1
|
A:HIS125
|
4.2
|
24.2
|
1.0
|
CG
|
A:HIS125
|
4.2
|
24.3
|
1.0
|
N
|
A:LEU-3
|
4.3
|
31.3
|
1.0
|
CG1
|
A:VAL46
|
4.3
|
28.0
|
1.0
|
CB
|
A:ASN-4
|
4.4
|
38.1
|
1.0
|
SD
|
A:MET144
|
4.4
|
55.0
|
1.0
|
CG
|
A:ASN-4
|
4.6
|
41.4
|
1.0
|
CB
|
A:VAL46
|
4.7
|
28.0
|
1.0
|
O
|
A:HOH627
|
4.9
|
30.4
|
1.0
|
CA
|
A:LEU-3
|
5.0
|
30.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6y75
Go back to
Zinc Binding Sites List in 6y75
Zinc binding site 2 out
of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:36.4
occ:1.00
|
NE2
|
B:HIS125
|
2.1
|
33.5
|
1.0
|
NE2
|
B:HIS48
|
2.1
|
34.7
|
1.0
|
N
|
B:ASN-4
|
2.2
|
46.0
|
1.0
|
O
|
B:HOH657
|
2.4
|
41.2
|
1.0
|
O
|
B:ASN-4
|
2.4
|
42.0
|
1.0
|
CE1
|
B:HIS125
|
3.1
|
33.0
|
1.0
|
CD2
|
B:HIS48
|
3.1
|
35.1
|
1.0
|
CE1
|
B:HIS48
|
3.1
|
34.5
|
1.0
|
CD2
|
B:HIS125
|
3.1
|
32.2
|
1.0
|
C
|
B:ASN-4
|
3.2
|
43.6
|
1.0
|
CA
|
B:ASN-4
|
3.2
|
45.0
|
1.0
|
ND2
|
B:ASN-4
|
3.8
|
50.3
|
1.0
|
CG1
|
B:VAL46
|
4.1
|
29.8
|
1.0
|
ND1
|
B:HIS125
|
4.2
|
32.5
|
1.0
|
ND1
|
B:HIS48
|
4.2
|
34.1
|
1.0
|
CG
|
B:HIS48
|
4.2
|
34.6
|
1.0
|
CG
|
B:HIS125
|
4.3
|
31.9
|
1.0
|
SD
|
B:MET144
|
4.4
|
90.7
|
1.0
|
CB
|
B:ASN-4
|
4.4
|
46.9
|
1.0
|
N
|
B:LEU-3
|
4.5
|
41.0
|
1.0
|
CB
|
B:VAL46
|
4.6
|
30.3
|
1.0
|
CG
|
B:ASN-4
|
4.6
|
48.9
|
1.0
|
CG2
|
B:VAL46
|
5.0
|
29.6
|
1.0
|
O
|
B:HOH630
|
5.0
|
52.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6y75
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Zinc Binding Sites List in 6y75
Zinc binding site 3 out
of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:33.3
occ:1.00
|
NE2
|
C:HIS48
|
1.9
|
34.0
|
1.0
|
NE2
|
C:HIS125
|
2.1
|
32.5
|
1.0
|
N
|
C:ASN-4
|
2.2
|
40.8
|
1.0
|
O
|
C:ASN-4
|
2.3
|
38.4
|
1.0
|
CD2
|
C:HIS48
|
2.9
|
34.9
|
1.0
|
CE1
|
C:HIS48
|
2.9
|
35.8
|
1.0
|
CD2
|
C:HIS125
|
3.1
|
31.0
|
1.0
|
C
|
C:ASN-4
|
3.1
|
38.4
|
1.0
|
CE1
|
C:HIS125
|
3.1
|
32.1
|
1.0
|
CA
|
C:ASN-4
|
3.2
|
40.3
|
1.0
|
ND2
|
C:ASN-4
|
4.0
|
42.8
|
1.0
|
ND1
|
C:HIS48
|
4.0
|
36.5
|
1.0
|
CG
|
C:HIS48
|
4.0
|
34.8
|
1.0
|
CG1
|
C:VAL46
|
4.1
|
31.6
|
1.0
|
ND1
|
C:HIS125
|
4.2
|
31.6
|
1.0
|
CG
|
C:HIS125
|
4.2
|
30.5
|
1.0
|
O
|
C:HOH414
|
4.4
|
35.5
|
1.0
|
N
|
C:LEU-3
|
4.4
|
37.1
|
1.0
|
CB
|
C:ASN-4
|
4.5
|
41.2
|
1.0
|
SD
|
C:MET144
|
4.5
|
63.7
|
1.0
|
CB
|
C:VAL46
|
4.6
|
34.2
|
1.0
|
CG
|
C:ASN-4
|
4.7
|
42.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6y75
Go back to
Zinc Binding Sites List in 6y75
Zinc binding site 4 out
of 4 in the BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of BIL2 Domain From T.Thermophila BUBL1 Locus (C1A-N143A) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:33.8
occ:1.00
|
NE2
|
D:HIS48
|
2.0
|
38.0
|
1.0
|
N
|
D:ASN-4
|
2.1
|
45.7
|
1.0
|
NE2
|
D:HIS125
|
2.2
|
29.6
|
1.0
|
O
|
D:ASN-4
|
2.4
|
40.5
|
1.0
|
O
|
D:HOH429
|
2.4
|
31.2
|
1.0
|
CD2
|
D:HIS48
|
3.0
|
39.1
|
1.0
|
CE1
|
D:HIS48
|
3.0
|
38.6
|
1.0
|
C
|
D:ASN-4
|
3.1
|
43.3
|
1.0
|
CE1
|
D:HIS125
|
3.1
|
31.3
|
1.0
|
CA
|
D:ASN-4
|
3.2
|
46.1
|
1.0
|
CD2
|
D:HIS125
|
3.2
|
29.4
|
1.0
|
ND2
|
D:ASN-4
|
3.7
|
55.0
|
1.0
|
ND1
|
D:HIS48
|
4.1
|
38.9
|
1.0
|
CG
|
D:HIS48
|
4.1
|
38.1
|
1.0
|
CG1
|
D:VAL46
|
4.1
|
29.1
|
1.0
|
ND1
|
D:HIS125
|
4.3
|
30.0
|
1.0
|
CG
|
D:HIS125
|
4.3
|
29.0
|
1.0
|
CB
|
D:ASN-4
|
4.3
|
49.5
|
1.0
|
N
|
D:LEU-3
|
4.5
|
40.7
|
1.0
|
SD
|
D:MET144
|
4.5
|
77.5
|
1.0
|
CG
|
D:ASN-4
|
4.5
|
53.5
|
1.0
|
CB
|
D:VAL46
|
4.6
|
29.8
|
1.0
|
|
Reference:
V.Chiarini,
A.Fiorillo,
S.Camerini,
M.Crescenzi,
S.Nakamura,
T.Battista,
L.Guidoni,
G.Colotti,
A.Ilari.
Structural Basis of Ubiquitination Mediated By Protein Splicing in Early Eukarya Biochim.Biophys.Acta 2021.
ISSN: ISSN 0006-3002
DOI: HTTPS://DOI.ORG/10.1016/J.BBAGEN.2021.129844
Page generated: Tue Oct 29 11:24:56 2024
|