Zinc in PDB 6sc9: DAB3/Hoip-Rbr-Hoipin-8
Enzymatic activity of DAB3/Hoip-Rbr-Hoipin-8
All present enzymatic activity of DAB3/Hoip-Rbr-Hoipin-8:
2.3.2.31;
Protein crystallography data
The structure of DAB3/Hoip-Rbr-Hoipin-8, PDB code: 6sc9
was solved by
Y.-C.I.Tsai,
H.Johansson,
D.House,
K.Rittinger,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
81.90 /
2.47
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.127,
87.052,
241.538,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21 /
25.2
|
Other elements in 6sc9:
The structure of DAB3/Hoip-Rbr-Hoipin-8 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the DAB3/Hoip-Rbr-Hoipin-8
(pdb code 6sc9). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
DAB3/Hoip-Rbr-Hoipin-8, PDB code: 6sc9:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 1 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2002
b:79.0
occ:1.00
|
SG
|
A:CYS702
|
2.3
|
83.9
|
1.0
|
SG
|
A:CYS722
|
2.6
|
69.6
|
1.0
|
SG
|
A:CYS699
|
2.6
|
75.3
|
1.0
|
SG
|
A:CYS725
|
2.6
|
84.5
|
1.0
|
CB
|
A:CYS702
|
3.2
|
66.0
|
1.0
|
CB
|
A:CYS725
|
3.2
|
72.5
|
1.0
|
CB
|
A:CYS722
|
3.4
|
69.6
|
1.0
|
CB
|
A:CYS699
|
3.6
|
73.2
|
1.0
|
CG2
|
A:VAL701
|
3.7
|
83.9
|
1.0
|
N
|
A:CYS702
|
3.9
|
88.8
|
1.0
|
N
|
A:CYS722
|
4.1
|
74.8
|
1.0
|
CA
|
A:CYS702
|
4.1
|
73.6
|
1.0
|
CA
|
A:CYS722
|
4.3
|
71.6
|
1.0
|
CA
|
A:CYS725
|
4.5
|
70.2
|
1.0
|
N
|
A:CYS725
|
4.5
|
66.5
|
1.0
|
C
|
A:VAL701
|
4.8
|
93.0
|
1.0
|
O
|
A:CYS722
|
4.9
|
68.3
|
1.0
|
C
|
A:CYS722
|
4.9
|
66.6
|
1.0
|
C
|
A:CYS702
|
4.9
|
84.9
|
1.0
|
CB
|
A:TRP704
|
5.0
|
76.3
|
1.0
|
CA
|
A:CYS699
|
5.0
|
76.4
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 2 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2003
b:0.1
occ:1.00
|
SG
|
A:CYS747
|
2.5
|
1.0
|
1.0
|
SG
|
A:CYS717
|
2.6
|
1.0
|
1.0
|
SG
|
A:CYS744
|
2.6
|
95.1
|
1.0
|
SG
|
A:CYS719
|
2.7
|
0.5
|
1.0
|
CB
|
A:CYS747
|
3.0
|
0.0
|
1.0
|
CB
|
A:CYS719
|
3.0
|
86.2
|
1.0
|
CB
|
A:CYS717
|
3.2
|
0.3
|
1.0
|
N
|
A:CYS747
|
3.3
|
0.9
|
1.0
|
CB
|
A:CYS744
|
