Calcium in PDB 8jxe: Rat Megalin Rap Complex Head

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

Nickel

(Ni)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Rat Megalin Rap Complex Head (pdb code 8jxe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Rat Megalin Rap Complex Head, PDB code: 8jxe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4706 b:221.8 occ:1.00 O A:VAL1336 2.3 216.6 1.0 O A:ALA1331 2.3 215.9 1.0 OE2 A:GLU1345 2.3 214.4 1.0 OD1 A:ASP1334 2.4 217.7 1.0 OD2 A:ASP1344 2.5 217.5 1.0 OD2 A:ASP1338 2.6 215.8 1.0 CD A:GLU1345 3.4 213.9 1.0 CG A:ASP1334 3.4 216.3 1.0 C A:VAL1336 3.5 216.2 1.0 C A:ALA1331 3.5 215.1 1.0 CG A:ASP1338 3.5 215.9 1.0 N A:CYS1333 3.7 216.1 1.0 CG A:ASP1344 3.7 217.2 1.0 CG A:GLU1345 3.7 213.7 1.0 N A:ASP1338 3.8 216.3 1.0 N A:ASP1334 3.8 216.9 1.0 N A:VAL1336 4.0 216.1 1.0 C A:LEU1332 4.1 214.2 1.0 OD2 A:ASP1334 4.1 215.0 1.0 CA A:LEU1332 4.1 214.0 1.0 CB A:ASP1338 4.1 216.2 1.0 N A:LEU1332 4.2 213.8 1.0 N A:GLY1335 4.3 215.8 1.0 CA A:VAL1336 4.3 215.7 1.0 OD1 A:ASP1338 4.3 215.5 1.0 N A:PHE1337 4.4 213.9 1.0 CA A:PHE1337 4.4 213.8 1.0 CG2 A:VAL1336 4.4 215.1 1.0 CB A:ASP1334 4.4 215.9 1.0 OE1 A:GLU1345 4.5 214.0 1.0 CA A:CYS1333 4.5 215.8 1.0 C A:CYS1333 4.5 216.0 1.0 CA A:ALA1331 4.5 214.9 1.0 OD1 A:ASP1344 4.6 217.2 1.0 CA A:ASP1334 4.6 216.1 1.0 C A:PHE1337 4.6 213.6 1.0 CB A:ASP1344 4.6 217.1 1.0 CA A:ASP1338 4.6 216.2 1.0 O A:ASP1344 4.8 217.3 1.0 C A:GLY1335 4.8 215.7 1.0 C A:ASP1334 4.9 215.7 1.0 O A:LEU1332 4.9 213.9 1.0 CB A:ALA1331 4.9 214.2 1.0 CB A:VAL1336 5.0 215.0 1.0

Calcium binding site 2 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4707 b:112.5 occ:1.00 OD1 A:ASP1391 2.3 121.2 1.0 OE2 A:GLU1394 2.3 105.4 1.0 ND2 A:ASN1407 2.4 108.2 1.0 OD2 A:ASP1391 2.4 120.8 1.0 OE1 A:GLU1394 2.5 109.0 1.0 O A:ILE1392 2.6 115.2 1.0 CG A:ASP1391 2.7 120.0 1.0 CD A:GLU1394 2.7 106.5 1.0 O A:MET1408 2.8 116.4 1.0 O A:SER1411 3.2 104.6 1.0 CG A:ASN1407 3.5 107.9 1.0 C A:ILE1392 3.8 114.5 1.0 N A:SER1411 3.8 109.2 1.0 C A:MET1408 3.9 115.2 1.0 OD1 A:ASN1407 4.0 108.4 1.0 C A:SER1411 4.0 106.3 1.0 N A:MET1408 4.1 115.4 1.0 CG A:GLU1394 4.2 104.6 1.0 CB A:ASP1391 4.2 119.2 1.0 C A:GLY1410 4.3 111.0 1.0 O A:ARG1409 4.3 119.3 1.0 CA A:SER1411 4.3 108.4 1.0 N A:ILE1392 4.4 114.3 1.0 C A:ARG1409 4.4 117.7 1.0 N A:GLY1410 4.4 110.7 1.0 CA A:GLY1410 4.5 111.6 1.0 N A:GLU1394 4.5 106.8 1.0 CB A:ASN1407 4.6 106.3 1.0 CA A:MET1408 4.6 113.9 1.0 CA A:ILE1392 4.7 113.8 1.0 N A:ASN1393 4.7 109.1 1.0 O A:GLY1379 4.7 129.7 1.0 CA A:ASN1393 4.7 107.3 1.0 N A:ARG1409 4.9 119.4 1.0 CA A:ASN1407 4.9 108.0 1.0 C A:ASN1407 4.9 110.5 1.0 C A:ASP1391 4.9 120.7 1.0 O A:GLY1410 5.0 109.1 1.0

