Calcium in PDB 8jxa: Cryo-Em Structure of Rat Megalin Bodyb

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

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Rat Megalin Bodyb (pdb code 8jxa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Cryo-Em Structure of Rat Megalin Bodyb, PDB code: 8jxa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4708 b:112.5 occ:1.00 O A:TRP1249 2.3 88.3 1.0 OD1 A:ASP1252 2.3 115.8 1.0 OD2 A:ASP1262 2.3 108.6 1.0 O A:HIS1254 2.3 106.7 1.0 OD2 A:ASP1256 2.3 105.4 1.0 OE2 A:GLU1263 2.3 117.1 1.0 CG A:ASP1252 3.2 115.9 1.0 CG A:ASP1262 3.4 108.7 1.0 C A:TRP1249 3.5 88.0 1.0 CG A:ASP1256 3.5 105.2 1.0 C A:HIS1254 3.5 106.6 1.0 CD A:GLU1263 3.5 117.3 1.0 OD2 A:ASP1252 3.9 115.8 1.0 N A:ASP1252 3.9 115.6 1.0 CB A:ASP1262 3.9 108.5 1.0 N A:ASP1256 4.0 105.3 1.0 N A:HIS1254 4.0 106.8 1.0 CG A:GLU1263 4.0 117.4 1.0 O A:ASP1262 4.1 109.1 1.0 CB A:ASP1252 4.2 115.8 1.0 CB A:ASP1256 4.2 105.0 1.0 CA A:HIS1254 4.2 106.5 1.0 N A:CYS1251 4.2 115.1 1.0 N A:GLU1250 4.3 98.4 1.0 CA A:GLU1250 4.3 98.9 1.0 CA A:TRP1249 4.4 87.6 1.0 OD1 A:ASP1256 4.4 105.2 1.0 CB A:TRP1249 4.4 87.4 1.0 CB A:HIS1254 4.4 106.5 1.0 OD1 A:ASP1262 4.5 108.7 1.0 C A:GLU1250 4.5 99.6 1.0 CA A:ASP1252 4.5 115.8 1.0 N A:PRO1255 4.5 107.3 1.0 OE1 A:GLU1263 4.5 117.6 1.0 C A:ASP1262 4.5 108.9 1.0 CA A:PRO1255 4.7 107.4 1.0 CA A:ASP1256 4.7 105.2 1.0 N A:GLY1253 4.8 114.5 1.0 C A:ASP1252 4.8 115.9 1.0 C A:PRO1255 4.8 107.4 1.0 CA A:ASP1262 4.9 108.5 1.0 C A:CYS1251 4.9 115.4 1.0 CA A:CYS1251 5.0 115.5 1.0

Calcium binding site 2 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4709 b:375.4 occ:1.00 OD2 A:ASP2938 2.3 367.9 1.0 O A:TRP2925 2.3 377.2 1.0 OD1 A:ASP2928 2.3 372.2 1.0 OE2 A:GLU2939 2.4 368.1 1.0 OD2 A:ASP2932 2.7 355.4 1.0 O A:ASP2930 2.8 362.6 1.0 CG A:ASP2928 3.3 372.2 1.0 C A:TRP2925 3.4 377.3 1.0 CG A:ASP2938 3.4 367.9 1.0 N A:CYS2927 3.4 375.6 1.0 N A:ASP2928 3.5 372.3 1.0 CD A:GLU2939 3.5 368.1 1.0 CA A:VAL2926 3.7 378.3 1.0 C A:VAL2926 3.8 378.3 1.0 CG A:ASP2932 3.8 355.3 1.0 OD2 A:ASP2928 3.9 372.2 1.0 N A:VAL2926 4.0 378.3 1.0 C A:ASP2930 4.1 362.5 1.0 CB A:ASP2938 4.1 367.9 1.0 CG A:GLU2939 4.1 368.0 1.0 CB A:ASP2928 4.2 372.2 1.0 CA A:CYS2927 4.3 375.6 1.0 CA A:ASP2928 4.4 372.2 1.0 CB A:ASP2932 4.4 355.2 1.0 N A:ASP2932 4.4 355.2 1.0 OD1 A:ASP2938 4.4 367.8 1.0 C A:CYS2927 4.4 375.6 1.0 N A:ASP2930 4.5 362.6 1.0 CB A:TRP2925 4.5 377.2 1.0 OE1 A:GLU2939 4.6 368.1 1.0 CA A:TRP2925 4.6 377.2 1.0 O A:VAL2926 4.6 378.3 1.0 N A:GLY2929 4.7 366.3 1.0 OD1 A:ASP2932 4.8 355.2 1.0 CA A:ASP2930 4.8 362.5 1.0 C A:ASP2938 4.9 367.9 1.0 C A:ASP2928 4.9 372.1 1.0 O A:ASP2938 4.9 368.0 1.0

