Nickel in PDB 4ypg: Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
Protein crystallography data
The structure of Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody, PDB code: 4ypg
was solved by
V.Oganesyan,
W.F.Dall'acqua,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
3.00
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
134.820,
153.260,
163.490,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.6 /
27.2
|
Nickel Binding Sites:
The binding sites of Nickel atom in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
(pdb code 4ypg). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the
Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody, PDB code: 4ypg:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
Nickel binding site 1 out
of 6 in 4ypg
Go back to
Nickel Binding Sites List in 4ypg
Nickel binding site 1 out
of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_01.jpg) Mono view
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni301
b:84.6
occ:1.00
|
NE2
|
A:HIS190
|
2.1
|
67.3
|
1.0
|
O
|
A:HOH402
|
2.4
|
49.8
|
1.0
|
CE1
|
A:HIS190
|
2.8
|
67.1
|
1.0
|
CD2
|
A:HIS190
|
3.3
|
67.1
|
1.0
|
ND1
|
A:HIS190
|
4.1
|
66.3
|
1.0
|
CG
|
A:HIS190
|
4.3
|
67.0
|
1.0
|
O
|
A:HOH417
|
4.6
|
29.0
|
1.0
|
|
Nickel binding site 2 out
of 6 in 4ypg
Go back to
Nickel Binding Sites List in 4ypg
Nickel binding site 2 out
of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_02.jpg) Mono view
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni301
b:84.4
occ:0.50
|
NH1
|
B:ARG87
|
3.1
|
51.6
|
1.0
|
OD2
|
B:ASP89
|
3.4
|
48.0
|
1.0
|
CG
|
B:ASP89
|
3.6
|
48.0
|
1.0
|
N
|
B:ASP89
|
3.8
|
49.1
|
1.0
|
CB
|
B:ASP89
|
4.0
|
48.0
|
1.0
|
OD1
|
B:ASP89
|
4.1
|
48.4
|
1.0
|
CB
|
B:SER88
|
4.1
|
50.5
|
1.0
|
CB
|
B:ARG87
|
4.2
|
51.8
|
1.0
|
N
|
B:SER88
|
4.2
|
51.0
|
1.0
|
CZ
|
B:ARG87
|
4.3
|
51.8
|
1.0
|
CA
|
B:SER88
|
4.6
|
50.5
|
1.0
|
CA
|
B:ASP89
|
4.6
|
48.2
|
1.0
|
C
|
B:SER88
|
4.7
|
49.4
|
1.0
|
OG
|
B:SER88
|
4.7
|
52.2
|
1.0
|
C
|
B:ARG87
|
4.9
|
51.1
|
1.0
|
NH2
|
B:ARG87
|
4.9
|
52.5
|
1.0
|
|
Nickel binding site 3 out
of 6 in 4ypg
Go back to
Nickel Binding Sites List in 4ypg
Nickel binding site 3 out
of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_03.jpg) Mono view
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni201
b:69.5
occ:1.00
|
N
|
C:THR-1
|
1.9
|
61.7
|
1.0
|
N
|
C:SER0
|
2.2
|
63.4
|
1.0
|
NE2
|
C:HIS7
|
2.2
|
61.9
|
1.0
|
N
|
C:CYS1
|
2.3
|
64.2
|
1.0
|
CA
|
C:THR-1
|
2.8
|
61.5
|
1.0
|
C
|
C:THR-1
|
2.8
|
62.3
|
1.0
|
CD2
|
C:HIS7
|
2.9
|
60.2
|
1.0
|
CA
|
C:CYS1
|
3.2
|
64.7
|
1.0
|
C
|
C:SER0
|
3.2
|
64.8
|
1.0
|
CA
|
C:SER0
|
3.2
|
64.4
|
1.0
|
CE1
|
C:HIS7
|
3.3
|
63.5
|
1.0
|
O
|
C:THR-1
|
4.0
|
61.9
|
1.0
|
CB
|
C:THR-1
|
4.1
|
62.3
|
1.0
|
CG
|
C:HIS7
|
4.1
|
61.2
|
1.0
|
OG1
|
C:THR-1
|
4.2
|
64.5
|
1.0
|
C
|
C:CYS1
|
4.2
|
66.3
|
1.0
|
N
|
C:ASP2
|
4.2
|
67.0
|
1.0
|
ND1
|
C:HIS7
|
4.3
|
63.5
|
1.0
|
CB
|
C:CYS1
|
4.3
|
64.5
|
1.0
|
CB
|
C:ALA97
|
4.3
|
50.2
|
1.0
|
OG
|
C:SER0
|
4.3
|
67.7
|
1.0
|
CB
|
C:SER0
|
4.3
|
66.3
|
1.0
|
O
|
C:SER0
|
4.4
|
65.9
|
1.0
|
OD1
|
C:ASP94
|
4.4
|
54.5