Calcium binding site 3 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4708 b:43.0 occ:1.00 O A:ASP2254 2.3 54.4 1.0 OD1 B:ASN2001 2.3 61.3 1.0 OD1 A:ASP2257 2.4 52.0 1.0 O A:PRO2279 2.6 46.8 1.0 C A:ASP2254 3.5 48.6 1.0 CG B:ASN2001 3.5 54.2 1.0 CG A:ASP2257 3.6 51.1 1.0 C A:PRO2279 3.6 34.4 1.0 OE1 B:GLU1982 4.0 53.6 1.0 CA A:PRO2279 4.1 29.0 1.0 OD2 A:ASP2257 4.1 50.5 1.0 CA A:ASP2254 4.3 38.8 1.0 CB A:ASP2254 4.4 41.9 1.0 CB B:ASN2001 4.4 43.7 1.0 ND2 B:ASN2001 4.4 54.5 1.0 N A:SER2255 4.4 42.7 1.0 CG2 A:THR2280 4.5 45.9 1.0 CA A:SER2255 4.6 39.0 1.0 CA B:ASN2001 4.6 42.4 1.0 CB A:PRO2279 4.7 34.9 1.0 N A:THR2280 4.7 28.8 1.0 O A:SER2255 4.7 53.2 1.0 C A:SER2255 4.7 43.5 1.0 N A:ASP2257 4.8 39.3 1.0 CB A:ASP2257 4.8 47.1 1.0 CA A:THR2280 5.0 38.6 1.0 CA A:ASP2257 5.0 37.4 1.0

Calcium binding site 4 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4709 b:187.0 occ:1.00 OD1 A:ASP2721 2.2 183.4 1.0 OD2 A:ASP2731 2.3 174.4 1.0 OD2 A:ASP2725 2.3 175.3 1.0 O A:ASP2723 2.3 184.5 1.0 O A:TRP2718 2.4 172.3 1.0 OE2 A:GLU2732 2.5 174.8 1.0 CG A:ASP2725 3.2 175.3 1.0 CG A:ASP2721 3.2 183.5 1.0 CG A:ASP2731 3.4 173.7 1.0 C A:ASP2723 3.5 184.1 1.0 CD A:GLU2732 3.5 174.0 1.0 C A:TRP2718 3.6 170.5 1.0 OD2 A:ASP2721 3.6 183.3 1.0 CB A:ASP2725 3.8 175.1 1.0 N A:ASP2725 3.8 176.5 1.0 OD1 A:ASP2731 3.9 173.1 1.0 CG A:GLU2732 3.9 174.4 1.0 OD1 A:ASP2725 4.0 175.1 1.0 N A:ASP2723 4.0 184.0 1.0 CA A:ASP2723 4.1 184.2 1.0 CB A:ASP2723 4.1 185.2 1.0 N A:ASP2721 4.1 184.6 1.0 CB A:TRP2718 4.3 170.0 1.0 CA A:TRP2718 4.4 170.0 1.0 N A:CYS2720 4.4 178.6 1.0 CB A:ASP2721 4.4 183.2 1.0 N A:LYS2719 4.5 169.6 1.0 CA A:LYS2719 4.5 169.0 1.0 CA A:ASP2725 4.5 175.4 1.0 C A:LYS2719 4.6 170.5 1.0 N A:ASN2724 4.6 178.1 1.0 OE1 A:GLU2732 4.6 174.1 1.0 CB A:ASP2731 4.6 173.8 1.0 CA A:ASP2721 4.7 184.6 1.0 C A:ASP2721 4.8 184.9 1.0 O A:ASP2731 4.8 174.4 1.0 CA A:ASN2724 4.8 178.7 1.0 C A:ASN2724 4.8 178.9 1.0 N A:ASN2722 4.9 188.7 1.0 CD1 A:ILE2714 5.0 164.0 1.0

