Calcium in PDB 8jxg: Rat Megalin Rap Complex Bodyb

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Calcium atom in the Rat Megalin Rap Complex Bodyb (pdb code 8jxg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 21 binding sites of Calcium where determined in the Rat Megalin Rap Complex Bodyb, PDB code: 8jxg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4707 b:139.7 occ:1.00 OD1 A:ASP1252 2.3 134.0 1.0 OD2 A:ASP1262 2.3 115.0 1.0 O A:TRP1249 2.3 121.2 1.0 OD2 A:ASP1256 2.4 118.3 1.0 OE2 A:GLU1263 2.4 126.4 1.0 OD2 A:ASP1252 2.4 135.3 1.0 O A:HIS1254 2.4 132.4 1.0 CG A:ASP1252 2.6 134.6 1.0 CD A:GLU1263 3.2 126.4 1.0 CG A:ASP1256 3.3 116.6 1.0 CG A:ASP1262 3.4 113.7 1.0 C A:TRP1249 3.5 120.7 1.0 CG A:GLU1263 3.5 125.6 1.0 C A:HIS1254 3.6 132.8 1.0 N A:ASP1256 4.0 116.3 1.0 OD1 A:ASP1256 4.0 116.6 1.0 CB A:ASP1252 4.0 134.7 1.0 CB A:ASP1262 4.1 111.9 1.0 N A:HIS1254 4.1 134.4 1.0 OE1 A:GLU1263 4.2 126.1 1.0 CB A:ASP1256 4.2 116.8 1.0 CA A:HIS1254 4.2 133.3 1.0 CA A:TRP1249 4.3 121.9 1.0 OD1 A:ASP1262 4.3 112.3 1.0 N A:ASP1252 4.4 132.8 1.0 CB A:HIS1254 4.5 133.6 1.0 N A:GLU1250 4.5 118.8 1.0 CB A:TRP1249 4.6 125.3 1.0 N A:PRO1255 4.6 128.3 1.0 CA A:GLU1250 4.7 118.6 1.0 CA A:ASP1252 4.7 134.4 1.0 CA A:PRO1255 4.7 128.4 1.0 CA A:ASP1256 4.7 117.0 1.0 N A:GLY1253 4.8 135.6 1.0 C A:PRO1255 4.8 126.5 1.0 N A:CYS1251 4.9 126.3 1.0 C A:GLU1250 4.9 118.7 1.0 CB A:GLU1263 4.9 123.8 1.0 C A:ASP1252 5.0 135.4 1.0 CG A:HIS1254 5.0 135.9 1.0

Calcium binding site 2 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4708 b:228.3 occ:1.00 O A:GLU2888 2.3 209.6 1.0 OD1 A:ASP2896 2.4 210.3 1.0 OD1 A:ASP2886 2.4 213.7 1.0 OE2 A:GLU2897 2.8 212.2 1.0 OD2 A:ASP2890 2.8 212.9 1.0 N A:CYS2885 2.8 214.0 1.0 O A:TRP2883 2.8 212.7 1.0 CA A:PHE2884 2.9 210.5 1.0 C A:PHE2884 3.0 211.0 1.0 N A:ASP2886 3.1 212.2 1.0 CG A:ASP2896 3.2 210.1 1.0 OD2 A:ASP2896 3.3 209.4 1.0 CG A:ASP2886 3.4 212.2 1.0 C A:GLU2888 3.5 209.8 1.0 C A:TRP2883 3.6 212.3 1.0 CA A:CYS2885 3.7 213.9 1.0 N A:PHE2884 3.7 210.3 1.0 CG A:ASP2890 3.9 211.8 1.0 N A:GLU2888 3.9 209.4 1.0 CD A:GLU2897 3.9 211.7 1.0 C A:CYS2885 3.9 212.6 1.0 O A:PHE2884 3.9 211.6 1.0 CB A:PHE2884 4.1 209.4 1.0 CA A:ASP2886 4.1 211.1 1.0 CB A:ASP2886 4.1 211.8 1.0 N A:GLY2887 4.1 212.5 1.0 OD2 A:ASP2886 4.3 210.4 1.0 CA A:GLU2888 4.4 209.6 1.0 N A:ASP2890 4.4 212.6 1.0 N A:ALA2889 4.5 211.9 1.0 OD1 A:ASP2890 4.6 211.1 1.0 C A:ASP2886 4.6 211.7 1.0 CA A:ALA2889 4.6 211.9 1.0 CB A:ASP2896 4.6 210.1 1.0 OE1 A:GLU2897 4.7 212.0 1.0 CG A:GLU2897 4.8 211.0 1.0 CB A:ASP2890 4.9 211.6 1.0 C A:ALA2889 4.9 212.2 1.0 C A:GLY2887 5.0 210.9 1.0

