Arsenic in PDB 6x91: Crystal Structure of Mbp-Fused Human APOBEC1
Enzymatic activity of Crystal Structure of Mbp-Fused Human APOBEC1
All present enzymatic activity of Crystal Structure of Mbp-Fused Human APOBEC1:
3.5.4.36;
Protein crystallography data
The structure of Crystal Structure of Mbp-Fused Human APOBEC1, PDB code: 6x91
was solved by
A.D.Wolfe,
S.-X.Li,
X.S.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.61 /
3.51
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
177.715,
179.209,
210.505,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
27.6 /
29.8
|
Other elements in 6x91:
The structure of Crystal Structure of Mbp-Fused Human APOBEC1 also contains other interesting chemical elements:
Arsenic Binding Sites:
The binding sites of Arsenic atom in the Crystal Structure of Mbp-Fused Human APOBEC1
(pdb code 6x91). This binding sites where shown within
5.0 Angstroms radius around Arsenic atom.
In total 8 binding sites of Arsenic where determined in the
Crystal Structure of Mbp-Fused Human APOBEC1, PDB code: 6x91:
Jump to Arsenic binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Arsenic binding site 1 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 1 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 1 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As1302
b:0.1
occ:1.00
|
AS
|
A:CAC1302
|
0.0
|
0.1
|
1.0
|
O1
|
A:CAC1302
|
1.6
|
0.8
|
1.0
|
O2
|
A:CAC1302
|
1.8
|
0.5
|
1.0
|
C2
|
A:CAC1302
|
2.0
|
0.3
|
1.0
|
C1
|
A:CAC1302
|
2.0
|
0.1
|
1.0
|
ZN
|
A:ZN1301
|
3.4
|
0.4
|
1.0
|
ND1
|
A:HIS1061
|
3.7
|
0.4
|
1.0
|
CG
|
A:HIS1061
|
4.4
|
0.7
|
1.0
|
CB
|
A:TRP1090
|
4.4
|
90.9
|
1.0
|
CB
|
A:HIS1061
|
4.4
|
0.7
|
1.0
|
CE1
|
A:HIS1061
|
4.5
|
0.9
|
1.0
|
O
|
A:SER1091
|
4.5
|
88.7
|
1.0
|
N
|
A:CYS1093
|
4.7
|
97.9
|
1.0
|
SG
|
A:CYS1096
|
4.7
|
0.9
|
1.0
|
O
|
A:TRP1090
|
4.7
|
93.2
|
1.0
|
SG
|
A:CYS1093
|
4.8
|
99.0
|
1.0
|
NH1
|
A:ARG1033
|
4.8
|
0.3
|
1.0
|
CB
|
A:CYS1093
|
4.9
|
96.7
|
1.0
|
CA
|
A:PRO1092
|
5.0
|
0.1
|
1.0
|
|
Arsenic binding site 2 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 2 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 2 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:As1302
b:0.9
occ:1.00
|
AS
|
B:CAC1302
|
0.0
|
0.9
|
1.0
|
O1
|
B:CAC1302
|
1.6
|
0.6
|
1.0
|
O2
|
B:CAC1302
|
1.8
|
0.7
|
1.0
|
C1
|
B:CAC1302
|
2.0
|
91.4
|
1.0
|
C2
|
B:CAC1302
|
2.0
|
0.2
|
1.0
|
ND1
|
B:HIS1061
|
3.3
|
0.8
|
1.0
|
ZN
|
B:ZN1301
|
3.8
|
0.4
|
1.0
|
CE1
|
B:HIS1061
|
4.0
|
0.6
|
1.0
|
CG
|
B:HIS1061
|
4.2
|
0.8
|
1.0
|
O
|
B:SER1091
|
4.3
|
96.3
|
1.0
|
CB
|
B:HIS1061
|
4.4
|
0.5
|
1.0
|
N
|
B:CYS1093
|
4.5
|
0.4
|
1.0
|
SG
|
B:CYS1096
|
4.7
|
0.1
|
1.0
|
CA
|
B:PRO1092