|
1.0
|
O
|
C:ASP94
|
4.6
|
51.2
|
1.0
|
CG
|
C:ASP94
|
4.7
|
54.5
|
1.0
|
CA
|
C:ASP94
|
4.9
|
51.7
|
1.0
|
CB
|
C:ASP94
|
4.9
|
53.0
|
1.0
|
|
Nickel binding site 4 out
of 6 in 4ypg
Go back to
Nickel Binding Sites List in 4ypg
Nickel binding site 4 out
of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_04.jpg) Mono view
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni201
b:64.7
occ:1.00
|
NE2
|
D:HIS7
|
2.0
|
55.8
|
1.0
|
N
|
D:THR-1
|
2.1
|
57.5
|
1.0
|
N
|
D:SER0
|
2.1
|
58.0
|
1.0
|
N
|
D:CYS1
|
2.2
|
56.4
|
1.0
|
CD2
|
D:HIS7
|
2.8
|
53.1
|
1.0
|
C
|
D:THR-1
|
2.9
|
57.6
|
1.0
|
CA
|
D:THR-1
|
3.0
|
57.9
|
1.0
|
C
|
D:SER0
|
3.0
|
57.6
|
1.0
|
CA
|
D:SER0
|
3.1
|
57.7
|
1.0
|
CA
|
D:CYS1
|
3.1
|
57.0
|
1.0
|
CE1
|
D:HIS7
|
3.2
|
59.9
|
1.0
|
O
|
D:THR-1
|
4.0
|
57.4
|
1.0
|
CG
|
D:HIS7
|
4.0
|
55.8
|
1.0
|
C
|
D:CYS1
|
4.1
|
60.6
|
1.0
|
CB
|
D:ALA97
|
4.1
|
51.4
|
1.0
|
OG1
|
D:THR-1
|
4.1
|
65.5
|
1.0
|
N
|
D:ASP2
|
4.1
|
63.9
|
1.0
|
CB
|
D:THR-1
|
4.1
|
61.6
|
1.0
|
ND1
|
D:HIS7
|
4.2
|
59.8
|
1.0
|
O
|
D:SER0
|
4.2
|
59.2
|
1.0
|
CB
|
D:SER0
|
4.2
|
61.8
|
1.0
|
CB
|
D:CYS1
|
4.3
|
55.0
|
1.0
|
OG
|
D:SER0
|
4.4
|
64.8
|
1.0
|
OD1
|
D:ASP94
|
4.5
|
51.9
|
1.0
|
CG
|
D:ASP94
|
4.6
|
52.7
|
1.0
|
O
|
D:ASP94
|
4.7
|
50.9
|
1.0
|
CA
|
D:ASP94
|
4.8
|
50.9
|
1.0
|
CB
|
D:ASP94
|
4.8
|
51.2
|
1.0
|
OD2
|
D:ASP94
|
5.0
|
55.0
|
1.0
|
CG2
|
D:THR-1
|
5.0
|
61.8
|
1.0
|
|
Nickel binding site 5 out
of 6 in 4ypg
Go back to
Nickel Binding Sites List in 4ypg
Nickel binding site 5 out
of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_05.jpg) Mono view
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ni301
b:72.5
occ:0.50
|
NH1
|
H:ARG87
|
3.1
|
59.7
|
1.0
|
OD2
|
H:ASP89
|
3.3
|
54.1
|
1.0
|
CG
|
H:ASP89
|
3.4
|
55.3
|
1.0
|
N
|
H:ASP89
|
3.6
|
56.1
|
1.0
|
CB
|
H:ASP89
|
3.8
|
54.5
|
1.0
|
OD1
|
H:ASP89
|
3.8
|
56.1
|
1.0
|
N
|
H:SER88
|
4.0
|
59.6
|
1.0
|
CB
|
H:ARG87
|
4.1
|
60.5
|
1.0
|
CB
|
H:SER88
|
4.2
|
58.5
|
1.0
|
CA
|
H:ASP89
|
4.3
|
54.7
|
1.0
|
CZ
|
H:ARG87
|
4.3
|
60.9
|
1.0
|
CA
|
H:SER88
|
4.5
|
58.5
|
1.0
|
C
|
H:SER88
|
4.5
|
56.9
|
1.0
|
C
|
H:ARG87
|
4.8
|
59.9
|
1.0
|
OG
|
H:SER88
|
4.8
|
60.4
|
1.0
|
CA
|
H:ARG87
|
4.9
|
61.3
|
1.0
|
NH2
|
H:ARG87
|
5.0
|
62.2
|
1.0
|
|
Nickel binding site 6 out
of 6 in 4ypg
Go back to
Nickel Binding Sites List in 4ypg
Nickel binding site 6 out
of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_06.jpg) Mono view
![](/pictures/NI/pdb/yp/4ypg-NI-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni301
b:77.1
occ:0.50
|
NE2
|
L:HIS190
|
1.9
|
76.2
|
1.0
|
O
|
L:HOH402
|
1.9
|
57.5
|
1.0
|
O
|
L:HOH401
|
2.0
|
49.5
|
1.0
|
CE1
|
L:HIS190
|
2.7
|
75.6
|
1.0
|
CD2
|
L:HIS190
|
3.0
|
78.0
|
1.0
|
ND1
|
L:HIS190
|
3.9
|
76.4
|
1.0
|
CG
|
L:HIS190
|
4.0
|
77.8
|
1.0
|
|
Reference:
V.Oganesyan,
L.Peng,
R.M.Woods,
H.Wu,
W.F.Dall'acqua.
Structural Insights Into the Neutralization Properties of the Fully Human, Anti-Interferon Monoclonal Antibody Sifalimumab. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 25925951
DOI: 10.1074/JBC.M115.652156
Page generated: Wed Dec 16 01:38:19 2020
|