Calcium binding site 3 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4709 b:218.3 occ:1.00 O A:TRP2925 2.3 208.7 1.0 O A:ASP2930 2.3 209.5 1.0 OE2 A:GLU2939 2.3 210.3 1.0 OD1 A:ASP2928 2.3 211.1 1.0 OD2 A:ASP2932 2.6 210.0 1.0 OD2 A:ASP2938 2.8 209.4 1.0 N A:ASP2930 3.1 209.6 1.0 C A:ASP2930 3.3 208.6 1.0 CD A:GLU2939 3.3 209.8 1.0 C A:TRP2925 3.4 208.4 1.0 CG A:ASP2928 3.5 210.2 1.0 CG A:ASP2932 3.5 209.8 1.0 N A:GLY2929 3.6 208.9 1.0 CA A:ASP2930 3.7 208.4 1.0 CG A:ASP2938 3.8 209.3 1.0 C A:GLY2929 3.9 209.1 1.0 CB A:ASP2938 4.0 209.3 1.0 OD2 A:ASP2928 4.0 208.9 1.0 CA A:TRP2925 4.0 209.5 1.0 CB A:ASP2932 4.0 210.1 1.0 OE1 A:GLU2939 4.1 209.4 1.0 CA A:GLY2929 4.1 208.8 1.0 CB A:ASP2930 4.2 207.8 1.0 N A:ASP2928 4.2 208.9 1.0 N A:ASP2932 4.2 210.7 1.0 CG A:GLU2939 4.2 209.4 1.0 CB A:TRP2925 4.3 209.6 1.0 C A:ASP2928 4.4 209.4 1.0 N A:ASN2931 4.5 205.3 1.0 N A:VAL2926 4.5 207.1 1.0 OD1 A:ASP2932 4.5 209.4 1.0 N A:CYS2927 4.6 209.0 1.0 CB A:ASP2928 4.6 209.3 1.0 CA A:ASP2928 4.6 208.9 1.0 C A:VAL2926 4.7 208.4 1.0 CA A:VAL2926 4.8 208.0 1.0 C A:CYS2927 4.8 208.5 1.0 CA A:ASP2932 4.8 210.4 1.0 OD1 A:ASP2938 4.9 208.8 1.0 O A:GLY2929 5.0 208.6 1.0 CA A:ASN2931 5.0 205.3 1.0

Calcium binding site 4 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4710 b:176.9 occ:1.00 OD2 A:ASP2979 2.2 158.6 1.0 OD2 A:ASP2985 2.2 163.9 1.0 OE2 A:GLU2986 2.3 162.8 1.0 O A:ASP2977 2.3 168.9 1.0 OD1 A:ASP2975 2.3 164.8 1.0 CD A:GLU2986 2.6 162.2 1.0 O A:TRP2972 2.9 160.9 1.0 CG A:ASP2975 3.1 163.1 1.0 OE1 A:GLU2986 3.1 162.0 1.0 CG A:ASP2979 3.1 158.5 1.0 C A:ASP2977 3.2 167.5 1.0 OD2 A:ASP2975 3.3 163.8 1.0 CG A:GLU2986 3.5 161.1 1.0 CG A:ASP2985 3.5 164.4 1.0 CA A:ALA2978 3.6 159.0 1.0 N A:ASP2979 3.6 158.7 1.0 C A:ALA2978 3.8 160.0 1.0 N A:ALA2978 3.8 159.3 1.0 OD1 A:ASP2979 3.9 158.8 1.0 CB A:ASP2979 4.0 158.1 1.0 C A:TRP2972 4.1 159.6 1.0 OD1 A:ASP2985 4.3 165.0 1.0 N A:ASP2975 4.3 161.9 1.0 N A:ASP2977 4.4 167.2 1.0 CB A:ASP2975 4.4 161.8 1.0 CA A:ASP2979 4.4 158.3 1.0 CA A:ASP2977 4.4 167.2 1.0 CB A:ASP2985 4.5 163.8 1.0 O A:ALA2978 4.6 159.6 1.0 CA A:ASP2975 4.7 162.3 1.0 N A:CYS2974 4.8 159.3 1.0 CB A:TRP2972 4.8 160.4 1.0 C A:ASP2975 4.8 162.7 1.0 CB A:GLU2986 4.8 159.6 1.0 O A:ASP2975 4.8 162.6 1.0 OD2 A:ASP2977 4.8 166.8 1.0 CA A:TRP2972 4.9 159.4 1.0 N A:GLU2986 4.9 161.3 1.0 CB A:ALA2978 4.9 157.3 1.0 CG A:ASP2977 4.9 166.8 1.0