|
4.7
|
91.5
|
1.0
|
CG
|
B:GLU1035
|
4.8
|
0.9
|
1.0
|
CB
|
B:TRP1090
|
4.9
|
0.3
|
1.0
|
SG
|
B:CYS1093
|
4.9
|
0.3
|
1.0
|
CB
|
B:CYS1093
|
4.9
|
0.7
|
1.0
|
CB
|
B:GLU1035
|
5.0
|
0.8
|
1.0
|
|
Arsenic binding site 3 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 3 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 3 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:As1302
b:0.3
occ:1.00
|
AS
|
C:CAC1302
|
0.0
|
0.3
|
1.0
|
O1
|
C:CAC1302
|
1.6
|
0.2
|
1.0
|
O2
|
C:CAC1302
|
1.8
|
76.7
|
1.0
|
C1
|
C:CAC1302
|
2.0
|
0.6
|
1.0
|
C2
|
C:CAC1302
|
2.0
|
98.9
|
1.0
|
ND1
|
C:HIS1061
|
3.4
|
0.4
|
1.0
|
ZN
|
C:ZN1301
|
3.4
|
0.5
|
1.0
|
CG
|
C:HIS1061
|
4.2
|
0.4
|
1.0
|
CE1
|
C:HIS1061
|
4.2
|
0.9
|
1.0
|
CB
|
C:HIS1061
|
4.3
|
0.4
|
1.0
|
SG
|
C:CYS1096
|
4.5
|
92.7
|
1.0
|
N
|
C:CYS1093
|
4.5
|
77.7
|
1.0
|
SG
|
C:CYS1093
|
4.6
|
82.5
|
1.0
|
O
|
C:SER1091
|
4.7
|
74.2
|
1.0
|
CB
|
C:CYS1093
|
4.7
|
80.1
|
1.0
|
CA
|
C:PRO1092
|
5.0
|
71.3
|
1.0
|
CA
|
C:HIS1061
|
5.0
|
0.8
|
1.0
|
|
Arsenic binding site 4 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 4 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 4 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As1302
b:0.8
occ:1.00
|
AS
|
D:CAC1302
|
0.0
|
0.8
|
1.0
|
O1
|
D:CAC1302
|
1.6
|
0.0
|
1.0
|
O2
|
D:CAC1302
|
1.8
|
0.8
|
1.0
|
C2
|
D:CAC1302
|
2.0
|
0.9
|
1.0
|
C1
|
D:CAC1302
|
2.0
|
0.1
|
1.0
|
ND1
|
D:HIS1061
|
3.3
|
0.8
|
1.0
|
ZN
|
D:ZN1301
|
3.8
|
0.3
|
1.0
|
CE1
|
D:HIS1061
|
4.0
|
0.2
|
1.0
|
CG
|
D:HIS1061
|
4.3
|
0.9
|
1.0
|
CB
|
D:HIS1061
|
4.5
|
0.1
|
1.0
|
O
|
D:SER1091
|
4.7
|
0.6
|
1.0
|
CB
|
D:TRP1090
|
4.7
|
0.4
|
1.0
|
SG
|
D:CYS1096
|
4.8
|
0.4
|
1.0
|
N
|
D:CYS1093
|
4.9
|
0.6
|
1.0
|
SG
|
D:CYS1093
|
5.0
|
0.8
|
1.0
|
|
Arsenic binding site 5 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 5 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 5 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:As1302
b:0.9
occ:1.00
|
AS
|
E:CAC1302
|
0.0
|
0.9
|
1.0
|
O1
|
E:CAC1302
|
1.6
|
0.6
|
1.0
|
O2
|
E:CAC1302
|
1.8
|
0.2
|
1.0
|
C2
|
E:CAC1302
|
2.0
|
0.2
|
1.0
|
C1
|
E:CAC1302
|
2.0
|
0.1
|
1.0
|
ND1
|
E:HIS1061
|
3.1
|
0.1
|
1.0
|
ZN
|
E:ZN1301
|
3.7
|
0.8
|
1.0
|
CE1
|
E:HIS1061
|
4.0
|
0.6
|
1.0
|
CG
|
E:HIS1061
|
4.0
|
0.8
|
1.0
|
CB
|
E:HIS1061
|
4.2
|
0.4
|
1.0
|
SG
|
E:CYS1096
|
4.3
|
0.5
|
1.0
|
SG
|
E:CYS1093
|
4.4
|
0.0
|
1.0
|
N
|
E:CYS1093
|
4.5
|
0.6
|
1.0
|
O
|
E:SER1091
|
4.6
|
97.2
|
1.0
|
CA
|
E:PRO1092
|
4.8
|
1.0
|
1.0
|
CB
|
E:TRP1090
|
4.8
|
0.8
|
1.0
|
CB
|
E:CYS1093
|
4.9
|
0.8
|
1.0
|
CA
|
E:HIS1061
|
4.9
|
0.3
|
1.0
|
O
|
E:TRP1090
|
4.9
|
0.6
|
1.0
|
|
