Calcium in PDB 8jfy: Cryo-Em Structure of Rdgc/CA2+-Cam Complex

All present enzymatic activity of Cryo-Em Structure of Rdgc/CA2+-Cam Complex:
3.1.3.16;

The structure of Cryo-Em Structure of Rdgc/CA2+-Cam Complex also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iron	(Fe)	2 atoms

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex (pdb code 8jfy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex, PDB code: 8jfy:
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 Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:77.0 occ:1.00 OD1 A:ASP94 2.4 83.1 1.0 OD2 A:ASP96 2.4 77.2 1.0 OE1 A:GLU105 2.4 86.3 1.0 O A:PHE100 2.4 69.8 1.0 OD1 A:ASP96 2.5 88.4 1.0 CG A:ASP96 2.7 83.9 1.0 CD A:GLU105 3.0 82.9 1.0 OD1 A:ASN98 3.1 74.8 1.0 OE2 A:GLU105 3.4 84.1 1.0 C A:PHE100 3.4 61.0 1.0 CG A:ASP94 3.5 75.9 1.0 CA A:ILE101 3.7 60.3 1.0 N A:SER102 3.8 62.4 1.0 CG A:GLU105 3.9 81.4 1.0 CG A:ASN98 4.0 79.7 1.0 N A:ILE101 4.0 59.5 1.0 CB A:ASP96 4.1 80.1 1.0 ND2 A:ASN98 4.3 82.3 1.0 OD2 A:ASP94 4.3 77.6 1.0 OG A:SER102 4.3 58.1 1.0 C A:ILE101 4.3 58.8 1.0 CA A:ASP94 4.3 70.8 1.0 N A:ASP96 4.3 86.5 1.0 CB A:ASP94 4.5 70.7 1.0 N A:PHE100 4.5 67.2 1.0 CB A:GLU105 4.6 73.2 1.0 CA A:PHE100 4.6 57.4 1.0 N A:LYS95 4.6 79.1 1.0 C A:ASP94 4.7 78.2 1.0 CA A:ASP96 4.8 83.6 1.0 CB A:SER102 4.8 62.5 1.0 CB A:ILE101 4.9 57.2 1.0 CA A:SER102 4.9 60.1 1.0 N A:GLY97 5.0 79.4 1.0

Calcium binding site 2 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:55.5 occ:1.00 OE1 A:GLU141 2.4 63.9 1.0 OD1 A:ASP132 2.4 67.5 1.0 O A:GLN136 2.4 70.4 1.0 OD1 A:ASP130 2.6 69.8 1.0 OE2 A:GLU141 2.9 70.8 1.0 CD A:GLU141 3.0 59.1 1.0 CB A:ASP134 3.4 72.0 1.0 CG A:ASP132 3.4 67.3 1.0 C A:GLN136 3.6 65.0 1.0 CG A:ASP130 3.8 68.9 1.0 OD2 A:ASP132 4.0 72.9 1.0 N A:ASP134 4.1 75.8 1.0 ND2 A:ASN138 4.1 75.5 1.0 N A:GLN136 4.2 71.5 1.0 CA A:ASP134 4.3 68.8 1.0 CG A:ASP134 4.3 79.8 1.0 N A:ASN138 4.3 56.6 1.0 CG A:ASN138 4.4 77.0 1.0 CG A:GLU141 4.5 58.1 1.0 N A:GLY135 4.5 70.8 1.0 CB A:ASP132 4.5 63.4 1.0 N A:VAL137 4.5 62.5 1.0 CA A:VAL137 4.5 58.9 1.0 CA A:GLN136 4.6 60.2 1.0 OD2 A:ASP130 4.6 72.2 1.0 N A:ASP132 4.7 61.9 1.0 CA A:ASP130 4.7 51.5 1.0 CB A:ASP130 4.7 56.5 1.0 OD2 A:ASP134 4.8 76.5 1.0 C A:ASP134 4.8 72.0 1.0 OD1 A:ASN138 4.9 78.5 1.0 CB A:ASN138 4.9 69.9 1.0 C A:VAL137 4.9 57.5 1.0 N A:GLY133 4.9 59.4 1.0