Calcium binding site 5 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4711 b:123.7 occ:1.00 OD2 A:ASP3019 2.2 128.6 1.0 OD2 A:ASP3025 2.3 119.5 1.0 OE2 A:GLU3026 2.3 118.3 1.0 OD1 A:ASP3015 2.3 121.5 1.0 O A:ARG3017 2.3 123.0 1.0 OD2 A:ASP3015 2.4 121.0 1.0 CG A:ASP3015 2.6 122.3 1.0 O A:PHE3012 3.0 123.2 1.0 CG A:ASP3019 3.3 129.5 1.0 CD A:GLU3026 3.4 116.8 1.0 C A:ARG3017 3.4 124.2 1.0 CG A:ASP3025 3.5 117.9 1.0 C A:PHE3012 3.9 123.5 1.0 CB A:ASP3019 4.0 127.3 1.0 CB A:ASP3015 4.0 121.5 1.0 N A:ASP3019 4.0 128.2 1.0 CG A:GLU3026 4.0 113.7 1.0 N A:ARG3017 4.1 125.4 1.0 CA A:ARG3017 4.2 125.6 1.0 OD1 A:ASP3019 4.2 129.0 1.0 CB A:ASP3025 4.2 116.8 1.0 N A:ASP3015 4.2 118.1 1.0 OE1 A:GLU3026 4.4 116.9 1.0 OD1 A:ASP3025 4.4 117.6 1.0 CB A:ARG3017 4.4 126.2 1.0 CA A:ASP3015 4.5 118.9 1.0 N A:ASN3018 4.5 122.4 1.0 C A:ASP3015 4.5 121.5 1.0 CA A:PHE3012 4.6 123.2 1.0 O A:ASP3015 4.6 119.7 1.0 CA A:ASP3019 4.7 126.8 1.0 CA A:ASN3018 4.7 123.4 1.0 N A:CYS3014 4.7 115.8 1.0 N A:ARG3013 4.7 120.6 1.0 CA A:ARG3013 4.8 116.7 1.0 CD1 A:PHE3012 4.8 124.7 1.0 CB A:PHE3012 4.8 123.4 1.0 C A:ASN3018 4.8 125.7 1.0 O A:ASP3025 4.8 118.9 1.0 C A:ARG3013 4.9 118.9 1.0 N A:ARG3016 5.0 128.7 1.0 C A:ASP3025 5.0 119.7 1.0