3.7
|
91.6
|
1.0
|
CA
|
A:CYS747
|
3.7
|
0.4
|
1.0
|
CB
|
A:ALA746
|
4.2
|
91.9
|
1.0
|
CA
|
A:CYS719
|
4.3
|
95.6
|
1.0
|
N
|
A:CYS719
|
4.4
|
0.7
|
1.0
|
C
|
A:ALA746
|
4.5
|
0.3
|
1.0
|
CD2
|
A:LEU714
|
4.6
|
0.2
|
1.0
|
C
|
A:CYS747
|
4.6
|
0.2
|
1.0
|
CA
|
A:CYS717
|
4.6
|
0.1
|
1.0
|
CA
|
A:ALA746
|
4.7
|
91.7
|
1.0
|
C
|
A:CYS717
|
4.8
|
0.7
|
1.0
|
N
|
A:ALA746
|
4.8
|
0.5
|
1.0
|
O
|
A:CYS717
|
4.9
|
0.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 3 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2004
b:61.5
occ:1.00
|
SG
|
A:CYS802
|
2.3
|
58.3
|
1.0
|
SG
|
A:CYS817
|
2.3
|
61.5
|
1.0
|
SG
|
A:CYS820
|
2.4
|
68.1
|
1.0
|
SG
|
A:CYS799
|
2.5
|
58.8
|
1.0
|
CB
|
A:CYS820
|
3.0
|
55.7
|
1.0
|
CB
|
A:CYS817
|
3.0
|
55.2
|
1.0
|
CB
|
A:CYS802
|
3.2
|
48.2
|
1.0
|
CB
|
A:CYS799
|
3.2
|
48.4
|
1.0
|
N
|
A:CYS820
|
3.5
|
63.9
|
1.0
|
CA
|
A:CYS820
|
3.8
|
61.7
|
1.0
|
N
|
A:CYS802
|
4.0
|
58.9
|
1.0
|
CA
|
A:CYS802
|
4.1
|
53.5
|
1.0
|
CA
|
A:CYS817
|
4.5
|
67.4
|
1.0
|
CB
|
A:GLN819
|
4.6
|
74.5
|
1.0
|
C
|
A:GLN819
|
4.6
|
69.1
|
1.0
|
C
|
A:CYS820
|
4.6
|
67.2
|
1.0
|
CA
|
A:CYS799
|
4.7
|
53.8
|
1.0
|
C
|
A:CYS802
|
4.7
|
60.2
|
1.0
|
CB
|
A:PHE804
|
4.7
|
60.0
|
1.0
|
N
|
A:HIS821
|
4.8
|
72.8
|
1.0
|
C
|
A:GLN801
|
4.9
|
67.3
|
1.0
|
CA
|
A:GLN819
|
5.0
|
63.7
|
1.0
|
N
|
A:GLN819
|
5.0
|
62.8
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 4 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2005
b:61.0
occ:1.00
|
NE2
|
A:HIS836
|
2.2
|
63.1
|
1.0
|
SG
|
A:CYS841
|
2.3
|
58.2
|
1.0
|
SG
|
A:CYS828
|
2.3
|
63.6
|
1.0
|
SG
|
A:CYS825
|
2.4
|
62.4
|
1.0
|
CB
|
A:CYS841
|
3.1
|
55.2
|
1.0
|
CD2
|
A:HIS836
|
3.2
|
63.5
|
1.0
|
CE1
|
A:HIS836
|
3.2
|
58.0
|
1.0
|
CB
|
A:CYS825
|
3.2
|
56.5
|
1.0
|
CB
|
A:CYS828
|
3.4
|
59.7
|
1.0
|
CA
|
A:CYS841
|
3.8
|
69.2
|
1.0
|
N
|
A:CYS828
|
3.8
|
56.8
|
1.0
|
CA
|
A:CYS828
|
4.2
|
58.4
|
1.0
|
ND1
|
A:HIS836
|
4.3
|
69.0
|
1.0
|
CG
|
A:HIS836
|
4.3
|
69.1
|
1.0
|
N
|
A:CYS841
|
4.4
|
52.1
|
1.0
|
CB
|
A:ARG827
|
4.6
|
77.3
|
1.0
|
CA
