Calcium in PDB 6wx6: Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up

The binding sites of Calcium atom in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up (pdb code 6wx6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up, PDB code: 6wx6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:23.2 occ:1.00 OE1 A:GLU134 2.4 15.7 1.0 OE1 F:GLU134 2.4 15.7 1.0 OE1 L:GLU134 2.4 15.7 1.0 O L:HOH240 3.1 18.7 1.0 O F:HOH240 3.1 18.7 1.0 O A:HOH341 3.1 18.6 1.0 CD L:GLU134 3.5 15.7 1.0 CD A:GLU134 3.5 15.7 1.0 CD F:GLU134 3.5 15.7 1.0 OD1 A:ASP131 3.8 15.6 1.0 OD1 F:ASP131 3.8 15.6 1.0 OD1 L:ASP131 3.9 15.6 1.0 OE2 L:GLU134 3.9 15.7 1.0 OE2 F:GLU134 3.9 15.7 1.0 OE2 A:GLU134 4.0 15.7 1.0 HB2 A:ASP131 4.0 15.6 1.0 HB2 F:ASP131 4.0 15.6 1.0 HB2 L:ASP131 4.0 15.6 1.0 HA A:ASP131 4.1 15.6 1.0 HA F:ASP131 4.1 15.6 1.0 HA L:ASP131 4.1 15.6 1.0 HB2 A:GLU134 4.5 15.7 1.0 HB2 F:GLU134 4.5 15.7 1.0 HB2 L:GLU134 4.5 15.7 1.0 O L:HOH213 4.6 18.2 1.0 O F:HOH214 4.6 18.2 1.0 O A:HOH314 4.6 18.1 1.0 CB A:ASP131 4.6 15.6 1.0 CB F:ASP131 4.6 15.6 1.0 CB L:ASP131 4.6 15.6 1.0 HB3 F:GLU134 4.7 15.7 1.0 HB3 A:GLU134 4.7 15.7 1.0 HB3 L:GLU134 4.7 15.7 1.0 CG A:ASP131 4.7 15.6 1.0 CG F:ASP131 4.7 15.6 1.0 CG L:ASP131 4.7 15.6 1.0 CG A:GLU134 4.7 15.7 1.0 CG F:GLU134 4.7 15.7 1.0 CG L:GLU134 4.7 15.7 1.0 CA A:ASP131 4.8 15.6 1.0 CA F:ASP131 4.8 15.6 1.0 CA L:ASP131 4.8 15.6 1.0 O F:HOH220 4.9 17.1 1.0 O L:HOH222 4.9 17.0 1.0 O A:HOH320 4.9 16.9 1.0 CB A:GLU134 4.9 15.7 1.0 CB F:GLU134 4.9 15.7 1.0 CB L:GLU134 4.9 15.7 1.0

Calcium binding site 2 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:23.2 occ:1.00 OE1 I:GLU134 2.4 15.7 1.0 OE1 B:GLU134 2.4 15.7 1.0 OE1 H:GLU134 2.4 15.7 1.0 O H:HOH240 3.1 18.5 1.0 O B:HOH341 3.1 18.6 1.0 O I:HOH243 3.1 18.7 1.0 CD H:GLU134 3.5 15.7 1.0 CD I:GLU134 3.5 15.7 1.0 CD B:GLU134 3.5 15.7 1.0 OD1 I:ASP131 3.8 15.6 1.0 OD1 B:ASP131 3.9 15.6 1.0 OD1 H:ASP131 3.9 15.6 1.0 OE2 H:GLU134 3.9 15.7 1.0 OE2 I:GLU134 3.9 15.7 1.0 OE2 B:GLU134 3.9 15.7 1.0 HB2 I:ASP131 4.0 15.6 1.0 HB2 B:ASP131 4.0 15.6 1.0 HB2 H:ASP131 4.0 15.6 1.0 HA I:ASP131 4.1 15.6 1.0 HA B:ASP131 4.1 15.6 1.0 HA H:ASP131 4.1 15.6 1.0 HB2 I:GLU134 4.5 15.7 1.0 HB2 B:GLU134 4.5 15.7 1.0 HB2 H:GLU134 4.5 15.7 1.0 O B:HOH314 4.6 17.9 1.0 O I:HOH214 4.6 18.1 1.0 O H:HOH215 4.6 18.1 1.0 CB I:ASP131 4.6 15.6 1.0 CB B:ASP131 4.6 15.6 1.0 CB H:ASP131 4.6 15.6 1.0 HB3 B:GLU134 4.7 15.7 1.0 HB3 H:GLU134 4.7 15.7 1.0 HB3 I:GLU134 4.7 15.7 1.0 CG I:ASP131 4.7 15.6 1.0 CG B:ASP131 4.7 15.6 1.0 CG H:ASP131 4.7 15.6 1.0 CG H:GLU134 4.7 15.7 1.0 CG I:GLU134 4.7 15.7 1.0 CG B:GLU134 4.7 15.7 1.0 CA I:ASP131 4.8 15.6 1.0 CA B:ASP131 4.8 15.6 1.0 CA H:ASP131 4.8 15.6 1.0 O H:HOH223 4.9 16.9 1.0 O I:HOH224 4.9 16.9 1.0 O B:HOH320 4.9 16.8 1.0 CB B:GLU134 4.9 15.7 1.0 CB I:GLU134 4.9 15.7 1.0 CB H:GLU134 4.9 15.7 1.0

