Calcium in PDB 8jxd: Cryo-Em Structure of Rat Megalin Leg

The binding sites of Calcium atom in the Cryo-Em Structure of Rat Megalin Leg (pdb code 8jxd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryo-Em Structure of Rat Megalin Leg, PDB code: 8jxd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Cryo-Em Structure of Rat Megalin Leg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Rat Megalin Leg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4702 b:247.3 occ:1.00 OD2 A:ASP3960 2.3 250.3 1.0 O A:VAL3952 2.3 248.7 1.0 O A:TYR3947 2.3 240.0 1.0 OD1 A:ASP3950 2.3 250.5 1.0 CD1 A:TYR3947 2.6 239.7 1.0 OE2 A:GLU3961 3.0 254.9 1.0 CE1 A:TYR3947 3.1 239.9 1.0 CG A:ASP3950 3.3 249.6 1.0 C A:TYR3947 3.4 240.2 1.0 CG A:ASP3960 3.5 250.1 1.0 C A:VAL3952 3.5 247.8 1.0 CG A:TYR3947 3.7 239.6 1.0 OD2 A:ASP3950 3.8 249.1 1.0 CD A:GLU3961 3.8 253.8 1.0 OE1 A:GLU3961 3.8 254.1 1.0 N A:ASP3954 4.0 245.2 1.0 CB A:TYR3947 4.1 239.3 1.0 CA A:TYR3947 4.2 239.5 1.0 N A:ASP3950 4.3 250.4 1.0 OD1 A:ASP3960 4.3 250.4 1.0 CB A:ASP3954 4.3 244.8 1.0 N A:VAL3952 4.3 247.1 1.0 CA A:VAL3952 4.4 247.2 1.0 CB A:ASP3950 4.4 249.3 1.0 N A:VAL3948 4.4 250.2 1.0 N A:ASN3953 4.5 249.1 1.0 CB A:ASP3960 4.5 249.2 1.0 CZ A:TYR3947 4.5 239.9 1.0 N A:CYS3949 4.5 255.6 1.0 CA A:ASN3953 4.6 249.2 1.0 CA A:VAL3948 4.6 250.3 1.0 C A:ASN3953 4.6 249.0 1.0 CB A:VAL3952 4.7 247.2 1.0 CA A:ASP3950 4.8 249.7 1.0 CA A:ASP3954 4.8 245.2 1.0 C A:VAL3948 4.8 250.3 1.0 CG1 A:VAL3952 4.9 246.8 1.0 CD2 A:TYR3947 4.9 239.7 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structure of Rat Megalin Leg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Rat Megalin Leg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4703 b:169.8 occ:1.00 OD1 A:ASP4009 2.3 170.2 1.0 OD1 A:ASN4025 2.4 153.4 1.0 O A:ILE4010 2.4 161.1 1.0 O A:SER4026 2.4 162.7 1.0 OE2 A:GLU4012 2.4 157.1 1.0 OE1 A:GLU4012 2.4 160.0 1.0 CD A:GLU4012 2.6 157.6 1.0 OD2 A:ASP4009 3.0 168.9 1.0 CG A:ASP4009 3.0 169.4 1.0 O A:SER4029 3.2 155.5 1.0 CG A:ASN4025 3.6 153.4 1.0 C A:ILE4010 3.6 160.1 1.0 C A:SER4026 3.6 161.6 1.0 N A:SER4029 3.6 158.4 1.0 N A:GLY4028 3.6 167.5 1.0 N A:SER4026 3.8 160.2 1.0 CG A:GLU4012 4.0 155.6 1.0 CA A:GLY4028 4.1 165.8 1.0 C A:SER4029 4.1 156.7 1.0 C A:GLY4028 4.2 166.1 1.0 ND2 A:ASN4025 4.2 154.8 1.0 N A:GLU4012 4.3 156.1 1.0 N A:ILE4010 4.3 160.8 1.0 CA A:SER4026 4.4 161.4 1.0 N A:ASN4011 4.5 153.5 1.0 CA A:SER4029 4.5 157.5 1.0 CA A:ILE4010 4.5 160.1 1.0 CA A:ASN4011 4.5 153.2 1.0 CB A:ASP4009 4.5 169.2 1.0 C A:LYS4027 4.5 169.2 1.0 N A:LYS4027 4.6 167.5 1.0 CB A:ASN4025 