Calcium binding site 6 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4712 b:119.2 occ:1.00 OD1 A:ASP3054 2.2 121.1 1.0 OD2 A:ASP3064 2.2 118.8 1.0 O A:ASP3056 2.3 114.0 1.0 OD2 A:ASP3058 2.3 116.8 1.0 OE2 A:GLU3065 2.3 119.2 1.0 O A:PHE3051 2.5 118.4 1.0 CG A:ASP3058 3.2 118.0 1.0 CD A:GLU3065 3.3 119.2 1.0 CG A:ASP3054 3.3 120.6 1.0 C A:ASP3056 3.4 116.1 1.0 CG A:ASP3064 3.5 117.7 1.0 CG A:GLU3065 3.6 118.4 1.0 C A:PHE3051 3.7 116.6 1.0 N A:ASP3056 3.7 116.9 1.0 N A:ASP3054 3.8 119.5 1.0 OD1 A:ASP3058 3.9 118.1 1.0 OD2 A:ASP3054 3.9 119.0 1.0 CA A:ASP3056 4.0 117.6 1.0 N A:CYS3053 4.1 121.2 1.0 CB A:ASP3058 4.1 118.4 1.0 N A:ASP3058 4.2 117.3 1.0 CB A:ASP3056 4.3 117.7 1.0 OD1 A:ASP3064 4.3 116.5 1.0 O A:ASP3064 4.4 116.9 1.0 CB A:ASP3064 4.4 116.2 1.0 CB A:ASP3054 4.4 118.8 1.0 CA A:VAL3052 4.4 116.2 1.0 N A:GLU3055 4.4 117.8 1.0 CA A:ASP3054 4.4 118.3 1.0 OE1 A:GLU3065 4.4 116.3 1.0 C A:VAL3052 4.5 116.5 1.0 C A:ASP3054 4.5 117.1 1.0 N A:VAL3052 4.5 118.0 1.0 N A:ASN3057 4.5 109.9 1.0 CA A:PHE3051 4.7 114.7 1.0 CB A:PHE3051 4.7 112.1 1.0 C A:ASP3064 4.8 115.1 1.0 CA A:ASP3058 4.8 119.0 1.0 CA A:CYS3053 4.8 122.7 1.0 C A:CYS3053 4.8 122.2 1.0 C A:GLU3055 4.8 117.5 1.0 CA A:ASN3057 4.9 108.9 1.0

Calcium binding site 7 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4713 b:202.0 occ:1.00 O A:ARG3094 2.3 189.3 1.0 OD1 A:ASP3101 2.5 191.6 1.0 O A:VAL3099 2.5 190.5 1.0 OE2 A:GLU3108 2.6 194.8 1.0 OD1 A:ASN3097 2.7 188.2 1.0 OD2 A:ASP3101 2.7 190.9 1.0 CG A:ASP3101 2.9 190.7 1.0 OE1 A:GLU3108 3.0 195.0 1.0 CB A:ASP3107 3.1 190.2 1.0 CD A:GLU3108 3.1 195.0 1.0 OD2 A:ASP3107 3.5 189.2 1.0 C A:ARG3094 3.5 189.5 1.0 CG A:ASN3097 3.7 187.7 1.0 C A:VAL3099 3.7 189.3 1.0 CG A:ASP3107 3.8 189.9 1.0 N A:ASP3101 4.1 192.6 1.0 N A:CYS3096 4.1 188.9 1.0 CA A:VAL3095 4.2 186.2 1.0 N A:ASN3097 4.2 188.5 1.0 CB A:ASP3101 4.3 189.4 1.0 N A:VAL3095 4.3 187.8 1.0 N A:VAL3099 4.4 189.2 1.0 CA A:ASP3107 4.5 189.0 1.0 CA A:ARG3094 4.5 189.4 1.0 CB A:ARG3094 4.5 188.5 1.0 ND2 A:ASN3097 4.5 186.7 1.0 CA A:VAL3099 4.5 189.3 1.0 C A:VAL3095 4.5 186.3 1.0 C A:ASP3107 4.6 188.6 1.0 CB A:ASN3097 4.6 186.7 1.0 CG A:GLU3108 4.6 194.4 1.0 O A:ASP3107 4.7 188.6 1.0 N A:ASP3100 4.7 190.0 1.0 CB A:VAL3099 4.7 188.8 1.0 CA A:ASP3101 4.8 190.5 1.0 CA A:ASP3100 4.9 190.5 1.0 CA A:ASN3097 4.9 188.1 1.0 CA A:CYS3096 5.0 188.8 1.0 C A:ASP3100 5.0 190.9 1.0