Calcium binding site 3 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4710 b:306.4 occ:1.00 OE2 A:GLU2986 2.3 305.1 1.0 O A:TRP2972 2.3 313.0 1.0 N A:CYS2974 2.5 319.2 1.0 OD1 A:ASP2975 2.7 304.0 1.0 C A:VAL2973 2.9 311.9 1.0 CA A:VAL2973 2.9 311.9 1.0 OD2 A:ASP2979 3.1 286.5 1.0 N A:ASP2975 3.2 304.1 1.0 C A:TRP2972 3.3 313.0 1.0 OD2 A:ASP2985 3.3 306.9 1.0 CA A:CYS2974 3.5 319.3 1.0 CD A:GLU2986 3.5 305.0 1.0 N A:VAL2973 3.5 311.9 1.0 CG A:ASP2985 3.7 307.0 1.0 CG A:ASP2975 3.7 303.9 1.0 O A:ASP2977 3.7 300.1 1.0 C A:CYS2974 3.7 319.2 1.0 O A:VAL2973 3.9 311.9 1.0 OD1 A:ASP2985 4.0 307.0 1.0 CG A:GLU2986 4.2 304.9 1.0 CA A:ASP2975 4.2 304.0 1.0 CB A:VAL2973 4.3 311.9 1.0 CG A:ASP2979 4.3 286.3 1.0 CB A:ASP2975 4.3 304.0 1.0 N A:GLY2976 4.3 300.3 1.0 OE1 A:GLU2986 4.4 305.1 1.0 CG2 A:VAL2973 4.5 311.9 1.0 CB A:ASP2985 4.5 307.1 1.0 N A:ASP2977 4.6 300.2 1.0 OD2 A:ASP2975 4.6 303.9 1.0 CA A:TRP2972 4.7 313.1 1.0 CD1 A:TRP2972 4.7 313.0 1.0 C A:ASP2975 4.8 303.9 1.0 C A:ASP2977 4.8 300.1 1.0 CB A:CYS2974 4.8 319.4 1.0 C A:ASP2985 4.9 307.1 1.0 N A:GLU2986 4.9 305.1 1.0 CB A:TRP2972 4.9 313.0 1.0 O A:CYS2974 4.9 319.3 1.0 O A:ASP2985 4.9 307.2 1.0 OD1 A:ASP2979 5.0 286.3 1.0

Calcium binding site 4 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4711 b:242.1 occ:1.00 OD2 A:ASP3025 2.2 231.4 1.0 OD1 A:ASP3015 2.2 229.2 1.0 O A:PHE3012 2.2 257.7 1.0 OD2 A:ASP3019 2.2 250.9 1.0 O A:ARG3017 2.2 234.0 1.0 CG A:ASP3015 3.1 229.3 1.0 CG A:ASP3025 3.2 231.5 1.0 OE2 A:GLU3026 3.2 215.3 1.0 C A:ARG3017 3.3 234.1 1.0 C A:PHE3012 3.3 257.9 1.0 CG A:ASP3019 3.5 251.0 1.0 OD2 A:ASP3015 3.5 229.5 1.0 CG A:GLU3026 3.8 215.3 1.0 CA A:PHE3012 3.9 258.2 1.0 N A:ARG3017 3.9 233.8 1.0 CA A:ARG3017 3.9 234.0 1.0 CB A:ASP3025 3.9 231.5 1.0 CD A:GLU3026 4.0 215.2 1.0 CB A:PHE3012 4.0 258.2 1.0 CB A:ARG3017 4.0 234.1 1.0 OD1 A:ASP3025 4.1 231.7 1.0 N A:ASP3015 4.2 228.9 1.0 CB A:ASP3019 4.3 251.0 1.0 CB A:ASP3015 4.3 229.2 1.0 OD1 A:ASP3019 4.4 251.0 1.0 N A:ASN3018 4.4 242.5 1.0 N A:CYS3014 4.5 230.1 1.0 N A:ARG3013 4.5 234.2 1.0 N A:ASP3019 4.5 250.8 1.0 CG A:ARG3017 4.6 234.1 1.0 O A:ASP3025 4.6 231.1 1.0 C A:ASP3025 4.6 230.9 1.0 CA A:ASP3015 4.7 228.9 1.0 CA A:ASN3018 4.7 242.6 1.0 CA A:ARG3013 4.8 233.9 1.0 C A:ASN3018 4.8 242.8 1.0 C A:ARG3013 4.9 233.8 1.0 CG A:PHE3012 4.9 258.3 1.0 C A:ASP3015 4.9 228.8 1.0 CA A:ASP3025 4.9 231.2 1.0 N A:ARG3016 5.0 219.8 1.0

