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Nickel in PDB 8juu: Rat Megalin

Other elements in 8juu:

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

Calcium (Ca) 88 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Rat Megalin (pdb code 8juu). 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, PDB code: 8juu:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 8juu

Go back to Nickel Binding Sites List in 8juu
Nickel binding site 1 out of 2 in the Rat Megalin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Rat Megalin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni4768

b:69.7
occ:1.00
NE2 A:HIS1963 2.1 84.7 1.0
OE2 A:GLU1923 2.3 77.4 1.0
SG J:CYS2 2.4 123.2 1.0
NE2 A:HIS1921 2.5 74.6 1.0
CE1 A:HIS1963 2.9 85.0 1.0
CE1 A:HIS1921 3.1 75.3 1.0
CD2 A:HIS1963 3.2 86.0 1.0
CD A:GLU1923 3.2 78.6 1.0
CA J:CYS2 3.4 157.7 1.0
CB J:CYS2 3.4 141.1 1.0
OE1 A:GLU1923 3.5 77.9 1.0
CD2 A:HIS1921 3.6 74.7 1.0
N J:CYS2 3.9 171.9 1.0
ND1 A:HIS1963 4.1 85.0 1.0
ND1 A:HIS1921 4.2 75.4 1.0
OG1 A:THR1939 4.2 74.6 1.0
CG A:HIS1963 4.3 84.4 1.0
CG A:HIS1921 4.4 75.6 1.0
CZ3 A:TRP1965 4.5 86.7 1.0
CE3 A:TRP1965 4.5 85.3 1.0
CG A:GLU1923 4.6 78.9 1.0
CH2 A:TRP1965 4.7 86.5 1.0
O A:PRO1964 4.7 75.6 1.0
C J:CYS2 4.8 166.9 1.0
CD2 A:TRP1965 4.8 83.4 1.0
CZ2 A:TRP1965 4.9 85.3 1.0
CB A:THR1939 4.9 73.7 1.0
CE2 A:TRP1965 5.0 84.3 1.0

Nickel binding site 2 out of 2 in 8juu

Go back to Nickel Binding Sites List in 8juu
Nickel binding site 2 out of 2 in the Rat Megalin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Rat Megalin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni4768

b:69.8
occ:1.00
NE2 B:HIS1963 2.1 92.3 1.0
NE2 B:HIS1921 2.3 79.4 1.0
OE2 B:GLU1923 2.4 95.9 1.0
SG D:CYS2 2.4 117.0 1.0
CE1 B:HIS1963 3.1 93.4 1.0
CE1 B:HIS1921 3.1 81.3 1.0
CD2 B:HIS1963 3.1 91.4 1.0
CD B:GLU1923 3.2 93.9 1.0
CD2 B:HIS1921 3.4 78.2 1.0
OE1 B:GLU1923 3.5 95.3 1.0
CB D:CYS2 3.6 136.2 1.0
CA D:CYS2 3.7 151.3 1.0
OG1 B:THR1939 4.1 80.2 1.0
N D:CYS2 4.2 165.2 1.0
ND1 B:HIS1963 4.2 90.3 1.0
ND1 B:HIS1921 4.2 81.2 1.0
CG B:HIS1963 4.3 89.5 1.0
CG B:GLU1923 4.3 90.8 1.0
CG B:HIS1921 4.4 79.2 1.0
O B:PRO1964 4.8 73.7 1.0
CE3 B:TRP1965 4.8 86.9 1.0
CZ3 B:TRP1965 4.8 88.6 1.0
CB B:THR1939 4.8 80.1 1.0
CG2 B:THR1939 4.9 81.0 1.0
C D:UNK1 5.0 179.2 1.0

Reference:

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
Page generated: Thu Oct 10 09:44:59 2024

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