Calcium in PDB 8jxj: Rat Megalin Rap Complex Leg

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

Calcium binding site 1 out of 8 in the Rat Megalin Rap Complex Leg


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4702 b:183.8 occ:1.00 OD1 A:ASP48 2.2 172.6 1.0 OD2 A:ASP58 2.2 167.5 1.0 O A:THR50 2.3 166.4 1.0 OD1 A:ASP52 2.3 160.2 1.0 O A:TRP45 2.5 159.8 1.0 OE2 A:GLU59 2.8 173.7 1.0 CG A:ASP48 3.0 170.4 1.0 CG A:ASP52 3.2 157.0 1.0 CG A:ASP58 3.3 165.5 1.0 OD2 A:ASP48 3.4 168.3 1.0 C A:THR50 3.4 160.8 1.0 C A:TRP45 3.6 157.3 1.0 N A:THR50 3.7 161.1 1.0 OD1 A:ASP58 3.7 164.0 1.0 CD A:GLU59 3.9 173.8 1.0 CB A:ASP52 3.9 155.9 1.0 CG2 A:THR50 3.9 160.0 1.0 N A:ASP52 4.0 156.8 1.0 CB A:TRP45 4.0 158.9 1.0 OD2 A:ASP52 4.0 155.5 1.0 CA A:THR50 4.0 158.2 1.0 CA A:TRP45 4.1 157.2 1.0 CB A:ASP48 4.3 169.3 1.0 CG A:GLU59 4.3 173.6 1.0 N A:GLY49 4.4 167.1 1.0 N A:ASP48 4.4 171.8 1.0 CB A:THR50 4.4 157.5 1.0 OG1 A:THR50 4.4 159.8 1.0 O A:ASP58 4.5 164.0 1.0 N A:ARG51 4.5 151.8 1.0 CA A:ASP52 4.6 153.2 1.0 CB A:ASP58 4.6 165.0 1.0 N A:ARG46 4.7 165.0 1.0 CA A:ASP48 4.7 171.2 1.0 C A:GLY49 4.8 167.4 1.0 OE1 A:GLU59 4.9 173.9 1.0 C A:ASP48 4.9 170.3 1.0 CA A:ARG51 4.9 153.4 1.0 C A:ARG51 4.9 156.9 1.0 CG A:TRP45 4.9 158.8 1.0 C A:ASP58 5.0 163.4 1.0

Calcium binding site 2 out of 8 in the Rat Megalin Rap Complex Leg


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4703 b:242.7 occ:1.00 O A:TRP85 2.3 238.4 1.0 OE1 A:GLU99 2.3 239.7 1.0 OE2 A:GLU99 2.4 239.6 1.0 O A:ASP90 2.5 232.4 1.0 CD A:GLU99 2.5 239.3 1.0 OD2 A:ASP92 2.9 233.9 1.0 N A:ASP88 3.2 235.5 1.0 C A:ASP90 3.4 231.3 1.0 N A:ASP90 3.4 232.7 1.0 C A:TRP85 3.5 239.5 1.0 CB A:ASP88 3.7 235.3 1.0 CG A:ASP92 3.7 234.4 1.0 CA A:ASP90 3.7 232.2 1.0 N A:CYS87 3.7 238.9 1.0 CB A:ASP90 3.7 233.1 1.0 NZ B:LYS4027 3.8 145.2 1.0 CA A:ASP88 3.8 235.3 1.0 CG A:GLU99 3.8 238.6 1.0 OD1 A:ASP92 3.9 234.9 1.0 N A:GLU89 4.0 229.1 1.0 C A:VAL86 4.1 238.6 1.0 C A:ASP88 4.1 236.1 1.0 CA A:VAL86 4.1 239.0 1.0 N A:VAL86 4.2 239.8 1.0 OD2 A:ASP98 4.3 242.3 1.0 C A:CYS87 4.3 239.5 1.0 CA A:CYS87 4.4 239.8 1.0 C A:GLU89 4.5 226.2 1.0 N A:LYS91 4.6 231.4 1.0 CA A:TRP85 4.6 238.9 1.0 CG A:ASP88 4.7 235.7 1.0 N A:ASP92 4.7 235.7 1.0 OD2 A:ASP88 4.7 236.2 1.0 O A:VAL86 4.8 238.8 1.0 CA A:GLU89 4.8 227.1 1.0 CG A:ASP90 4.8 231.9 1.0 O A:ASP88 4.9 235.5 1.0 CB A:ASP92 4.9 235.2 1.0 CE B:LYS4027 5.0 143.7 1.0

