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Nickel in PDB 8jxe: Rat Megalin Rap Complex Head

Other elements in 8jxe:

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

Calcium (Ca) 12 atoms

Nickel Binding Sites:

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

Nickel binding site 1 out of 2 in 8jxe

Go back to Nickel Binding Sites List in 8jxe
Nickel binding site 1 out of 2 in the Rat Megalin Rap Complex Head


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 Head within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni4712

b:71.5
occ:1.00
OE2 A:GLU1923 2.1 35.7 1.0
NE2 A:HIS1921 2.3 40.9 1.0
SG J:CYS2 2.4 29.9 1.0
NE2 A:HIS1963 2.5 42.4 1.0
CD A:GLU1923 3.0 39.1 1.0
CE1 A:HIS1963 3.1 45.0 1.0
CD2 A:HIS1921 3.2 37.6 1.0
CE1 A:HIS1921 3.2 43.3 1.0
OE1 A:GLU1923 3.3 51.7 1.0
CD2 A:HIS1963 3.6 38.9 1.0
CB J:CYS2 3.7 37.7 1.0
CA J:CYS2 3.8 40.2 1.0
OG1 A:THR1939 4.0 48.7 1.0
N J:CYS2 4.2 45.5 1.0
ND1 A:HIS1963 4.3 46.2 1.0
CG A:HIS1921 4.3 34.0 1.0
ND1 A:HIS1921 4.3 45.8 1.0
CG A:GLU1923 4.4 30.7 1.0
CE3 A:TRP1965 4.6 41.6 1.0
CG A:HIS1963 4.6 40.0 1.0
O A:PRO1964 4.6 56.1 1.0
CZ3 A:TRP1965 4.6 46.9 1.0
CD2 A:TRP1965 4.7 37.0 1.0
CB A:THR1939 4.8 41.4 1.0
CH2 A:TRP1965 4.8 44.3 1.0
O A:LEU1922 4.9 48.1 1.0
CE2 A:TRP1965 5.0 40.1 1.0

Nickel binding site 2 out of 2 in 8jxe

Go back to Nickel Binding Sites List in 8jxe
Nickel binding site 2 out of 2 in the Rat Megalin Rap Complex Head


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 Head within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni4712

b:80.6
occ:1.00
NE2 B:HIS1963 2.1 43.7 1.0
NE2 B:HIS1921 2.2 48.1 1.0
SG D:CYS2 2.3 13.1 1.0
OE2 B:GLU1923 2.4 52.5 1.0
CE1 B:HIS1921 2.8 48.5 1.0
CD2 B:HIS1963 2.8 38.1 1.0
CD B:GLU1923 2.9 42.5 1.0
OE1 B:GLU1923 3.0 48.7 1.0
CD2 B:HIS1921 3.2 44.4 1.0
OG1 B:THR1939 3.2 47.2 1.0
CE1 B:HIS1963 3.2 45.4 1.0
ND1 B:HIS1921 3.8 44.9 1.0
CB D:CYS2 4.0 15.0 1.0
CB B:THR1939 4.0 43.5 1.0
CG B:HIS1921 4.0 35.7 1.0
CG B:HIS1963 4.1 36.5 1.0
CG B:GLU1923 4.1 37.9 1.0
CG2 B:THR1939 4.1 36.3 1.0
ND1 B:HIS1963 4.2 46.2 1.0
CA D:CYS2 4.5 16.3 1.0
N D:CYS2 4.8 25.0 1.0
CE3 B:TRP1965 5.0 42.1 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 09:45:34 2024

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