Calcium binding site 3 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:23.6 occ:1.00 OE1 C:GLU134 2.4 15.7 1.0 OE1 K:GLU134 2.4 15.6 1.0 OE1 G:GLU134 2.4 15.7 1.0 O G:HOH241 3.1 18.5 1.0 O K:HOH240 3.1 18.7 1.0 O C:HOH341 3.1 18.6 1.0 CD C:GLU134 3.5 15.7 1.0 CD K:GLU134 3.5 15.6 1.0 CD G:GLU134 3.5 15.7 1.0 OD1 G:ASP131 3.8 15.6 1.0 OD1 K:ASP131 3.9 15.5 1.0 OD1 C:ASP131 3.9 15.5 1.0 OE2 C:GLU134 3.9 15.7 1.0 OE2 K:GLU134 3.9 15.6 1.0 OE2 G:GLU134 4.0 15.7 1.0 HB2 G:ASP131 4.0 15.6 1.0 HB2 K:ASP131 4.0 15.5 1.0 HB2 C:ASP131 4.0 15.5 1.0 HA G:ASP131 4.1 15.6 1.0 HA K:ASP131 4.1 15.5 1.0 HA C:ASP131 4.1 15.5 1.0 HB2 G:GLU134 4.5 15.7 1.0 HB2 K:GLU134 4.5 15.6 1.0 HB2 C:GLU134 4.5 15.7 1.0 O G:HOH214 4.6 18.3 1.0 O K:HOH214 4.6 18.0 1.0 O C:HOH314 4.6 18.2 1.0 CB G:ASP131 4.6 15.6 1.0 CB K:ASP131 4.6 15.5 1.0 CB C:ASP131 4.6 15.5 1.0 HB3 G:GLU134 4.7 15.7 1.0 HB3 K:GLU134 4.7 15.6 1.0 HB3 C:GLU134 4.7 15.7 1.0 CG G:ASP131 4.7 15.6 1.0 CG K:ASP131 4.7 15.5 1.0 CG C:ASP131 4.7 15.5 1.0 CG K:GLU134 4.7 15.6 1.0 CG C:GLU134 4.7 15.7 1.0 CG G:GLU134 4.8 15.7 1.0 CA G:ASP131 4.8 15.6 1.0 CA K:ASP131 4.8 15.5 1.0 CA C:ASP131 4.8 15.5 1.0 O C:HOH323 4.9 16.9 1.0 O K:HOH220 4.9 16.9 1.0 CB G:GLU134 4.9 15.7 1.0 CB K:GLU134 4.9 15.6 1.0 CB C:GLU134 4.9 15.7 1.0