Calcium binding site 3 out of 8 in the Rat Megalin Rap Complex Leg


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4704 b:253.7 occ:1.00 OD2 A:ASP3954 2.3 241.9 1.0 OD1 A:ASP3950 2.3 246.9 1.0 O A:VAL3952 2.3 239.7 1.0 OD1 A:ASP3960 2.4 235.7 1.0 OE2 A:GLU3961 2.6 235.7 1.0 O A:TYR3947 2.6 241.1 1.0 CG A:ASP3960 2.9 234.6 1.0 CG A:ASP3950 3.3 245.7 1.0 CG A:ASP3954 3.4 241.4 1.0 OD2 A:ASP3960 3.4 232.7 1.0 CD A:GLU3961 3.5 233.9 1.0 C A:VAL3952 3.5 238.9 1.0 C A:TYR3947 3.6 241.4 1.0 OD2 A:ASP3950 3.6 244.4 1.0 CB A:ASP3960 3.8 234.8 1.0 OE1 A:GLU3961 3.9 233.5 1.0 CA A:TYR3947 3.9 241.8 1.0 CB A:TYR3947 3.9 241.3 1.0 N A:VAL3952 4.0 240.5 1.0 N A:ASP3954 4.0 242.5 1.0 CB A:ASP3954 4.1 241.6 1.0 CA A:VAL3952 4.2 239.3 1.0 N A:ASP3950 4.2 246.6 1.0 OD1 A:ASP3954 4.4 240.6 1.0 CB A:VAL3952 4.4 238.9 1.0 CG A:TYR3947 4.6 241.9 1.0 N A:ASN3953 4.6 234.3 1.0 CB A:ASP3950 4.6 245.3 1.0 CG A:GLU3961 4.6 233.4 1.0 N A:CYS3949 4.7 246.5 1.0 CA A:ASP3954 4.7 241.8 1.0 O A:ASP3960 4.7 234.5 1.0 C A:ASP3960 4.7 234.6 1.0 N A:ASN3951 4.7 245.0 1.0 CA A:ASP3950 4.8 245.8 1.0 N A:VAL3948 4.8 247.1 1.0 CA A:ASN3953 4.8 235.7 1.0 CA A:ASP3960 4.9 234.5 1.0 CD1 A:TYR3947 4.9 241.0 1.0 C A:ASP3950 4.9 245.7 1.0 C A:ASN3953 5.0 237.0 1.0

Calcium binding site 4 out of 8 in the Rat Megalin Rap Complex Leg


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4705 b:152.7 occ:1.00 OE1 A:GLU4012 2.3 150.7 1.0 OD1 A:ASN4025 2.4 141.0 1.0 O A:SER4026 2.5 143.7 1.0 O A:SER4029 2.5 147.8 1.0 OE2 A:GLU4012 2.6 154.2 1.0 CD A:GLU4012 2.8 152.8 1.0 OD1 A:ASP4009 2.9 164.5 1.0 O A:ILE4010 3.1 160.1 1.0 N A:SER4029 3.3 153.3 1.0 OD2 A:ASP4009 3.4 164.5 1.0 C A:SER4029 3.5 149.6 1.0 CG A:ASN4025 3.5 136.9 1.0 CG A:ASP4009 3.5 165.2 1.0 C A:SER4026 3.6 143.2 1.0 N A:SER4026 3.7 144.6 1.0 N A:GLY4028 3.8 158.6 1.0 CA A:SER4029 4.0 151.6 1.0 C A:GLY4028 4.0 159.1 1.0 C A:ILE4010 4.0 160.4 1.0 CA A:GLY4028 4.1 158.1 1.0 CG A:GLU4012 4.2 151.1 1.0 ND2 A:ASN4025 4.3 133.2 1.0 CA A:SER4026 4.3 144.1 1.0 C A:LYS4027 4.6 154.7 1.0 N A:GLU4012 4.6 149.8 1.0 N A:ILE4010 4.6 162.5 1.0 C A:ASN4025 4.6 138.4 1.0 N A:TYR4030 4.6 141.9 1.0 CA A:ASN4025 4.6 135.3 1.0 N A:LYS4027 4.6 151.7 1.0 CB A:ASN4025 4.6 135.9 1.0 CA A:ILE4010 4.7 160.8 1.0 CB A:GLU4012 4.8 145.8 1.0 CB A:ILE4010 4.8 154.7 1.0 OG A:SER4026 4.8 142.6 1.0 CA A:LYS4027 4.9 153.4 1.0 N A:ASN4011 4.9 145.6 1.0 O A:GLY4028 5.0 158.1 1.0 CA A:TYR4030 5.0 140.0 1.0 CA A:ASN4011 5.0 140.6 1.0