Calcium binding site 3 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:178.1 occ:1.00 O A:THR27 2.4 172.3 1.0 OD1 A:ASP25 2.4 176.7 1.0 OD2 A:ASP23 2.4 170.2 1.0 OE1 A:GLU32 2.4 162.5 1.0 OD1 A:ASP23 2.5 170.0 1.0 OD2 A:ASP25 2.6 174.9 1.0 CG A:ASP25 2.7 175.6 1.0 CG A:ASP23 2.8 170.2 1.0 OE2 A:GLU32 2.8 162.2 1.0 CD A:GLU32 2.8 162.3 1.0 OD1 A:ASP21 2.9 166.1 1.0 CG2 A:THR29 3.5 163.6 1.0 C A:THR27 3.6 172.7 1.0 N A:THR29 4.0 164.7 1.0 CG A:ASP21 4.1 167.6 1.0 CB A:ASP25 4.2 174.8 1.0 OG1 A:THR29 4.2 164.7 1.0 CG A:GLU32 4.2 161.1 1.0 CB A:ASP23 4.3 169.7 1.0 CA A:ILE28 4.3 167.3 1.0 N A:THR27 4.3 172.2 1.0 CB A:THR29 4.4 164.7 1.0 N A:ILE28 4.4 169.4 1.0 C A:ILE28 4.4 166.8 1.0 N A:ASP25 4.5 175.4 1.0 CA A:THR27 4.6 172.4 1.0 CG2 A:THR27 4.7 170.8 1.0 CA A:THR29 4.8 165.1 1.0 CA A:ASP25 4.8 175.2 1.0 OD2 A:ASP21 4.9 167.3 1.0 N A:ASP23 4.9 171.1 1.0 CA A:ASP21 4.9 167.9 1.0 N A:GLY26 5.0 172.5 1.0

Calcium binding site 4 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:187.8 occ:1.00 OD2 A:ASP57 2.4 181.6 1.0 O A:THR63 2.4 175.7 1.0 OD1 A:ASN61 2.4 181.6 1.0 OE2 A:GLU68 2.4 178.3 1.0 OD1 A:ASP57 2.5 182.9 1.0 OE1 A:GLU68 2.5 178.9 1.0 CD A:GLU68 2.6 178.5 1.0 ND2 A:ASN61 2.7 181.0 1.0 CG A:ASP57 2.7 181.8 1.0 CG A:ASN61 2.8 181.6 1.0 C A:THR63 3.6 176.5 1.0 CB A:ASP59 3.7 183.0 1.0 CG A:GLU68 3.9 177.8 1.0 O A:ASN61 3.9 180.9 1.0 CG A:ASP59 4.2 182.7 1.0 CB A:ASP57 4.2 181.1 1.0 CB A:ASN61 4.2 181.0 1.0 CA A:ILE64 4.3 176.2 1.0 N A:ILE64 4.3 176.2 1.0 C A:ASN61 4.4 181.7 1.0 N A:ASN61 4.5 182.4 1.0 N A:THR63 4.5 177.1 1.0 CB A:GLU68 4.6 177.7 1.0 OD1 A:ASP59 4.6 182.4 1.0 CA A:ASN61 4.6 182.1 1.0 CA A:THR63 4.6 176.9 1.0 CG2 A:THR63 4.7 175.7 1.0 OD2 A:ASP59 4.8 182.6 1.0 N A:ASP65 4.8 175.3 1.0 OD2 A:ASP65 4.8 175.0 1.0 CA A:ASP59 4.9 183.3 1.0 O A:ASP57 5.0 181.1 1.0

Calcium binding site 5 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca704 b:147.5 occ:1.00 OE1 D:GLU550 2.5 168.6 1.0 OD1 D:ASP541 2.5 146.5 1.0 OD1 D:ASP539 2.6 152.8 1.0 OG1 D:THR547 2.6 169.1 1.0 C D:ILE546 2.9 167.1 1.0 O D:ILE546 3.1 167.6 1.0 CA D:ILE546 3.1 165.6 1.0 CD D:GLU550 3.2 166.7 1.0 O D:SER543 3.2 147.5 1.0 CG D:ASP541 3.3 145.7 1.0 OD2 D:ASP541 3.4 144.8 1.0 OE2 D:GLU550 3.4 166.3 1.0 N D:THR547 3.4 170.1 1.0 CB D:SER543 3.5 146.3 1.0 C D:SER543 3.7 148.2 1.0 CB D:THR547 3.7 169.2 1.0 CG D:ASP539 3.8 152.3 1.0 N D:SER543 3.8 148.2 1.0 N D:ILE546 3.8 164.8 1.0 CA D:SER543 3.9 146.7 1.0 CA D:THR547 4.2 169.6 1.0 OD2 D:ASP539 4.2 151.7 1.0 O D:GLY544 4.2 159.8 1.0 OG D:SER543 4.3 145.9 1.0 CB D:ILE546 4.5 165.2 1.0 CG D:GLU550 4.5 167.1 1.0 CG1 D:ILE546 4.6 165.4 1.0 CD1 D:ILE546 4.7 165.6 1.0 N D:GLY544 4.7 159.6 1.0 CB D:ASP541 4.8 143.7 1.0 C D:GLU545 4.8 171.3 1.0 C D:GLY544 4.8 160.0 1.0 C D:ASN542 4.8 130.3 1.0 N D:ASN542 4.9 132.1 1.0 CB D:ASP539 5.0 152.9 1.0 CG2 D:THR547 5.0 168.9 1.0