Calcium binding site 5 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4710 b:211.1 occ:1.00 OD2 A:ASP2772 2.2 205.2 1.0 OD1 A:ASP2762 2.3 200.6 1.0 O A:TYR2764 2.3 203.2 1.0 OD1 A:ASP2766 2.3 203.2 1.0 O A:TYR2759 2.8 195.7 1.0 N A:ASP2766 3.0 203.4 1.0 CA A:ASN2765 3.0 203.4 1.0 C A:TYR2764 3.2 203.0 1.0 CG A:ASP2772 3.3 204.7 1.0 CG A:ASP2762 3.4 200.6 1.0 CG A:ASP2766 3.4 202.9 1.0 C A:ASN2765 3.4 203.7 1.0 OE2 A:GLU2773 3.4 205.4 1.0 N A:ASN2765 3.5 203.2 1.0 OD2 A:ASP2762 3.8 200.3 1.0 C A:TYR2759 3.8 195.1 1.0 CD A:GLU2773 4.0 205.1 1.0 CB A:ASP2772 4.0 204.3 1.0 OD2 A:ASP2766 4.1 203.0 1.0 OE1 A:GLU2773 4.1 204.5 1.0 CA A:ASP2766 4.1 202.4 1.0 OD1 A:ASP2772 4.2 204.6 1.0 ND2 A:ASN2765 4.2 202.6 1.0 CB A:ASN2765 4.3 202.9 1.0 CB A:ASP2766 4.3 202.2 1.0 CA A:TYR2764 4.5 202.9 1.0 O A:ASN2765 4.5 203.1 1.0 CA A:TYR2759 4.5 195.7 1.0 N A:ASP2762 4.6 201.3 1.0 CB A:ASP2762 4.6 201.0 1.0 N A:TYR2764 4.7 203.6 1.0 N A:CYS2767 4.7 201.5 1.0 N A:ARG2760 4.7 196.6 1.0 C A:ASP2766 4.7 202.2 1.0 CG A:ASN2765 4.7 202.6 1.0 CB A:TYR2759 4.8 195.5 1.0 N A:CYS2761 4.8 204.9 1.0 CA A:ARG2760 4.8 197.1 1.0

Calcium binding site 6 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4711 b:56.9 occ:1.00 O A:HIS1644 2.4 60.2 1.0 O A:ALA1618 2.6 46.2 1.0 OD1 A:ASP1621 2.7 48.4 1.0 OD2 A:ASP1621 3.3 52.7 1.0 CG A:ASP1621 3.4 47.6 1.0 C A:HIS1644 3.6 48.7 1.0 C A:ALA1618 3.8 41.2 1.0 OH B:TYR2168 4.2 68.3 1.0 CZ B:TYR2168 4.2 62.6 1.0 O A:TYR1619 4.3 44.8 1.0 CE1 B:TYR2168 4.4 57.0 1.0 CA A:TYR1619 4.4 33.3 1.0 ND1 A:HIS1645 4.4 40.8 1.0 CA A:HIS1644 4.5 41.8 1.0 N A:HIS1645 4.5 39.5 1.0 CA A:HIS1645 4.5 38.7 1.0 N A:TYR1619 4.5 38.9 1.0 CE2 B:TYR2168 4.6 60.2 1.0 C A:TYR1619 4.6 36.1 1.0 ND1 A:HIS1644 4.7 53.1 1.0 CA A:ALA1618 4.8 29.9 1.0 CB A:HIS1645 4.8 37.7 1.0 CB A:ASP1621 4.9 42.3 1.0