Calcium binding site 5 out of 8 in the Rat Megalin Rap Complex Leg


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4702 b:164.9 occ:1.00 OD2 B:ASP58 2.2 155.5 1.0 OD1 B:ASP48 2.2 160.6 1.0 OE2 B:GLU59 2.3 157.4 1.0 OD2 B:ASP52 2.3 154.8 1.0 O B:THR50 2.3 151.0 1.0 O B:TRP45 2.4 148.4 1.0 CG B:ASP52 3.2 153.2 1.0 CG B:ASP48 3.3 158.2 1.0 CG B:ASP58 3.3 155.8 1.0 CD B:GLU59 3.3 157.1 1.0 C B:THR50 3.4 148.7 1.0 N B:THR50 3.6 151.0 1.0 C B:TRP45 3.6 144.1 1.0 N B:ASP48 3.6 158.2 1.0 CG B:GLU59 3.7 159.1 1.0 OD1 B:ASP58 3.7 158.3 1.0 OD1 B:ASP52 3.9 151.1 1.0 OD2 B:ASP48 3.9 154.9 1.0 CA B:THR50 4.0 148.3 1.0 N B:CYS47 4.0 164.7 1.0 CB B:ASP52 4.1 152.2 1.0 N B:GLY49 4.2 156.6 1.0 CB B:ASP48 4.2 158.2 1.0 NZ A:LYS4337 4.3 113.8 1.0 O B:ASP58 4.3 156.8 1.0 CA B:ASP48 4.3 158.0 1.0 CB B:THR50 4.3 148.2 1.0 N B:ASP52 4.4 153.2 1.0 OE1 B:GLU59 4.4 156.4 1.0 C B:ARG46 4.4 157.8 1.0 CA B:ARG46 4.5 157.7 1.0 N B:ARG46 4.5 156.4 1.0 CA B:TRP45 4.5 140.7 1.0 N B:ARG51 4.6 140.6 1.0 C B:ASP48 4.6 157.4 1.0 C B:CYS47 4.6 162.8 1.0 CA B:CYS47 4.6 163.5 1.0 CB B:ASP58 4.6 154.4 1.0 CB B:TRP45 4.7 141.2 1.0 C B:GLY49 4.7 156.2 1.0 C B:ASP58 4.7 156.2 1.0 CA B:ASP52 4.9 150.8 1.0 CA B:ARG51 5.0 140.7 1.0

Calcium binding site 6 out of 8 in the Rat Megalin Rap Complex Leg


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4703 b:221.1 occ:1.00 OD2 B:ASP98 2.3 234.7 1.0 O B:TRP85 2.3 217.2 1.0 O B:ASP90 2.4 218.1 1.0 OD1 B:ASP88 2.5 225.6 1.0 OE2 B:GLU99 2.8 229.5 1.0 OD1 B:ASP92 2.9 229.2 1.0 CG B:ASP88 3.1 224.9 1.0 OD2 B:ASP88 3.2 224.6 1.0 C B:ASP90 3.4 217.4 1.0 CG B:ASP92 3.4 227.7 1.0 CG B:ASP98 3.5 234.9 1.0 C B:TRP85 3.5 217.5 1.0 CD B:GLU99 3.7 229.6 1.0 N B:ASP90 3.8 217.3 1.0 CB B:ASP90 3.8 219.1 1.0 CA B:ASP90 3.9 217.7 1.0 CB B:ASP92 4.0 227.0 1.0 CG B:GLU99 4.1 229.3 1.0 OD2 B:ASP92 4.1 226.6 1.0 CB B:ASP98 4.2 234.4 1.0 N B:ASP92 4.2 226.2 1.0 CA B:TRP85 4.3 217.4 1.0 N B:ASP88 4.3 225.4 1.0 CB B:TRP85 4.3 217.3 1.0 CB B:ASP88 4.4 224.0 1.0 OD1 B:ASP98 4.5 234.3 1.0 N B:VAL86 4.5 221.2 1.0 N B:LYS91 4.6 216.8 1.0 OE1 B:GLU99 4.7 230.0 1.0 CA B:ASP88 4.7 225.2 1.0 C B:ASP88 4.7 226.5 1.0 N B:GLU89 4.7 230.4 1.0 CA B:VAL86 4.7 221.3 1.0 CA B:ASP92 4.7 226.5 1.0 N B:CYS87 4.7 230.4 1.0 C B:VAL86 4.9 221.9 1.0 C B:GLU89 5.0 227.2 1.0