|
A:CYS825
|
4.7
|
54.4
|
1.0
|
C
|
A:ARG827
|
4.9
|
61.7
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 5 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2006
b:64.7
occ:1.00
|
SG
|
A:CYS893
|
2.1
|
78.3
|
1.0
|
SG
|
A:CYS874
|
2.3
|
62.0
|
1.0
|
SG
|
A:CYS871
|
2.5
|
63.2
|
1.0
|
SG
|
A:CYS890
|
2.6
|
67.3
|
1.0
|
CB
|
A:CYS874
|
2.7
|
52.2
|
1.0
|
CB
|
A:CYS893
|
3.2
|
68.6
|
1.0
|
CB
|
A:CYS871
|
3.2
|
58.0
|
1.0
|
CB
|
A:CYS890
|
3.5
|
66.7
|
1.0
|
N
|
A:CYS874
|
3.5
|
65.4
|
1.0
|
CA
|
A:CYS874
|
3.6
|
70.6
|
1.0
|
N
|
A:CYS893
|
4.0
|
68.8
|
1.0
|
CA
|
A:CYS893
|
4.2
|
65.9
|
1.0
|
C
|
A:CYS874
|
4.4
|
68.8
|
1.0
|
N
|
A:LYS875
|
4.7
|
70.0
|
1.0
|
CB
|
A:HIS895
|
4.7
|
64.1
|
1.0
|
CA
|
A:CYS871
|
4.7
|
67.1
|
1.0
|
C
|
A:LYS873
|
4.7
|
57.8
|
1.0
|
CB
|
A:GLN892
|
4.8
|
79.1
|
1.0
|
C
|
A:GLN892
|
4.9
|
73.9
|
1.0
|
CA
|
A:CYS890
|
4.9
|
71.6
|
1.0
|
C
|
A:CYS893
|
4.9
|
61.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 6 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2007
b:50.8
occ:1.00
|
ND1
|
A:HIS926
|
2.1
|
46.7
|
1.0
|
SG
|
A:CYS901
|
2.3
|
46.3
|
1.0
|
SG
|
A:CYS898
|
2.4
|
46.7
|
1.0
|
SG
|
A:CYS930
|
2.5
|
50.6
|
1.0
|
CG
|
A:HIS926
|
3.0
|
49.1
|
1.0
|
CE1
|
A:HIS926
|
3.1
|
49.5
|
1.0
|
CB
|
A:CYS901
|
3.1
|
34.6
|
1.0
|
CB
|
A:CYS898
|
3.3
|
53.8
|
1.0
|
CB
|
A:HIS926
|
3.3
|
42.6
|
1.0
|
N
|
A:CYS901
|
3.5
|
47.8
|
1.0
|
CB
|
A:CYS930
|
3.6
|
43.2
|
1.0
|
CA
|
A:CYS901
|
3.9
|
54.6
|
1.0
|
CB
|
A:PHE932
|
3.9
|
49.4
|
1.0
|
CA
|
A:HIS926
|
4.1
|
55.5
|
1.0
|
NE2
|
A:HIS926
|
4.2
|
58.5
|
1.0
|
CD2
|
A:HIS926
|
4.2
|
51.8
|
1.0
|
C
|
A:GLY900
|
4.4
|
50.9
|
1.0
|
CA
|
A:CYS898
|
4.7
|
50.2
|
1.0
|
CA
|
A:GLY900
|
4.7
|
47.8
|
1.0
|
C
|
A:CYS901
|
4.8
|
52.1
|
1.0
|
CG
|
A:PHE932
|
4.8
|
50.0
|
1.0
|
N
|
A:GLY900
|
4.8
|
48.0
|
1.0
|
CD
|
A:PRO927
|
4.8
|
46.8
|
1.0
|
N
|
A:PHE932
|
4.8
|
41.6
|
1.0
|
CA
|
A:CYS930
|
5.0
|
47.5
|
1.0
|
CA
|
A:PHE932
|
5.0
|
46.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 7 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2008