Calcium binding site 6 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca705 b:190.3 occ:1.00 OD1 D:ASN581 2.3 182.5 1.0 OE1 D:GLU590 2.4 175.9 1.0 O D:LYS585 2.4 178.6 1.0 OD1 D:ASP583 2.4 181.8 1.0 OD1 D:ASP579 2.9 179.6 1.0 OD2 D:ASP583 2.9 180.2 1.0 CG D:ASP583 3.0 180.8 1.0 CG D:ASN581 3.0 182.1 1.0 OE2 D:GLU590 3.0 176.4 1.0 CD D:GLU590 3.0 175.6 1.0 ND2 D:ASN581 3.1 181.5 1.0 C D:LYS585 3.5 177.4 1.0 CG D:ASP579 3.9 180.1 1.0 N D:VAL586 4.3 175.7 1.0 CA D:VAL586 4.3 176.0 1.0 N D:LYS585 4.3 177.3 1.0 CA D:LYS585 4.4 176.2 1.0 CB D:ASP583 4.4 180.7 1.0 CB D:ASN581 4.4 181.8 1.0 OD2 D:ASP579 4.5 179.9 1.0 N D:ASN581 4.5 181.0 1.0 CG D:GLU590 4.5 175.8 1.0 N D:ASP583 4.5 181.5 1.0 N D:ASP587 4.5 174.3 1.0 OE1 D:GLU545 4.7 170.9 1.0 N D:LEU580 4.7 184.9 1.0 CB D:LYS585 4.7 176.0 1.0 N D:GLY582 4.9 181.6 1.0 CB D:ASP579 4.9 180.4 1.0 CA D:ASN581 4.9 182.2 1.0 CA D:ASP579 4.9 180.2 1.0 C D:VAL586 4.9 175.3 1.0 CA D:ASP583 5.0 181.4 1.0

Calcium binding site 7 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:77.0 occ:1.00 OD1 B:ASP94 2.4 83.1 1.0 OD2 B:ASP96 2.4 77.2 1.0 OE1 B:GLU105 2.4 86.3 1.0 O B:PHE100 2.4 69.8 1.0 OD1 B:ASP96 2.5 88.4 1.0 CG B:ASP96 2.7 83.9 1.0 CD B:GLU105 3.0 82.9 1.0 OD1 B:ASN98 3.1 74.8 1.0 OE2 B:GLU105 3.4 84.1 1.0 C B:PHE100 3.4 61.0 1.0 CG B:ASP94 3.5 75.9 1.0 CA B:ILE101 3.7 60.3 1.0 N B:SER102 3.8 62.4 1.0 CG B:GLU105 3.9 81.4 1.0 CG B:ASN98 4.0 79.7 1.0 N B:ILE101 4.0 59.5 1.0 CB B:ASP96 4.1 80.1 1.0 ND2 B:ASN98 4.3 82.3 1.0 OD2 B:ASP94 4.3 77.6 1.0 OG B:SER102 4.3 58.1 1.0 C B:ILE101 4.3 58.8 1.0 CA B:ASP94 4.3 70.8 1.0 N B:ASP96 4.3 86.5 1.0 CB B:ASP94 4.5 70.7 1.0 N B:PHE100 4.5 67.2 1.0 CB B:GLU105 4.6 73.2 1.0 CA B:PHE100 4.6 57.4 1.0 N B:LYS95 4.6 79.1 1.0 C B:ASP94 4.7 78.2 1.0 CA B:ASP96 4.8 83.6 1.0 CB B:SER102 4.8 62.5 1.0 CB B:ILE101 4.9 57.2 1.0 CA B:SER102 4.9 60.1 1.0 N B:GLY97 5.0 79.4 1.0

Calcium binding site 8 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:55.5 occ:1.00 OE1 B:GLU141 2.4 63.9 1.0 OD1 B:ASP132 2.4 67.5 1.0 O B:GLN136 2.4 70.4 1.0 OD1 B:ASP130 2.6 69.8 1.0 OE2 B:GLU141 2.9 70.8 1.0 CD B:GLU141 3.0 59.1 1.0 CB B:ASP134 3.4 72.0 1.0 CG B:ASP132 3.4 67.3 1.0 C B:GLN136 3.6 65.0 1.0 CG B:ASP130 3.8 68.9 1.0 OD2 B:ASP132 4.0 72.9 1.0 N B:ASP134 4.1 75.8 1.0 ND2 B:ASN138 4.1 75.5 1.0 N B:GLN136 4.2 71.5 1.0 CA B:ASP134 4.3 68.8 1.0 CG B:ASP134 4.3 79.8 1.0 N B:ASN138 4.3 56.6 1.0 CG B:ASN138 4.4 77.0 1.0 CG B:GLU141 4.5 58.1 1.0 N B:GLY135 4.5 70.8 1.0 CB B:ASP132 4.5 63.4 1.0 N B:VAL137 4.5 62.5 1.0 CA B:VAL137 4.5 58.9 1.0 CA B:GLN136 4.6 60.2 1.0 OD2 B:ASP130 4.6 72.2 1.0 N B:ASP132 4.7 61.9 1.0 CA B:ASP130 4.7 51.5 1.0 CB B:ASP130 4.7 56.5 1.0 OD2 B:ASP134 4.8 76.5 1.0 C B:ASP134 4.8 72.0 1.0 OD1 B:ASN138 4.9 78.5 1.0 CB B:ASN138 4.9 69.9 1.0 C B:VAL137 4.9 57.5 1.0 N B:GLY133 4.9 59.4 1.0