Calcium binding site 4 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:23.5 occ:1.00 OE1 E:GLU134 2.4 15.7 1.0 OE1 D:GLU134 2.4 15.7 1.0 OE1 J:GLU134 2.4 15.7 1.0 O J:HOH241 3.1 18.5 1.0 O E:HOH241 3.1 18.7 1.0 O D:HOH340 3.1 18.5 1.0 CD E:GLU134 3.5 15.7 1.0 CD D:GLU134 3.5 15.7 1.0 CD J:GLU134 3.5 15.7 1.0 OD1 D:ASP131 3.8 15.6 1.0 OD1 J:ASP131 3.9 15.6 1.0 OD1 E:ASP131 3.9 15.6 1.0 OE2 E:GLU134 3.9 15.7 1.0 OE2 J:GLU134 4.0 15.7 1.0 OE2 D:GLU134 4.0 15.7 1.0 HB2 D:ASP131 4.0 15.6 1.0 HB2 E:ASP131 4.0 15.6 1.0 HB2 J:ASP131 4.0 15.6 1.0 HA D:ASP131 4.1 15.6 1.0 HA E:ASP131 4.1 15.6 1.0 HA J:ASP131 4.1 15.6 1.0 HB2 D:GLU134 4.5 15.7 1.0 HB2 J:GLU134 4.5 15.7 1.0 HB2 E:GLU134 4.5 15.7 1.0 O D:HOH313 4.6 18.2 1.0 O J:HOH214 4.6 18.0 1.0 O E:HOH213 4.6 18.2 1.0 CB D:ASP131 4.6 15.6 1.0 CB J:ASP131 4.6 15.6 1.0 CB E:ASP131 4.6 15.6 1.0 HB3 D:GLU134 4.7 15.7 1.0 HB3 J:GLU134 4.7 15.7 1.0 HB3 E:GLU134 4.7 15.7 1.0 CG D:ASP131 4.7 15.6 1.0 CG J:ASP131 4.7 15.6 1.0 CG E:ASP131 4.7 15.6 1.0 CG E:GLU134 4.7 15.7 1.0 CG D:GLU134 4.7 15.7 1.0 CG J:GLU134 4.8 15.7 1.0 CA D:ASP131 4.8 15.6 1.0 CA E:ASP131 4.8 15.6 1.0 CA J:ASP131 4.8 15.6 1.0 O J:HOH222 4.9 17.1 1.0 O D:HOH320 4.9 16.9 1.0 O E:HOH222 4.9 16.9 1.0 CB D:GLU134 4.9 15.7 1.0 CB J:GLU134 4.9 15.7 1.0 CB E:GLU134 4.9 15.7 1.0

Calcium binding site 5 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca201 b:23.6 occ:1.00 OE1 M:GLU134 2.4 15.6 1.0 OE1 R:GLU134 2.4 15.6 1.0 OE1 X:GLU134 2.4 15.6 1.0 O X:HOH239 3.1 18.6 1.0 O M:HOH342 3.1 18.5 1.0 O R:HOH241 3.1 18.5 1.0 CD M:GLU134 3.5 15.6 1.0 CD R:GLU134 3.5 15.6 1.0 CD X:GLU134 3.5 15.6 1.0 OD1 M:ASP131 3.8 15.5 1.0 OD1 X:ASP131 3.8 15.5 1.0 OD1 R:ASP131 3.9 15.5 1.0 OE2 R:GLU134 3.9 15.6 1.0 OE2 M:GLU134 3.9 15.6 1.0 OE2 X:GLU134 4.0 15.6 1.0 HB2 M:ASP131 4.0 15.5 1.0 HB2 X:ASP131 4.0 15.5 1.0 HB2 R:ASP131 4.0 15.5 1.0 HA M:ASP131 4.1 15.5 1.0 HA X:ASP131 4.1 15.5 1.0 HA R:ASP131 4.1 15.5 1.0 HB2 X:GLU134 4.5 15.6 1.0 HB2 M:GLU134 4.5 15.6 1.0 HB2 R:GLU134 4.5 15.6 1.0 O R:HOH214 4.6 18.3 1.0 O X:HOH214 4.6 18.0 1.0 O M:HOH316 4.6 18.1 1.0 CB M:ASP131 4.6 15.5 1.0 CB X:ASP131 4.6 15.5 1.0 CB R:ASP131 4.6 15.5 1.0 HB3 X:GLU134 4.7 15.6 1.0 HB3 M:GLU134 4.7 15.6 1.0 HB3 R:GLU134 4.7 15.6 1.0 CG M:ASP131 4.7 15.5 1.0 CG X:ASP131 4.7 15.5 1.0 CG R:ASP131 4.7 15.5 1.0 CG M:GLU134 4.7 15.6 1.0 CG R:GLU134 4.7 15.6 1.0 CG X:GLU134 4.7 15.6 1.0 CA M:ASP131 4.8 15.5 1.0 CA X:ASP131 4.8 15.5 1.0 CA R:ASP131 4.8 15.5 1.0 O M:HOH322 4.9 16.8 1.0 O X:HOH219 4.9 17.0 1.0 O R:HOH222 4.9 17.0 1.0 CB X:GLU134 4.9 15.6 1.0 CB M:GLU134 4.9 15.6 1.0 CB R:GLU134 4.9 15.6 1.0

