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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

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Nickel binding site 1 out of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody


Mono view


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

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Nickel binding site 2 out of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody


Mono view


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

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Nickel binding site 3 out of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody


Mono view


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

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Nickel binding site 4 out of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody


Mono view


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

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Nickel binding site 5 out of 6 in the Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody


Mono view


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


Mono view


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

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