Nickel in PDB 8jut: Rat Megalin Rap Complex

The structure of Rat Megalin Rap Complex also contains other interesting chemical elements:

Calcium

(Ca)

88 atoms

The binding sites of Nickel atom in the Rat Megalin Rap Complex (pdb code 8jut). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Rat Megalin Rap Complex, PDB code: 8jut:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Rat Megalin Rap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Rat Megalin Rap Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni4768 b:26.4 occ:1.00 OE2 A:GLU1923 2.3 51.7 1.0 SG J:CYS2 2.3 122.1 1.0 NE2 A:HIS1963 2.3 56.3 1.0 NE2 A:HIS1921 2.5 44.2 1.0 CE1 A:HIS1963 2.9 57.6 1.0 CD A:GLU1923 3.2 54.4 1.0 CB J:CYS2 3.2 146.8 1.0 OE1 A:GLU1923 3.3 53.0 1.0 CE1 A:HIS1921 3.4 45.9 1.0 CA J:CYS2 3.4 172.6 1.0 CD2 A:HIS1921 3.5 44.5 1.0 CD2 A:HIS1963 3.5 55.5 1.0 ND1 A:HIS1963 4.1 56.4 1.0 OG1 A:THR1939 4.2 42.7 1.0 N J:CYS2 4.3 201.5 1.0 CE3 A:TRP1965 4.3 49.7 1.0 CG A:HIS1963 4.4 54.0 1.0 CZ3 A:TRP1965 4.5 51.8 1.0 ND1 A:HIS1921 4.5 46.7 1.0 CD2 A:TRP1965 4.5 48.5 1.0 CG A:GLU1923 4.6 55.5 1.0 CG A:HIS1921 4.6 46.7 1.0 C J:CYS2 4.6 183.0 1.0 O A:PRO1964 4.7 42.4 1.0 CH2 A:TRP1965 4.8 53.8 1.0 CE2 A:TRP1965 4.8 50.2 1.0 CZ2 A:TRP1965 5.0 53.0 1.0

Nickel binding site 2 out of 2 in the Rat Megalin Rap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Rat Megalin Rap Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni4768 b:26.3 occ:1.00 SG Q:CYS2 2.0 117.2 1.0 NE2 B:HIS1963 2.3 54.3 1.0 NE2 B:HIS1921 2.6 46.8 1.0 OE2 B:GLU1923 2.6 53.5 1.0 CE1 B:HIS1963 3.1 55.1 1.0 CE1 B:HIS1921 3.2 47.1 1.0 CB Q:CYS2 3.3 137.9 1.0 CA Q:CYS2 3.3 164.0 1.0 CD B:GLU1923 3.4 54.4 1.0 OE1 B:GLU1923 3.4 53.6 1.0 CD2 B:HIS1963 3.4 53.8 1.0 N Q:CYS2 3.6 182.9 1.0 CD2 B:HIS1921 3.7 47.9 1.0 ND1 B:HIS1963 4.3 54.1 1.0 OG1 B:THR1939 4.4 45.8 1.0 C Q:UNK1 4.4 203.2 1.0 ND1 B:HIS1921 4.4 48.2 1.0 CG B:HIS1963 4.5 52.3 1.0 CE3 B:TRP1965 4.5 57.0 1.0 CZ3 B:TRP1965 4.6 59.0 1.0 CD2 B:TRP1965 4.7 53.7 1.0 CG B:HIS1921 4.7 48.6 1.0 C Q:CYS2 4.8 188.9 1.0 CG B:GLU1923 4.8 55.1 1.0 CH2 B:TRP1965 4.9 59.9 1.0 CE2 B:TRP1965 4.9 54.4 1.0 O Q:UNK1 4.9 194.6 1.0 N Q:UNK1 5.0 224.0 1.0

S.Goto, A.Tsutsumi, Y.Lee, M.Hosojima, H.Kabasawa, K.Komochi, S.Nagatoishi, K.Takemoto, K.Tsumoto, T.Nishizawa, M.Kikkawa, A.Saito. Cryo-Em Structures Elucidate the Multiligand Receptor Nature of Megalin. Proc.Natl.Acad.Sci.Usa V. 121 59121 2024.
ISSN: ESSN 1091-6490
PubMed: 38771880
DOI: 10.1073/PNAS.2318859121