Calcium binding site 6 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca201 b:23.9 occ:1.00 OE1 U:GLU134 2.4 15.7 1.0 OE1 N:GLU134 2.4 15.8 1.0 OE1 T:GLU134 2.4 15.7 1.0 O T:HOH242 3.1 18.6 1.0 O U:HOH240 3.1 18.7 1.0 O N:HOH341 3.1 18.6 1.0 CD N:GLU134 3.5 15.8 1.0 CD U:GLU134 3.5 15.7 1.0 CD T:GLU134 3.5 15.7 1.0 OD1 T:ASP131 3.8 15.6 1.0 OD1 U:ASP131 3.8 15.6 1.0 OD1 N:ASP131 3.9 15.6 1.0 OE2 N:GLU134 3.9 15.8 1.0 OE2 U:GLU134 3.9 15.7 1.0 OE2 T:GLU134 4.0 15.7 1.0 HB2 T:ASP131 4.0 15.6 1.0 HB2 U:ASP131 4.0 15.6 1.0 HB2 N:ASP131 4.0 15.6 1.0 HA T:ASP131 4.0 15.6 1.0 HA U:ASP131 4.1 15.6 1.0 HA N:ASP131 4.1 15.6 1.0 HB2 T:GLU134 4.5 15.7 1.0 HB2 U:GLU134 4.5 15.7 1.0 HB2 N:GLU134 4.5 15.8 1.0 O N:HOH314 4.6 18.3 1.0 O T:HOH213 4.6 18.0 1.0 O U:HOH214 4.6 18.1 1.0 CB T:ASP131 4.6 15.6 1.0 CB U:ASP131 4.6 15.6 1.0 CB N:ASP131 4.6 15.6 1.0 HB3 U:GLU134 4.7 15.7 1.0 HB3 T:GLU134 4.7 15.7 1.0 HB3 N:GLU134 4.7 15.8 1.0 CG T:ASP131 4.7 15.6 1.0 CG U:ASP131 4.7 15.6 1.0 CG N:ASP131 4.7 15.6 1.0 CG N:GLU134 4.7 15.8 1.0 CG U:GLU134 4.7 15.7 1.0 CG T:GLU134 4.8 15.7 1.0 CA T:ASP131 4.8 15.6 1.0 CA U:ASP131 4.8 15.6 1.0 CA N:ASP131 4.8 15.6 1.0 O N:HOH322 4.9 16.9 1.0 O U:HOH220 4.9 17.0 1.0 CB T:GLU134 4.9 15.7 1.0 CB U:GLU134 4.9 15.7 1.0 CB N:GLU134 4.9 15.8 1.0

Calcium binding site 7 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca201 b:23.5 occ:1.00 OE1 S:GLU134 2.4 15.8 1.0 OE1 O:GLU134 2.4 15.7 1.0 OE1 W:GLU134 2.4 15.7 1.0 O S:HOH240 3.1 18.7 1.0 O O:HOH341 3.1 18.6 1.0 O W:HOH243 3.1 18.9 1.0 CD S:GLU134 3.5 15.8 1.0 CD O:GLU134 3.5 15.7 1.0 CD W:GLU134 3.5 15.7 1.0 OD1 O:ASP131 3.8 15.6 1.0 OD1 S:ASP131 3.9 15.6 1.0 OD1 W:ASP131 3.9 15.6 1.0 OE2 S:GLU134 3.9 15.8 1.0 OE2 W:GLU134 4.0 15.7 1.0 OE2 O:GLU134 4.0 15.7 1.0 HB2 O:ASP131 4.0 15.6 1.0 HB2 S:ASP131 4.0 15.6 1.0 HB2 W:ASP131 4.0 15.6 1.0 HA O:ASP131 4.1 15.6 1.0 HA S:ASP131 4.1 15.6 1.0 HA W:ASP131 4.1 15.6 1.0 HB2 O:GLU134 4.5 15.7 1.0 HB2 S:GLU134 4.5 15.8 1.0 HB2 W:GLU134 4.5 15.7 1.0 O W:HOH215 4.6 18.1 1.0 O S:HOH214 4.6 18.1 1.0 O O:HOH314 4.6 18.0 1.0 CB O:ASP131 4.6 15.6 1.0 CB S:ASP131 4.6 15.6 1.0 CB W:ASP131 4.6 15.6 1.0 HB3 O:GLU134 4.7 15.7 1.0 HB3 S:GLU134 4.7 15.8 1.0 HB3 W:GLU134 4.7 15.7 1.0 CG O:ASP131 4.7 15.6 1.0 CG S:ASP131 4.7 15.6 1.0 CG W:ASP131 4.7 15.6 1.0 CG S:GLU134 4.7 15.8 1.0 CG O:GLU134 4.7 15.7 1.0 CG W:GLU134 4.7 15.7 1.0 CA O:ASP131 4.8 15.6 1.0 CA S:ASP131 4.8 15.6 1.0 CA W:ASP131 4.8 15.6 1.0 O W:HOH224 4.9 16.9 1.0 O S:HOH222 4.9 16.9 1.0 O O:HOH321 4.9 17.0 1.0 CB O:GLU134 4.9 15.7 1.0 CB S:GLU134 4.9 15.8 1.0 CB W:GLU134 4.9 15.7 1.0