Calcium binding site 5 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4712 b:234.8 occ:1.00 OD1 A:ASP3054 2.2 242.0 1.0 OD2 A:ASP3064 2.2 231.6 1.0 O A:PHE3051 2.3 228.5 1.0 OD2 A:ASP3058 2.3 221.4 1.0 OE2 A:GLU3065 2.3 243.1 1.0 O A:ASP3056 2.4 237.2 1.0 CD A:GLU3065 2.7 243.1 1.0 OE1 A:GLU3065 3.1 243.2 1.0 CG A:ASP3054 3.2 242.0 1.0 CG A:ASP3064 3.2 231.5 1.0 CG A:ASP3058 3.4 221.2 1.0 C A:PHE3051 3.5 228.4 1.0 C A:ASP3056 3.6 237.1 1.0 CG A:GLU3065 3.6 243.0 1.0 CB A:ASP3064 3.7 231.6 1.0 OD2 A:ASP3054 3.7 242.0 1.0 N A:ASP3054 4.0 242.2 1.0 N A:ASP3058 4.1 221.1 1.0 OD1 A:ASP3064 4.1 231.4 1.0 CB A:PHE3051 4.1 228.2 1.0 N A:ASP3056 4.1 237.5 1.0 CB A:ASP3058 4.2 221.1 1.0 N A:CYS3053 4.2 251.3 1.0 CB A:ASP3054 4.2 242.1 1.0 CA A:PHE3051 4.3 228.3 1.0 CA A:ASP3056 4.3 237.3 1.0 OD1 A:ASP3058 4.4 221.2 1.0 N A:VAL3052 4.4 235.7 1.0 CA A:VAL3052 4.5 235.9 1.0 CA A:ASP3054 4.5 242.1 1.0 N A:ASN3057 4.6 218.5 1.0 CB A:ASP3056 4.6 237.3 1.0 C A:VAL3052 4.7 236.0 1.0 CA A:ASP3058 4.8 221.1 1.0 C A:ASP3064 4.8 231.7 1.0 C A:ASP3054 4.8 242.2 1.0 CA A:ASN3057 4.8 218.3 1.0 N A:GLU3055 4.9 244.4 1.0 CA A:ASP3064 4.9 231.4 1.0 C A:ASN3057 4.9 218.2 1.0 N A:GLU3065 4.9 242.8 1.0 CA A:CYS3053 4.9 251.4 1.0 C A:CYS3053 5.0 251.4 1.0 CB A:GLU3065 5.0 243.1 1.0

Calcium binding site 6 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


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 Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4713 b:337.1 occ:1.00 O A:ARG3094 2.4 331.7 1.0 OD1 A:ASN3097 2.4 326.2 1.0 O A:VAL3099 2.6 340.8 1.0 OE2 A:GLU3108 2.9 327.7 1.0 CG A:ARG3094 3.1 331.7 1.0 C A:ARG3094 3.3 331.6 1.0 CG A:ASN3097 3.6 326.2 1.0 OD1 A:ASP3107 3.7 331.9 1.0 C A:VAL3099 3.8 340.9 1.0 CB A:ARG3094 3.8 331.7 1.0 CA A:ARG3094 3.8 331.7 1.0 CD A:GLU3108 4.0 327.7 1.0 CD A:ARG3094 4.0 331.7 1.0 OD2 A:ASP3107 4.1 332.0 1.0 N A:ASN3097 4.1 326.2 1.0 N A:VAL3099 4.2 340.8 1.0 ND2 A:ASN3097 4.3 326.2 1.0 CG A:ASP3107 4.3 331.9 1.0 CA A:VAL3099 4.4 340.9 1.0 N A:CYS3096 4.4 326.5 1.0 N A:VAL3095 4.4 322.2 1.0 CB A:VAL3099 4.4 340.9 1.0 OE1 A:GLU3108 4.4 327.8 1.0 N A:ASP3101 4.6 331.2 1.0 OD2 A:ASP3101 4.6 331.1 1.0 CB A:ASN3097 4.6 326.2 1.0 SG A:CYS3102 4.7 341.2 1.0 CA A:VAL3095 4.8 322.1 1.0 CA A:ASN3097 4.8 326.2 1.0 C A:VAL3095 4.8 322.1 1.0 N A:ASP3100 4.9 340.2 1.0 C A:ASN3097 5.0 326.3 1.0 N A:CYS3102 5.0 341.2 1.0

