Zinc in PDB 8dtn: The Complex of Nanobody 6101 with BCL11A ZF6
Protein crystallography data
The structure of The Complex of Nanobody 6101 with BCL11A ZF6, PDB code: 8dtn
was solved by
M.Yin,
K.Tenglin,
L.Zhai,
L.M.Dassama,
S.H.Orkin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.28 /
2.20
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.933,
54.933,
408.619,
90,
90,
120
|
R / Rfree (%)
|
19.5 /
23.2
|
Other elements in 8dtn:
The structure of The Complex of Nanobody 6101 with BCL11A ZF6 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the The Complex of Nanobody 6101 with BCL11A ZF6
(pdb code 8dtn). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
The Complex of Nanobody 6101 with BCL11A ZF6, PDB code: 8dtn:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8dtn
Go back to
Zinc Binding Sites List in 8dtn
Zinc binding site 1 out
of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn901
b:22.9
occ:1.00
|
NE2
|
B:HIS818
|
2.1
|
24.2
|
1.0
|
NE2
|
B:HIS823
|
2.1
|
31.1
|
1.0
|
SG
|
B:CYS805
|
2.3
|
24.9
|
1.0
|
SG
|
B:CYS802
|
2.3
|
27.5
|
1.0
|
CE1
|
B:HIS823
|
3.0
|
26.2
|
1.0
|
CD2
|
B:HIS818
|
3.0
|
27.2
|
1.0
|
CE1
|
B:HIS818
|
3.1
|
28.3
|
1.0
|
CB
|
B:CYS802
|
3.1
|
27.3
|
1.0
|
CD2
|
B:HIS823
|
3.1
|
27.6
|
1.0
|
CB
|
B:CYS805
|
3.4
|
23.1
|
1.0
|
N
|
B:CYS805
|
3.7
|
28.1
|
1.0
|
CA
|
B:CYS805
|
4.1
|
24.4
|
1.0
|
ND1
|
B:HIS823
|
4.1
|
25.2
|
1.0
|
ND1
|
B:HIS818
|
4.2
|
27.1
|
1.0
|
CG
|
B:HIS818
|
4.2
|
26.0
|
1.0
|
CG
|
B:HIS823
|
4.2
|
27.6
|
1.0
|
CB
|
B:ILE804
|
4.5
|
27.0
|
1.0
|
CA
|
B:CYS802
|
4.5
|
29.8
|
1.0
|
O
|
B:HOH1026
|
4.7
|
29.1
|
1.0
|
C
|
B:ILE804
|
4.7
|
27.7
|
1.0
|
C
|
B:CYS805
|
4.8
|
24.3
|
1.0
|
CA
|
B:ILE804
|
4.9
|
28.3
|
1.0
|
CB
|
B:MSE807
|
5.0
|
24.3
|
1.0
|
N
|
B:ILE804
|
5.0
|
26.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8dtn
Go back to
Zinc Binding Sites List in 8dtn
Zinc binding site 2 out
of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn901
b:26.5
occ:1.00
|
NE2
|
D:HIS818
|
2.0
|
27.7
|
1.0
|
NE2
|
D:HIS823
|
2.1
|
28.5
|
1.0
|
SG
|
D:CYS802
|
2.3
|
27.1
|
1.0
|
SG
|
D:CYS805
|
2.4
|
27.1
|
1.0
|
CE1
|
D:HIS823
|
3.0
|
28.0
|
1.0
|
CD2
|
D:HIS818
|
3.0
|
29.8
|
1.0
|
CE1
|
D:HIS818
|
3.0
|
28.1
|
1.0
|
CD2
|
D:HIS823
|
3.1
|
30.9
|
1.0
|
CB
|
D:CYS802
|
3.1
|
27.9
|
1.0
|
CB
|
D:CYS805
|
3.3
|
28.4
|
1.0
|
N
|
D:CYS805
|
3.6
|
30.5
|
1.0
|
CA
|
D:CYS805
|
4.0
|
29.4
|
1.0
|
ND1
|
D:HIS823
|
4.1
|
30.1
|
1.0
|
ND1
|
D:HIS818
|
4.1
|
27.2
|
1.0
|
CG
|
D:HIS818
|
4.1
|
29.6
|
1.0
|
CG
|
D:HIS823
|
4.2
|
35.5
|
1.0
|
CB
|
D:ILE804
|
4.4
|
30.4
|
1.0
|
CA
|
D:CYS802
|
4.6
|
25.7
|
1.0
|
C
|
D:ILE804
|
4.7
|
32.1
|
1.0
|
C
|
D:CYS805
|
4.8
|
27.2
|
1.0
|
CB
|
D:TRP822
|