Calcium binding site 8 out of 8 in the Cryo-Em Structure of Human Apoferritin Light Chain Vitrified Using Back-It-Up


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 Human Apoferritin Light Chain Vitrified Using Back-It-Up within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca201 b:23.1 occ:1.00 OE1 V:GLU134 2.4 15.7 1.0 OE1 Q:GLU134 2.4 15.7 1.0 OE1 P:GLU134 2.4 15.7 1.0 O P:HOH340 3.1 18.4 1.0 O Q:HOH241 3.1 18.6 1.0 O V:HOH242 3.1 18.5 1.0 CD Q:GLU134 3.5 15.7 1.0 CD V:GLU134 3.5 15.7 1.0 CD P:GLU134 3.5 15.7 1.0 OD1 P:ASP131 3.8 15.6 1.0 OD1 V:ASP131 3.9 15.6 1.0 OD1 Q:ASP131 3.9 15.6 1.0 OE2 Q:GLU134 3.9 15.7 1.0 OE2 V:GLU134 3.9 15.7 1.0 OE2 P:GLU134 4.0 15.7 1.0 HB2 P:ASP131 4.0 15.6 1.0 HB2 V:ASP131 4.0 15.6 1.0 HB2 Q:ASP131 4.0 15.6 1.0 HA P:ASP131 4.1 15.6 1.0 HA V:ASP131 4.1 15.6 1.0 HA Q:ASP131 4.1 15.6 1.0 HB2 P:GLU134 4.5 15.7 1.0 HB2 V:GLU134 4.5 15.7 1.0 HB2 Q:GLU134 4.5 15.7 1.0 O Q:HOH213 4.6 18.2 1.0 O P:HOH314 4.6 17.9 1.0 O V:HOH215 4.6 18.2 1.0 CB P:ASP131 4.6 15.6 1.0 CB V:ASP131 4.6 15.6 1.0 CB Q:ASP131 4.6 15.6 1.0 HB3 P:GLU134 4.7 15.7 1.0 HB3 V:GLU134 4.7 15.7 1.0 HB3 Q:GLU134 4.7 15.7 1.0 CG P:ASP131 4.7 15.6 1.0 CG V:ASP131 4.7 15.6 1.0 CG Q:ASP131 4.7 15.6 1.0 CG V:GLU134 4.7 15.7 1.0 CG Q:GLU134 4.7 15.7 1.0 CG P:GLU134 4.7 15.7 1.0 CA P:ASP131 4.8 15.6 1.0 CA V:ASP131 4.8 15.6 1.0 CA Q:ASP131 4.8 15.6 1.0 O P:HOH320 4.9 16.7 1.0 O V:HOH223 4.9 16.8 1.0 O Q:HOH222 4.9 17.0 1.0 CB P:GLU134 4.9 15.7 1.0 CB V:GLU134 4.9 15.7 1.0 CB Q:GLU134 4.9 15.7 1.0

Y.Z.Tan, J.L.Rubinstein. Through-Grid Wicking Enables High-Speed Cryoem Specimen Preparation To Be Published.