Calcium binding site 9 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:178.1 occ:1.00 O B:THR27 2.4 172.3 1.0 OD1 B:ASP25 2.4 176.7 1.0 OD2 B:ASP23 2.4 170.2 1.0 OE1 B:GLU32 2.4 162.5 1.0 OD1 B:ASP23 2.5 170.0 1.0 OD2 B:ASP25 2.6 174.9 1.0 CG B:ASP25 2.7 175.6 1.0 CG B:ASP23 2.8 170.2 1.0 OE2 B:GLU32 2.8 162.2 1.0 CD B:GLU32 2.8 162.3 1.0 OD1 B:ASP21 2.9 166.1 1.0 CG2 B:THR29 3.5 163.6 1.0 C B:THR27 3.6 172.7 1.0 N B:THR29 4.0 164.7 1.0 CG B:ASP21 4.1 167.6 1.0 CB B:ASP25 4.2 174.8 1.0 OG1 B:THR29 4.2 164.7 1.0 CG B:GLU32 4.2 161.1 1.0 CB B:ASP23 4.3 169.7 1.0 CA B:ILE28 4.3 167.3 1.0 N B:THR27 4.3 172.2 1.0 CB B:THR29 4.4 164.7 1.0 N B:ILE28 4.4 169.4 1.0 C B:ILE28 4.4 166.8 1.0 N B:ASP25 4.5 175.4 1.0 CA B:THR27 4.6 172.4 1.0 CG2 B:THR27 4.7 170.8 1.0 CA B:THR29 4.8 165.1 1.0 CA B:ASP25 4.8 175.2 1.0 OD2 B:ASP21 4.9 167.3 1.0 N B:ASP23 4.9 171.1 1.0 CA B:ASP21 4.9 167.9 1.0 N B:GLY26 5.0 172.5 1.0

Calcium binding site 10 out of 12 in the Cryo-Em Structure of Rdgc/CA2+-Cam Complex


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 Rdgc/CA2+-Cam Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:187.8 occ:1.00 OD2 B:ASP57 2.4 181.6 1.0 O B:THR63 2.4 175.7 1.0 OD1 B:ASN61 2.4 181.6 1.0 OE2 B:GLU68 2.4 178.3 1.0 OD1 B:ASP57 2.5 182.9 1.0 OE1 B:GLU68 2.5 178.9 1.0 CD B:GLU68 2.6 178.5 1.0 ND2 B:ASN61 2.7 181.0 1.0 CG B:ASP57 2.7 181.8 1.0 CG B:ASN61 2.8 181.6 1.0 C B:THR63 3.6 176.5 1.0 CB B:ASP59 3.7 183.0 1.0 CG B:GLU68 3.9 177.8 1.0 O B:ASN61 3.9 180.9 1.0 CG B:ASP59 4.2 182.7 1.0 CB B:ASP57 4.2 181.1 1.0 CB B:ASN61 4.2 181.0 1.0 CA B:ILE64 4.3 176.2 1.0 N B:ILE64 4.3 176.2 1.0 C B:ASN61 4.4 181.7 1.0 N B:ASN61 4.5 182.4 1.0 N B:THR63 4.5 177.1 1.0 CB B:GLU68 4.6 177.7 1.0 OD1 B:ASP59 4.6 182.4 1.0 CA B:ASN61 4.6 182.1 1.0 CA B:THR63 4.6 176.9 1.0 CG2 B:THR63 4.7 175.7 1.0 OD2 B:ASP59 4.8 182.6 1.0 N B:ASP65 4.8 175.3 1.0 OD2 B:ASP65 4.8 175.0 1.0 CA B:ASP59 4.9 183.3 1.0 O B:ASP57 5.0 181.1 1.0

Z.M.Liu, W.Liu, C.Wu, J.Liu. Cryo-Em Structure of Rdgc/CA2+-Cam Complex To Be Published.