Calcium binding site 7 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of Rat Megalin Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4714 b:114.5 occ:1.00 OE2 A:GLU3157 2.3 101.8 1.0 O A:VAL3172 2.4 96.8 1.0 OE1 A:GLU3157 2.4 102.0 1.0 O A:ILE3155 2.4 116.4 1.0 OD1 A:ASP3154 2.5 125.1 1.0 CD A:GLU3157 2.7 101.8 1.0 OD1 A:ASN3171 2.7 98.6 1.0 O A:SER3175 2.8 93.8 1.0 N A:SER3175 3.3 94.2 1.0 N A:GLY3174 3.3 104.5 1.0 CG A:ASP3154 3.4 125.4 1.0 OD2 A:ASP3154 3.4 125.5 1.0 C A:VAL3172 3.6 96.5 1.0 C A:ILE3155 3.7 116.4 1.0 C A:SER3175 3.7 93.7 1.0 CG A:ASN3171 3.9 98.4 1.0 CA A:GLY3174 3.9 104.8 1.0 C A:GLY3174 3.9 104.2 1.0 CA A:SER3175 4.1 94.0 1.0 CG A:GLU3157 4.1 101.5 1.0 C A:VAL3173 4.1 102.2 1.0 N A:VAL3172 4.2 96.4 1.0 CA A:VAL3173 4.3 102.2 1.0 N A:ILE3155 4.3 117.5 1.0 N A:VAL3173 4.4 102.0 1.0 O A:GLY3142 4.5 142.0 1.0 N A:GLU3157 4.5 101.5 1.0 CA A:ILE3155 4.5 116.7 1.0 ND2 A:ASN3171 4.5 98.4 1.0 CA A:VAL3172 4.6 96.2 1.0 N A:ASP3156 4.6 106.0 1.0 CA A:ASP3156 4.7 105.7 1.0 CB A:ASP3154 4.8 125.7 1.0 C A:ASP3154 4.9 126.0 1.0 N A:TYR3176 4.9 85.8 1.0 CB A:ILE3155 5.0 116.9 1.0 O A:GLY3174 5.0 104.7 1.0

Calcium binding site 8 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of Rat Megalin Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4715 b:77.9 occ:1.00 O A:GLU3323 2.5 76.5 1.0 OD2 A:ASP3294 2.5 83.0 1.0 O A:ALA3291 2.7 68.5 1.0 OD1 A:ASP3294 3.1 82.6 1.0 CG A:ASP3294 3.2 82.9 1.0 C A:GLU3323 3.6 75.6 1.0 C A:ALA3291 4.0 68.8 1.0 CA A:GLU3323 4.2 75.7 1.0 CD2 A:HIS3324 4.4 66.0 1.0 NE2 A:HIS3324 4.5 66.3 1.0 O A:ILE3292 4.6 73.8 1.0 CB A:ASP3294 4.6 82.9 1.0 CA A:ILE3292 4.7 73.6 1.0 N A:HIS3324 4.7 65.8 1.0 N A:ILE3292 4.8 73.8 1.0 CG A:GLU3323 4.8 76.7 1.0 CA A:ALA3291 4.9 68.5 1.0 CG A:HIS3324 4.9 66.1 1.0 O A:PHE3322 5.0 68.2 1.0 C A:ILE3292 5.0 73.3 1.0

Calcium binding site 9 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of Rat Megalin Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4716 b:71.8 occ:1.00 OE1 A:GLU3367 2.6 60.3 1.0 O A:VAL3344 3.0 71.8 1.0 CD A:GLU3367 3.6 60.1 1.0 OE2 A:GLU3367 3.8 60.2 1.0 C A:VAL3344 4.1 71.8 1.0 OE2 A:GLU3685 4.2 92.8 1.0 OG1 A:THR3684 4.3 94.4 1.0 OD2 A:ASP3681 4.3 112.0 1.0 CG A:GLU3685 4.7 92.5 1.0 CD A:GLU3685 4.7 93.0 1.0 CA A:VAL3344 4.8 72.0 1.0 O A:ILE3366 4.9 56.7 1.0 CG A:GLU3367 4.9 59.9 1.0

Calcium binding site 10 out of 20 in the Cryo-Em Structure of Rat Megalin Bodyb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of Rat Megalin Bodyb within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4717 b:74.3 occ:1.00 O A:PRO3410 2.8 51.0 1.0 O A:ALA3386 3.0 54.5 1.0 O A:HIS3387 4.0 59.0 1.0 C A:PRO3410 4.0 50.3 1.0 C A:ALA3386 4.2 53.9 1.0 CA A:HIS3387 4.3 58.5 1.0 ND2 A:ASN3428 4.5 51.7 1.0 C A:HIS3387 4.6 58.6 1.0 N A:HIS3387 4.8 58.1 1.0 CA A:PRO3410 4.8 51.5 1.0 ND1 A:HIS3411 4.9 45.2 1.0 CB A:HIS3411 5.0 45.6 1.0 O A:LEU3409 5.0 60.2 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