Calcium binding site 7 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4706 b:222.9 occ:1.00 OD1 B:ASP1334 2.2 215.3 1.0 OD2 B:ASP1344 2.2 217.6 1.0 O B:ALA1331 2.3 210.9 1.0 O B:VAL1336 2.3 216.6 1.0 OE2 B:GLU1345 2.4 217.0 1.0 OD2 B:ASP1338 2.5 218.0 1.0 CG B:ASP1344 3.2 217.4 1.0 CG B:ASP1334 3.2 214.2 1.0 C B:ALA1331 3.3 210.3 1.0 CD B:GLU1345 3.4 215.7 1.0 CB B:ASP1344 3.4 216.7 1.0 C B:VAL1336 3.4 216.0 1.0 CG B:ASP1338 3.6 217.7 1.0 CG B:GLU1345 3.7 215.7 1.0 OD2 B:ASP1334 3.7 213.6 1.0 N B:ASP1334 3.8 214.9 1.0 CA B:ALA1331 3.9 209.6 1.0 N B:VAL1336 3.9 216.3 1.0 CB B:ALA1331 4.0 209.1 1.0 CB B:ASP1334 4.2 214.1 1.0 N B:CYS1333 4.2 212.6 1.0 CA B:VAL1336 4.2 215.7 1.0 N B:GLU1345 4.2 216.6 1.0 N B:ASP1338 4.3 218.7 1.0 OD1 B:ASP1344 4.3 217.9 1.0 N B:GLY1335 4.3 215.7 1.0 C B:ASP1344 4.3 216.6 1.0 CB B:ASP1338 4.3 217.9 1.0 CA B:ASP1334 4.4 214.3 1.0 N B:PHE1337 4.4 215.9 1.0 N B:LEU1332 4.5 206.9 1.0 CA B:ASP1344 4.5 216.7 1.0 OE1 B:GLU1345 4.5 214.6 1.0 OD1 B:ASP1338 4.5 217.4 1.0 CA B:PHE1337 4.6 215.7 1.0 C B:ASP1334 4.7 214.4 1.0 C B:CYS1333 4.7 212.5 1.0 C B:LEU1332 4.7 206.4 1.0 C B:PHE1337 4.7 216.0 1.0 O B:ASP1344 4.7 216.0 1.0 CA B:CYS1333 4.8 212.8 1.0 CA B:LEU1332 4.9 206.2 1.0 CB B:VAL1336 4.9 215.2 1.0 CB B:GLU1345 4.9 215.3 1.0 C B:GLY1335 4.9 215.6 1.0 CA B:GLU1345 4.9 216.0 1.0 CA B:ASP1338 4.9 218.5 1.0

Calcium binding site 8 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4707 b:113.8 occ:1.00 OD1 B:ASP1391 2.5 128.0 1.0 OD1 B:ASN1407 2.6 108.3 1.0 O B:SER1411 2.6 108.0 1.0 OE2 B:GLU1394 2.7 110.0 1.0 OE1 B:GLU1394 2.8 112.7 1.0 OD2 B:ASP1391 2.9 125.3 1.0 O B:ILE1392 2.9 117.6 1.0 CG B:ASP1391 3.0 125.8 1.0 O B:MET1408 3.0 114.5 1.0 N B:SER1411 3.1 108.8 1.0 CD B:GLU1394 3.1 110.6 1.0 C B:SER1411 3.4 108.4 1.0 C B:GLY1410 3.5 114.0 1.0 CA B:SER1411 3.6 108.0 1.0 CG B:ASN1407 3.7 107.4 1.0 C B:MET1408 3.8 113.7 1.0 CA B:GLY1410 3.9 112.9 1.0 N B:GLY1410 4.0 112.0 1.0 N B:MET1408 4.0 115.3 1.0 C B:ILE1392 4.1 118.1 1.0 C B:ARG1409 4.2 119.6 1.0 O B:GLY1410 4.2 115.2 1.0 ND2 B:ASN1407 4.3 107.2 1.0 O B:ARG1409 4.4 120.9 1.0 CA B:MET1408 4.5 113.1 1.0 CB B:ASP1391 4.5 123.7 1.0 N B:PHE1412 4.6 103.1 1.0 CG B:GLU1394 4.6 108.4 1.0 N B:ILE1392 4.6 119.3 1.0 O B:GLY1379 4.7 134.5 1.0 N B:ARG1409 4.7 119.0 1.0 CA B:ILE1392 4.9 117.7 1.0 C B:ASN1407 4.9 110.3 1.0 N B:GLU1394 4.9 108.8 1.0 CB B:ASN1407 5.0 107.3 1.0 CB B:MET1408 5.0 114.1 1.0 CA B:ASN1407 5.0 108.4 1.0 CA B:ARG1409 5.0 119.1 1.0