4.7 152.9 1.0 CA A:LYS4027 4.7 168.3 1.0 CA A:ASN4025 4.8 152.4 1.0 C A:ASN4025 4.8 154.2 1.0 C A:ASP4009 4.8 169.0 1.0 CB A:GLU4012 4.8 154.5 1.0 C A:ASN4011 5.0 154.4 1.0 CB A:ILE4010 5.0 160.2 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structure of Rat Megalin Leg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Rat Megalin Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4702 b:119.7 occ:1.00 OD2 B:ASP58 2.2 129.2 1.0 OD1 B:ASP48 2.3 133.8 1.0 OD2 B:ASP52 2.3 123.8 1.0 OE2 B:GLU59 2.4 127.5 1.0 O B:THR50 2.4 122.9 1.0 O B:TRP45 2.4 135.2 1.0 CD B:GLU59 3.2 129.3 1.0 CG B:ASP48 3.3 133.2 1.0 CG B:ASP52 3.3 122.4 1.0 CG B:ASP58 3.4 130.3 1.0 C B:THR50 3.6 119.7 1.0 C B:TRP45 3.6 131.6 1.0 CB B:ASP52 3.7 121.5 1.0 CG B:GLU59 3.8 130.8 1.0 N B:ASP52 3.8 120.7 1.0 OG1 B:THR50 3.9 125.4 1.0 OD2 B:ASP48 4.0 130.3 1.0 CB B:ASP58 4.1 129.2 1.0 OE1 B:GLU59 4.1 130.4 1.0 N B:ASP48 4.2 134.2 1.0 N B:THR50 4.2 120.2 1.0 O B:ASP58 4.3 130.5 1.0 CB B:ASP48 4.3 133.3 1.0 OD1 B:ASP58 4.4 132.6 1.0 CA B:ASP52 4.4 120.3 1.0 OD1 B:ASP52 4.4 121.3 1.0 CA B:THR50 4.4 119.9 1.0 CA B:ARG46 4.4 131.3 1.0 N B:ARG46 4.5 129.6 1.0 N B:CYS47 4.5 136.0 1.0 CB B:TRP45 4.5 130.7 1.0 C B:ASP58 4.5 129.6 1.0 CA B:TRP45 4.5 130.4 1.0 N B:ARG51 4.6 105.2 1.0 CA B:ASP48 4.7 133.1 1.0 C B:ARG46 4.7 130.0 1.0 CA B:ARG51 4.7 106.5 1.0 C B:ARG51 4.7 111.4 1.0 N B:GLY49 4.8 119.8 1.0 CB B:THR50 4.8 122.0 1.0 C B:ASP48 5.0 132.3 1.0 N B:GLU59 5.0 127.2 1.0 CA B:ASP58 5.0 129.7 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structure of Rat Megalin Leg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Rat Megalin Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4703 b:235.2 occ:1.00 OD1 B:ASP88 2.4 214.4 1.0 O B:TRP85 2.4 205.8 1.0 OD2 B:ASP98 2.4 224.0 1.0 OD1 B:ASP92 2.4 215.2 1.0 OE2 B:GLU99 2.5 221.1 1.0 N B:CYS87 2.7 218.9 1.0 CA B:VAL86 2.9 210.5 1.0 N B:ASP88 3.0 214.7 1.0 CG B:ASP92 3.0 214.5 1.0 C B:VAL86 3.0 210.0 1.0 CG B:ASP88 3.1 213.6 1.0 C B:TRP85 3.3 205.9 1.0 OD2 B:ASP92 3.4 215.0 1.0 CG B:ASP98 3.5 223.3 1.0 N B:VAL86 3.6 211.4 1.0 CA B:CYS87 3.6 218.9 1.0 CD B:GLU99 3.7 219.9 1.0 C B:CYS87 3.8 219.0 1.0 O B:ASP90 3.8 205.0 1.0 OD2 B:ASP88 3.9 212.9 1.0 CB B:ASP88 3.9 213.4 1.0 CA B:ASP88 3.9 213.4 1.0 OD1 B:ASP98 3.9 222.4 1.0 O B:VAL86 4.0 208.9 1.0 CB B:ASP92 4.0 213.2 1.0 CB B:VAL86 4.1 209.4 1.0 CG2 B:VAL86 4.4 209.3 1.0 OE1 B:GLU99 4.4 219.9 1.0 N B:GLU89 4.4 213.5 1.0 C B:ASP88 4.5 214.1 1.0 CG B:GLU99 4.6 220.1 1.0 CB B:ASP98 4.7 223.7 1.0 CA B:TRP85 4.7 204.7 1.0 N B:ASP92 4.8 212.7 1.0 N B:ASP90 4.8 206.6 1.0 