Calcium binding site 8 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4714 b:101.1 occ:1.00 OE1 A:GLU3157 2.4 91.2 1.0 O A:ILE3155 2.4 98.2 1.0 O A:VAL3172 2.4 93.4 1.0 OD1 A:ASN3171 2.6 89.1 1.0 OE2 A:GLU3157 2.7 88.3 1.0 OD1 A:ASP3154 2.8 101.6 1.0 CD A:GLU3157 2.8 89.0 1.0 O A:GLY3174 3.0 95.9 1.0 O A:SER3175 3.1 76.0 1.0 OD2 A:ASP3154 3.5 101.9 1.0 CG A:ASP3154 3.5 103.2 1.0 C A:ILE3155 3.6 96.5 1.0 C A:VAL3172 3.6 90.9 1.0 C A:GLY3174 3.7 92.4 1.0 CG A:ASN3171 3.8 87.5 1.0 N A:GLY3174 3.9 88.9 1.0 C A:SER3175 4.0 78.4 1.0 N A:VAL3172 4.0 87.6 1.0 N A:ILE3155 4.3 96.7 1.0 CG A:GLU3157 4.3 88.0 1.0 CA A:GLY3174 4.3 91.8 1.0 N A:SER3175 4.4 77.6 1.0 CA A:ILE3155 4.4 93.8 1.0 CA A:VAL3172 4.4 87.3 1.0 N A:GLU3157 4.5 81.4 1.0 ND2 A:ASN3171 4.5 88.7 1.0 CA A:SER3175 4.6 77.2 1.0 N A:VAL3173 4.6 92.8 1.0 N A:ASP3156 4.6 97.0 1.0 O A:GLY3142 4.6 99.4 1.0 C A:VAL3173 4.6 88.2 1.0 CA A:VAL3173 4.7 91.1 1.0 CB A:ILE3155 4.7 97.3 1.0 CA A:ASP3156 4.7 97.0 1.0 N A:TYR3176 4.8 85.6 1.0 C A:ASN3171 4.9 87.5 1.0 CB A:ASN3171 4.9 85.2 1.0 CA A:ASN3171 4.9 85.6 1.0 CB A:ASP3154 5.0 106.2 1.0 CB A:TYR3176 5.0 77.0 1.0

Calcium binding site 9 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4715 b:67.0 occ:1.00 O A:ALA3291 2.3 67.1 1.0 O A:GLU3323 2.3 47.1 1.0 OD1 A:ASP3294 2.5 63.2 1.0 CG A:ASP3294 3.5 66.2 1.0 C A:GLU3323 3.5 48.5 1.0 C A:ALA3291 3.6 58.8 1.0 OD2 A:ASP3294 3.8 60.8 1.0 CD2 A:HIS3324 4.0 48.5 1.0 CA A:GLU3323 4.2 38.8 1.0 CA A:ILE3292 4.4 56.1 1.0 N A:ILE3292 4.4 59.8 1.0 CA A:ALA3291 4.5 52.4 1.0 N A:HIS3324 4.5 49.8 1.0 O A:ILE3292 4.5 66.4 1.0 NE2 A:HIS3324 4.5 48.0 1.0 C A:ILE3292 4.7 55.2 1.0 CB A:ALA3291 4.8 44.5 1.0 CA A:HIS3324 4.8 38.1 1.0 CB A:ASP3294 4.8 62.1 1.0 CG A:GLU3323 4.9 56.5 1.0 CG A:HIS3324 4.9 48.5 1.0 CD A:PRO3325 5.0 33.2 1.0

Calcium binding site 10 out of 21 in the Rat Megalin Rap Complex Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4716 b:56.9 occ:1.00 OE1 A:GLU3367 2.4 57.8 1.0 O A:VAL3344 2.5 62.4 1.0 CD A:GLU3367 3.4 58.1 1.0 C A:VAL3344 3.6 56.6 1.0 OE2 A:GLU3367 3.7 68.8 1.0 CA A:VAL3344 4.2 54.8 1.0 O A:GLY3343 4.2 50.9 1.0 OE1 A:GLU3685 4.3 75.9 1.0 OG1 A:THR3684 4.4 72.2 1.0 N A:HIS3345 4.7 50.0 1.0 N A:ALA3346 4.7 48.1 1.0 CG A:GLU3367 4.7 47.2 1.0 CG1 A:VAL3344 4.8 57.0 1.0 O A:ILE3366 4.8 52.5 1.0 CA A:GLU3367 4.9 42.7 1.0 CA A:HIS3345 5.0 47.7 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