Calcium binding site 9 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4708 b:51.3 occ:1.00 O B:ASP2254 2.3 49.2 1.0 ND2 A:ASN2001 2.4 58.4 1.0 OD1 B:ASP2257 2.5 58.5 1.0 O B:PRO2279 2.5 46.4 1.0 CG B:ASP2257 3.4 54.8 1.0 C B:PRO2279 3.5 38.1 1.0 C B:ASP2254 3.5 51.3 1.0 OD2 B:ASP2257 3.7 53.0 1.0 CG A:ASN2001 3.7 51.2 1.0 OE1 A:GLU1982 3.9 56.9 1.0 CA B:PRO2279 4.1 31.1 1.0 CG2 B:THR2280 4.2 43.6 1.0 CA B:ASP2254 4.4 45.0 1.0 OD1 A:ASN2001 4.4 47.5 1.0 N B:SER2255 4.5 45.1 1.0 CA B:SER2255 4.5 39.8 1.0 N B:THR2280 4.6 35.8 1.0 CB A:ASN2001 4.6 46.8 1.0 CB B:ASP2254 4.7 46.3 1.0 C B:SER2255 4.8 45.5 1.0 CB B:PRO2279 4.8 37.9 1.0 CB B:ASP2257 4.8 47.4 1.0 CA B:THR2280 4.8 39.7 1.0 CA A:ASN2001 4.8 42.8 1.0 O B:SER2255 4.9 55.5 1.0 CG B:ASP2254 4.9 59.2 1.0 N B:ASP2257 5.0 49.9 1.0

Calcium binding site 10 out of 12 in the Rat Megalin Rap Complex Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Rat Megalin Rap Complex Head within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4709 b:185.2 occ:1.00 OD1 B:ASP2721 2.1 179.4 1.0 OD2 B:ASP2731 2.2 175.4 1.0 O B:ASP2723 2.2 179.2 1.0 OD2 B:ASP2725 2.3 176.5 1.0 O B:TRP2718 2.3 175.2 1.0 OE2 B:GLU2732 2.6 175.1 1.0 CG B:ASP2721 3.2 179.2 1.0 C B:ASP2723 3.2 178.4 1.0 CG B:ASP2725 3.3 176.2 1.0 CG B:ASP2731 3.4 174.3 1.0 C B:TRP2718 3.4 175.0 1.0 N B:ASP2723 3.5 179.2 1.0 CD B:GLU2732 3.5 174.1 1.0 OD2 B:ASP2721 3.6 179.1 1.0 CA B:ASP2723 3.6 178.9 1.0 CB B:ASP2723 3.7 179.0 1.0 CB B:ASP2725 3.8 176.0 1.0 N B:ASP2725 4.0 176.4 1.0 CG B:GLU2732 4.0 173.8 1.0 CA B:TRP2718 4.1 174.5 1.0 N B:ASP2721 4.2 180.2 1.0 OD1 B:ASP2725 4.2 175.7 1.0 CB B:ASP2731 4.3 173.7 1.0 OD1 B:ASP2731 4.3 174.0 1.0 CB B:TRP2718 4.4 174.3 1.0 N B:ASN2724 4.4 173.5 1.0 CB B:ASP2721 4.4 179.2 1.0 N B:ASN2722 4.4 182.7 1.0 N B:LYS2719 4.5 174.6 1.0 CA B:ASP2725 4.6 176.5 1.0 C B:ASP2721 4.6 180.2 1.0 OE1 B:GLU2732 4.6 173.5 1.0 N B:CYS2720 4.6 178.0 1.0 CA B:ASP2721 4.6 179.9 1.0 C B:ASN2722 4.7 181.9 1.0 CA B:LYS2719 4.7 173.5 1.0 C B:LYS2719 4.8 173.3 1.0 CA B:ASN2724 4.9 173.8 1.0 C B:ASN2724 5.0 174.2 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