C B:ASP90 4.9 204.9 1.0 O B:CYS87 5.0 218.1 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structure of Rat Megalin Leg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of Rat Megalin Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4704 b:181.6 occ:1.00 OD2 B:ASP3785 2.2 163.5 1.0 OD2 B:ASP3781 2.3 187.1 1.0 OD1 B:ASP3791 2.3 160.0 1.0 O B:GLU3783 2.3 169.2 1.0 CG B:ASP3791 2.6 160.3 1.0 CG B:ASP3785 2.7 161.9 1.0 OD2 B:ASP3791 2.8 162.3 1.0 O B:TRP3778 2.8 193.4 1.0 CG B:ASP3781 3.1 187.6 1.0 OD1 B:ASP3785 3.2 161.6 1.0 OD1 B:ASP3781 3.4 187.3 1.0 CB B:ASP3785 3.5 160.0 1.0 C B:GLU3783 3.6 169.2 1.0 N B:ASP3785 3.7 158.5 1.0 N B:ASP3781 3.8 186.8 1.0 CB B:ASP3791 3.8 158.3 1.0 C B:TRP3778 3.9 193.0 1.0 N B:GLU3783 4.2 171.1 1.0 CA B:ASP3785 4.2 157.0 1.0 N B:CYS3780 4.2 186.3 1.0 CA B:TRP3778 4.3 194.1 1.0 CB B:ASP3781 4.3 187.6 1.0 CB B:TRP3778 4.4 194.4 1.0 CA B:GLU3783 4.4 170.5 1.0 CA B:CYS3780 4.5 186.7 1.0 C B:ASN3784 4.5 152.4 1.0 N B:ASN3784 4.5 151.7 1.0 CA B:ASP3781 4.5 187.3 1.0 CA B:ASN3784 4.5 150.8 1.0 C B:CYS3780 4.7 187.2 1.0 CG B:GLU3792 4.7 162.2 1.0 C B:ASP3781 4.8 187.7 1.0 N B:GLN3782 4.8 195.8 1.0 OE1 B:GLU3783 4.9 173.6 1.0 CB B:GLU3783 4.9 170.6 1.0 C B:VAL3779 5.0 177.3 1.0 N B:VAL3779 5.0 178.5 1.0

Calcium binding site 6 out of 6 in the Cryo-Em Structure of Rat Megalin Leg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of Rat Megalin Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4705 b:347.7 occ:1.00 OE2 B:GLU3831 2.3 342.8 1.0 OD2 B:ASP3824 2.3 319.8 1.0 OD2 B:ASP3830 2.4 328.6 1.0 OD1 B:ASP3820 2.4 349.3 1.0 O B:LEU3817 2.5 328.0 1.0 O B:ARG3822 2.8 342.6 1.0 OD2 B:ASP3820 2.8 349.1 1.0 CG B:ASP3820 2.9 349.0 1.0 C B:LEU3817 3.1 328.1 1.0 CG B:ASP3830 3.3 327.9 1.0 CG B:ASP3824 3.3 319.0 1.0 CD B:GLU3831 3.5 342.4 1.0 N B:ALA3818 3.7 336.6 1.0 CA B:ALA3818 3.7 336.5 1.0 CB B:ASP3830 3.7 327.4 1.0 CB B:ASP3824 3.8 318.7 1.0 N B:ASP3824 3.8 319.6 1.0 N B:CYS3819 4.0 349.4 1.0 C B:ARG3822 4.0 342.1 1.0 C B:ALA3818 4.1 336.8 1.0 CA B:LEU3817 4.1 327.9 1.0 OE1 B:GLU3831 4.2 342.8 1.0 N B:ASP3820 4.3 349.5 1.0 CB B:ASP3820 4.4 349.1 1.0 OD1 B:ASP3824 4.4 318.6 1.0 OD1 B:ASP3830 4.4 327.8 1.0 CG B:GLU3831 4.4 342.1 1.0 CA B:ASP3824 4.5 318.7 1.0 CB B:LEU3817 4.5 327.4 1.0 CG B:ARG3822 4.7 342.2 1.0 N B:ARG3822 4.8 342.5 1.0 CA B:ASP3820 4.9 349.2 1.0 C B:ALA3823 4.9 328.1 1.0 C B:ASP3830 4.9 328.3 1.0 CA B:ALA3823 4.9 328.0 1.0 N B:ALA3823 4.9 328.4 1.0 CA B:ASP3830 4.9 327.4 1.0 O B:ALA3818 4.9 336.6 1.0 CA B:ARG3822 5.0 342.2 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