b:60.6
occ:1.00
|
NE2
|
A:HIS925
|
2.1
|
62.4
|
1.0
|
NE2
|
A:HIS923
|
2.1
|
58.0
|
1.0
|
SG
|
A:CYS916
|
2.3
|
66.7
|
1.0
|
SG
|
A:CYS911
|
2.3
|
68.4
|
1.0
|
CE1
|
A:HIS925
|
3.1
|
62.5
|
1.0
|
CD2
|
A:HIS923
|
3.1
|
49.3
|
1.0
|
CE1
|
A:HIS923
|
3.1
|
64.7
|
1.0
|
CB
|
A:CYS916
|
3.1
|
72.0
|
1.0
|
CD2
|
A:HIS925
|
3.1
|
56.1
|
1.0
|
CB
|
A:CYS911
|
3.4
|
53.9
|
1.0
|
ND1
|
A:HIS925
|
4.2
|
65.8
|
1.0
|
ND1
|
A:HIS923
|
4.2
|
59.5
|
1.0
|
CG
|
A:HIS923
|
4.2
|
52.1
|
1.0
|
CG
|
A:HIS925
|
4.3
|
56.5
|
1.0
|
CB
|
A:GLU913
|
4.5
|
64.2
|
1.0
|
CA
|
A:CYS916
|
4.5
|
76.0
|
1.0
|
CG
|
A:GLU913
|
4.7
|
83.3
|
1.0
|
CG2
|
A:VAL918
|
4.7
|
54.4
|
1.0
|
CA
|
A:CYS911
|
4.8
|
64.8
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6sc9
Go back to
Zinc Binding Sites List in 6sc9
Zinc binding site 8 out
of 8 in the DAB3/Hoip-Rbr-Hoipin-8
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2009
b:66.7
occ:1.00
|
ND1
|
A:HIS1001
|
2.0
|
75.1
|
1.0
|
CB
|
A:CYS998
|
2.3
|
57.3
|
1.0
|
SG
|
A:CYS969
|
2.5
|
64.9
|
1.0
|
SG
|
A:CYS986
|
2.5
|
62.7
|
1.0
|
CE1
|
A:HIS1001
|
2.9
|
73.3
|
1.0
|
CB
|
A:CYS969
|
3.1
|
70.0
|
1.0
|
CG
|
A:HIS1001
|
3.1
|
69.5
|
1.0
|
CB
|
A:CYS986
|
3.2
|
78.5
|
1.0
|
SG
|
A:CYS998
|
3.5
|
90.6
|
1.0
|
CA
|
A:CYS998
|
3.5
|
63.0
|
1.0
|
CB
|
A:HIS1001
|
3.6
|
53.2
|
1.0
|
N
|
A:CYS998
|
3.6
|
58.4
|
1.0
|
NE2
|
A:HIS1001
|
4.0
|
72.2
|
1.0
|
CD2
|
A:HIS1001
|
4.1
|
68.5
|
1.0
|
CB
|
A:VAL971
|
4.4
|
81.9
|
1.0
|
CA
|
A:CYS969
|
4.6
|
77.1
|
1.0
|
CG2
|
A:VAL971
|
4.6
|
68.9
|
1.0
|
N
|
A:HIS1001
|
4.6
|
66.1
|
1.0
|
CB
|
A:LYS988
|
4.6
|
70.8
|
1.0
|
C
|
A:CYS998
|
4.7
|
66.3
|
1.0
|
CA
|
A:CYS986
|
4.7
|
87.9
|
1.0
|
CA
|
A:HIS1001
|
4.7
|
60.4
|
1.0
|
C
|
A:LEU997
|
4.9
|
62.8
|
1.0
|
C
|
A:CYS969
|
5.0
|
77.7
|
1.0
|
O
|
A:CYS969
|
5.0
|
82.3
|
1.0
|
|
Reference:
Y.-C.I.Tsai,
D.House,
K.Rittinger.
DAB3/Hoip-Rbr Apo Structure Cell Chem Biol 2019.
ISSN: ESSN 2451-9456
Page generated: Tue Oct 29 07:10:14 2024
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