Nickel in PDB 4ypg: Structural Insights Into the Neutralization Properties of A Human Anti-Interferon Monoclonal Antibody

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

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 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 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 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 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 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 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

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