Arsenic binding site 6 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 6 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 6 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:As1302
b:0.9
occ:1.00
|
AS
|
F:CAC1302
|
0.0
|
0.9
|
1.0
|
O1
|
F:CAC1302
|
1.6
|
0.2
|
1.0
|
O2
|
F:CAC1302
|
1.8
|
99.5
|
1.0
|
C1
|
F:CAC1302
|
2.0
|
94.0
|
1.0
|
C2
|
F:CAC1302
|
2.0
|
0.8
|
1.0
|
ND1
|
F:HIS1061
|
3.3
|
0.3
|
1.0
|
ZN
|
F:ZN1301
|
3.8
|
0.7
|
1.0
|
CE1
|
F:HIS1061
|
4.1
|
0.0
|
1.0
|
CG
|
F:HIS1061
|
4.2
|
0.1
|
1.0
|
O
|
F:SER1091
|
4.3
|
94.5
|
1.0
|
CB
|
F:HIS1061
|
4.3
|
0.7
|
1.0
|
N
|
F:CYS1093
|
4.5
|
0.2
|
1.0
|
SG
|
F:CYS1096
|
4.7
|
98.6
|
1.0
|
CA
|
F:PRO1092
|
4.8
|
0.7
|
1.0
|
CB
|
F:CYS1093
|
4.9
|
0.6
|
1.0
|
SG
|
F:CYS1093
|
5.0
|
0.5
|
1.0
|
CB
|
F:TRP1090
|
5.0
|
0.4
|
1.0
|
|
Arsenic binding site 7 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 7 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 7 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:As1302
b:0.0
occ:1.00
|
AS
|
G:CAC1302
|
0.0
|
0.0
|
1.0
|
O1
|
G:CAC1302
|
1.6
|
0.1
|
1.0
|
O2
|
G:CAC1302
|
1.8
|
78.2
|
1.0
|
C1
|
G:CAC1302
|
2.0
|
0.9
|
1.0
|
C2
|
G:CAC1302
|
2.0
|
92.1
|
1.0
|
ND1
|
G:HIS1061
|
3.4
|
0.4
|
1.0
|
ZN
|
G:ZN1301
|
3.8
|
0.2
|
1.0
|
CE1
|
G:HIS1061
|
4.3
|
0.3
|
1.0
|
CG
|
G:HIS1061
|
4.4
|
0.4
|
1.0
|
CB
|
G:HIS1061
|
4.5
|
0.3
|
1.0
|
O
|
G:SER1091
|
4.5
|
71.4
|
1.0
|
N
|
G:CYS1093
|
4.5
|
82.2
|
1.0
|
SG
|
G:CYS1093
|
4.6
|
89.7
|
1.0
|
SG
|
G:CYS1096
|
4.7
|
0.5
|
1.0
|
CB
|
G:CYS1093
|
4.8
|
83.1
|
1.0
|
CA
|
G:PRO1092
|
4.9
|
71.2
|
1.0
|
CB
|
G:TRP1090
|
4.9
|
70.7
|
1.0
|
|
Arsenic binding site 8 out
of 8 in 6x91
Go back to
Arsenic Binding Sites List in 6x91
Arsenic binding site 8 out
of 8 in the Crystal Structure of Mbp-Fused Human APOBEC1
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 8 of Crystal Structure of Mbp-Fused Human APOBEC1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:As1302
b:0.0
occ:1.00
|
AS
|
H:CAC1302
|
0.0
|
0.0
|
1.0
|
O1
|
H:CAC1302
|
1.6
|
0.4
|
1.0
|
O2
|
H:CAC1302
|
1.8
|
0.3
|
1.0
|
C1
|
H:CAC1302
|
2.0
|
0.0
|
1.0
|
C2
|
H:CAC1302
|
2.0
|
0.7
|
1.0
|
ZN
|
H:ZN1301
|
3.6
|
0.7
|
1.0
|
O
|
H:SER1091
|
4.2
|
0.1
|
1.0
|
CB
|
H:TRP1090
|
4.5
|
0.3
|
1.0
|
N
|
H:CYS1093
|
4.6
|
0.9
|
1.0
|
CA
|
H:PRO1092
|
4.6
|
0.2
|
1.0
|
O
|
H:TRP1090
|
4.7
|
0.8
|
1.0
|
SG
|
H:CYS1096
|
4.9
|
0.4
|
1.0
|
C
|
H:SER1091
|
4.9
|
0.9
|
1.0
|
SG
|
H:CYS1093
|
5.0
|
0.8
|
1.0
|
|
Reference:
A.D.Wolfe,
S.Li,
C.Goedderz,
X.S.Chen.
The Structure of APOBEC1 and Insights Into Its Rna and Dna Substrate Selectivity. Nar Cancer V. 2 AA027 2020.
ISSN: ISSN 2632-8674
PubMed: 33094286
DOI: 10.1093/NARCAN/ZCAA027
Page generated: Wed Jul 10 13:34:41 2024
|