4.8
|
27.9
|
1.0
|
N
|
D:ILE804
|
4.9
|
27.9
|
1.0
|
CA
|
D:ILE804
|
4.9
|
29.1
|
1.0
|
O
|
D:HOH1022
|
4.9
|
26.9
|
1.0
|
N
|
D:LYS806
|
5.0
|
25.1
|
1.0
|
CB
|
D:MSE807
|
5.0
|
24.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8dtn
Go back to
Zinc Binding Sites List in 8dtn
Zinc binding site 3 out
of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn901
b:25.6
occ:1.00
|
NE2
|
F:HIS823
|
2.0
|
36.3
|
1.0
|
NE2
|
F:HIS818
|
2.1
|
28.5
|
1.0
|
SG
|
F:CYS805
|
2.3
|
24.4
|
1.0
|
SG
|
F:CYS802
|
2.4
|
25.5
|
1.0
|
CE1
|
F:HIS823
|
3.0
|
36.4
|
1.0
|
CD2
|
F:HIS818
|
3.0
|
26.7
|
1.0
|
CD2
|
F:HIS823
|
3.0
|
30.1
|
1.0
|
CE1
|
F:HIS818
|
3.1
|
29.5
|
1.0
|
CB
|
F:CYS802
|
3.2
|
28.2
|
1.0
|
CB
|
F:CYS805
|
3.3
|
27.7
|
1.0
|
N
|
F:CYS805
|
3.7
|
27.8
|
1.0
|
CA
|
F:CYS805
|
4.1
|
30.4
|
1.0
|
ND1
|
F:HIS823
|
4.1
|
38.2
|
1.0
|
CG
|
F:HIS823
|
4.2
|
34.3
|
1.0
|
ND1
|
F:HIS818
|
4.2
|
29.7
|
1.0
|
CG
|
F:HIS818
|
4.2
|
29.2
|
1.0
|
CB
|
F:ILE804
|
4.5
|
34.4
|
1.0
|
CA
|
F:CYS802
|
4.7
|
26.3
|
1.0
|
C
|
F:ILE804
|
4.7
|
30.5
|
1.0
|
C
|
F:CYS805
|
4.8
|
28.8
|
1.0
|
O
|
F:HOH1023
|
4.9
|
34.2
|
1.0
|
CA
|
F:ILE804
|
5.0
|
29.2
|
1.0
|
N
|
F:LYS806
|
5.0
|
29.5
|
1.0
|
CB
|
F:TRP822
|
5.0
|
25.8
|
1.0
|
N
|
F:ILE804
|
5.0
|
27.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8dtn
Go back to
Zinc Binding Sites List in 8dtn
Zinc binding site 4 out
of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/dt/8dtn-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn901
b:27.1
occ:1.00
|
NE2
|
H:HIS818
|
2.0
|
32.5
|
1.0
|
NE2
|
H:HIS823
|
2.1
|
31.1
|
1.0
|
SG
|
H:CYS805
|
2.3
|
28.1
|
1.0
|
SG
|
H:CYS802
|
2.4
|
28.2
|
1.0
|
CE1
|
H:HIS818
|
2.9
|
33.0
|
1.0
|
CE1
|
H:HIS823
|
3.0
|
34.4
|
1.0
|
CD2
|
H:HIS818
|
3.0
|
28.6
|
1.0
|
CD2
|
H:HIS823
|
3.2
|
33.8
|
1.0
|
CB
|
H:CYS802
|
3.2
|
30.9
|
1.0
|
CB
|
H:CYS805
|
3.3
|
27.2
|
1.0
|
N
|
H:CYS805
|
3.7
|
30.2
|
1.0
|
CA
|
H:CYS805
|
4.0
|
31.3
|
1.0
|
ND1
|
H:HIS818
|
4.1
|
29.5
|
1.0
|
ND1
|
H:HIS823
|
4.1
|
34.4
|
1.0
|
CG
|
H:HIS818
|
4.1
|
29.4
|
1.0
|
CG
|
H:HIS823
|
4.2
|
37.5
|
1.0
|
CB
|
H:ILE804
|
4.3
|
32.9
|
1.0
|
C
|
H:ILE804
|
4.7
|
35.1
|
1.0
|
CA
|
H:CYS802
|
4.7
|
32.1
|
1.0
|
C
|
H:CYS805
|
4.7
|
30.8
|
1.0
|
O
|
H:HOH1022
|
4.8
|
35.8
|
1.0
|
CA
|
H:ILE804
|
4.9
|
34.6
|
1.0
|
N
|
H:LYS806
|
4.9
|
26.9
|
1.0
|
N
|
H:ILE804
|
4.9
|
35.3
|
1.0
|
CB
|
H:TRP822
|
5.0
|
29.4
|
1.0
|
|
Reference:
M.Yin,
M.Izadi,
K.Tenglin,
T.Viennet,
L.Zhai,
G.Zheng,
H.Arthanari,
L.M.K.Dassama,
S.H.Orkin.
Evolution of Nanobodies Specific For BCL11A. Proc.Natl.Acad.Sci.Usa V. 120 59120 2023.
ISSN: ESSN 1091-6490
PubMed: 36626555
DOI: 10.1073/PNAS.2218959120
Page generated: Sat Apr 8 08:22:07 2023
|