Calcium binding site 7 out of 8 in the Rat Megalin Rap Complex Leg


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4704 b:255.1 occ:1.00 OD1 B:ASP3950 2.1 238.0 1.0 OD2 B:ASP3960 2.2 246.6 1.0 O B:VAL3952 2.2 247.6 1.0 O B:TYR3947 2.2 231.4 1.0 OE1 B:GLU3961 2.4 241.4 1.0 OE2 B:GLU3961 2.4 240.5 1.0 OD2 B:ASP3954 2.4 237.5 1.0 CD B:GLU3961 2.7 240.6 1.0 CG B:ASP3960 3.2 245.2 1.0 CG B:ASP3950 3.2 237.2 1.0 C B:VAL3952 3.3 247.1 1.0 CG B:ASP3954 3.3 237.1 1.0 C B:TYR3947 3.4 231.3 1.0 CB B:ASP3960 3.6 244.9 1.0 OD2 B:ASP3950 3.6 236.9 1.0 N B:VAL3952 3.7 247.9 1.0 CB B:ASP3954 3.9 236.2 1.0 CA B:VAL3952 4.1 247.5 1.0 N B:ASP3954 4.2 236.7 1.0 CG B:GLU3961 4.2 238.8 1.0 OD1 B:ASP3960 4.2 244.3 1.0 CA B:TYR3947 4.3 229.9 1.0 OD1 B:ASP3954 4.3 237.0 1.0 N B:VAL3948 4.3 237.8 1.0 N B:ASN3953 4.3 235.1 1.0 N B:ASN3951 4.4 245.1 1.0 N B:ASP3950 4.4 237.2 1.0 CA B:VAL3948 4.4 235.8 1.0 C B:ASN3953 4.5 234.4 1.0 CB B:ASP3950 4.5 236.6 1.0 CA B:ASN3953 4.5 234.4 1.0 CB B:TYR3947 4.5 228.0 1.0 CB B:VAL3952 4.6 247.1 1.0 N B:CYS3949 4.6 241.2 1.0 C B:ASP3960 4.7 245.9 1.0 C B:ASP3950 4.7 238.4 1.0 O B:ASP3960 4.7 244.3 1.0 CA B:ASP3954 4.7 236.2 1.0 CA B:ASP3950 4.7 236.3 1.0 CA B:ASP3960 4.8 245.8 1.0 C B:VAL3948 4.8 235.1 1.0 C B:ASN3951 4.8 244.9 1.0 CB B:GLU3961 5.0 238.3 1.0

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


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 Leg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4705 b:162.4 occ:1.00 OD1 B:ASP4009 2.3 156.3 1.0 OE1 B:GLU4012 2.3 153.4 1.0 O B:SER4026 2.3 143.8 1.0 OE2 B:GLU4012 2.4 148.4 1.0 O B:ILE4010 2.5 147.8 1.0 O B:SER4029 2.6 151.3 1.0 CD B:GLU4012 2.6 150.5 1.0 OD1 B:ASN4025 2.9 151.4 1.0 CG B:ASP4009 3.0 158.9 1.0 OD2 B:ASP4009 3.0 159.8 1.0 N B:SER4029 3.2 149.2 1.0 N B:GLY4028 3.4 155.6 1.0 C B:SER4029 3.6 151.2 1.0 C B:SER4026 3.6 142.5 1.0 C B:ILE4010 3.6 147.2 1.0 C B:GLY4028 3.8 152.9 1.0 CA B:GLY4028 3.9 153.8 1.0 CA B:SER4029 3.9 151.2 1.0 CG B:ASN4025 4.1 150.1 1.0 N B:SER4026 4.1 144.3 1.0 CG B:GLU4012 4.1 147.7 1.0 N B:GLU4012 4.3 149.2 1.0 C B:LYS4027 4.3 148.3 1.0 N B:ILE4010 4.4 151.4 1.0 O B:GLY3996 4.4 171.0 1.0 CA B:SER4026 4.4 142.9 1.0 N B:ASN4011 4.5 143.6 1.0 CA B:ASN4011 4.5 146.0 1.0 CB B:ASP4009 4.5 159.7 1.0 N B:LYS4027 4.5 144.5 1.0 CA B:LYS4027 4.5 145.7 1.0 CA B:ILE4010 4.6 150.0 1.0 ND2 B:ASN4025 4.7 149.4 1.0 N B:TYR4030 4.7 143.5 1.0 O B:GLY4028 4.8 155.2 1.0 C B:ASN4011 4.9 148.8 1.0 CB B:GLU4012 4.9 144.4 1.0 C B:ASP4009 5.0 160.7 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