Calcium in PDB 4zcv: Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form

The structure of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form, PDB code: 4zcv was solved by S.P.D.Harborne, J.J.Ruprecht, E.R.S.Kunji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.10 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.920, 77.010, 119.560, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form (pdb code 4zcv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form, PDB code: 4zcv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:32.4 occ:1.00 OD1 A:ASP32 2.3 31.2 1.0 OD1 A:ASN34 2.3 56.7 1.0 OD1 A:ASP36 2.3 44.1 1.0 O A:VAL38 2.3 44.3 1.0 OE1 A:GLU43 2.3 33.2 1.0 OE2 A:GLU43 2.4 33.6 1.0 CD A:GLU43 2.6 32.9 1.0 CG A:ASP36 3.1 46.9 1.0 CG A:ASN34 3.3 51.0 1.0 OD2 A:ASP36 3.3 55.0 1.0 CG A:ASP32 3.4 30.4 1.0 C A:VAL38 3.5 37.8 1.0 ND2 A:ASN34 3.8 53.7 1.0 OD2 A:ASP40 3.8 49.8 1.0 CG A:GLU43 4.1 31.8 1.0 CA A:ASP32 4.1 41.1 1.0 OD2 A:ASP32 4.3 31.7 1.0 CA A:VAL39 4.3 26.9 1.0 CB A:ASP32 4.3 28.3 1.0 N A:ASP36 4.3 42.0 1.0 N A:VAL39 4.3 28.0 1.0 CG2 A:VAL38 4.3 35.6 1.0 N A:VAL38 4.4 45.5 1.0 CB A:ASP36 4.4 44.1 1.0 N A:ASN34 4.4 50.5 1.0 C A:ASP32 4.5 41.2 1.0 CA A:VAL38 4.5 41.4 1.0 N A:ARG33 4.5 32.7 1.0 N A:ASP40 4.5 26.4 1.0 CB A:ASN34 4.6 54.5 1.0 N A:GLY35 4.6 53.1 1.0 CG A:ASP40 4.8 43.2 1.0 CA A:ASP36 4.8 44.1 1.0 C A:VAL39 4.9 27.8 1.0 CA A:ASN34 4.9 56.1 1.0 CB A:GLU43 4.9 29.1 1.0

Calcium binding site 2 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:40.6 occ:1.00 OD1 A:ASN70 2.3 50.9 1.0 O A:LYS74 2.3 27.9 1.0 OE1 A:GLU79 2.4 57.1 1.0 OD1 A:ASP72 2.4 38.4 1.0 OD1 A:ASP68 2.4 56.5 1.0 OE2 A:GLU79 2.4 43.0 1.0 CD A:GLU79 2.7 44.5 1.0 CG A:ASN70 3.2 48.4 1.0 CG A:ASP72 3.3 36.4 1.0 C A:LYS74 3.3 27.9 1.0 CG A:ASP68 3.5 43.3 1.0 ND2 A:ASN70 3.6 55.8 1.0 OD2 A:ASP72 3.6 51.1 1.0 OD2 A:ASP76 4.1 64.5 1.0 N A:LYS74 4.2 27.7 1.0 CA A:LYS74 4.2 33.0 1.0 N A:LEU75 4.2 28.1 1.0 CG A:GLU79 4.2 38.1 1.0 CA A:LEU75 4.3 29.4 1.0 CA A:ASP68 4.3 37.0 1.0 OD2 A:ASP68 4.3 40.4 1.0 N A:ASP76 4.3 31.5 1.0 CB A:ASP68 4.4 37.2 1.0 N A:ASP72 4.4 29.2 1.0 CB A:LYS74 4.4 36.0 1.0 CB A:ASP72 4.6 30.2 1.0 N A:ASN70 4.6 35.7 1.0 CB A:ASN70 4.6 43.7 1.0 CG A:ASP76 4.7 56.4 1.0 C A:ASP68 4.7 37.0 1.0 N A:LYS71 4.8 43.4 1.0 N A:VAL69 4.8 35.9 1.0 C A:LEU75 4.8 31.1 1.0 CA A:ASP72 5.0 29.3 1.0 CA A:ASN70 5.0 39.2 1.0

Calcium binding site 3 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:93.1 occ:1.00 OE1 A:GLU110 2.4 75.7 1.0 O A:HOH1112 2.5 90.9 1.0 OD2 A:ASP103 2.5 0.1 1.0 CD A:GLU110 2.8 79.6 1.0 OE2 A:GLU110 3.1 87.2 1.0 O A:LYS105 3.1 69.6 1.0 N A:GLU107 3.2 65.1 1.0 ND2 A:ASN101 3.4 0.9 1.0 OD1 A:ASN101 3.5 0.2 1.0 CB A:GLU107 3.6 74.8 1.0 CG A:ASP103 3.6 0.2 1.0 C A:LYS105 3.7 66.3 1.0 CG A:ASN101 3.8 0.3 1.0 C A:ILE106 3.8 53.9 1.0 CA A:ILE106 3.8 50.4 1.0 CG A:GLU110 3.9 75.2 1.0 CA A:GLU107 4.0 64.9 1.0 N A:ILE106 4.1 52.6 1.0 OD1 A:ASP103 4.1 0.8 1.0 OD1 A:ASP99 4.5 75.4 1.0 CG A:GLU107 4.6 82.1 1.0 CB A:GLU110 4.7 70.4 1.0 CB A:LYS105 4.7 79.4 1.0 CA A:LYS105 4.7 72.6 1.0 O A:ILE106 4.8 49.4 1.0 CB A:ASP103 4.9 0.6 1.0 CD A:GLU107 4.9 92.9 1.0

Calcium binding site 4 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:37.8 occ:1.00 OD1 B:ASP36 2.3 57.7 1.0 OD1 B:ASN34 2.3 47.7 1.0 O B:VAL38 2.3 34.5 1.0 O B:HOH1102 2.3 17.8 1.0 OE1 B:GLU43 2.4 33.8 1.0 OD1 B:ASP32 2.4 41.1 1.0 OE2 B:GLU43 2.4 46.5 1.0 CD B:GLU43 2.7 34.1 1.0 CG B:ASP36 3.1 49.8 1.0 OD2 B:ASP36 3.4 45.0 1.0 CG B:ASN34 3.4 51.9 1.0 C B:VAL38 3.5 32.5 1.0 CG B:ASP32 3.6 41.4 1.0 ND2 B:ASN34 3.8 57.0 1.0 OD2 B:ASP40 3.8 59.7 1.0 CG B:GLU43 4.2 34.3 1.0 CA B:VAL39 4.3 32.4 1.0 N B:ASP36 4.3 48.2 1.0 N B:VAL39 4.3 31.3 1.0 CA B:ASP32 4.4 45.8 1.0 CB B:ASP36 4.4 49.3 1.0 CG2 B:VAL38 4.4 37.4 1.0 OD2 B:ASP32 4.4 39.0 1.0 N B:VAL38 4.4 33.8 1.0 N B:ASN34 4.4 54.7 1.0 O B:HOH1103 4.5 48.5 1.0 CB B:ASP32 4.5 42.4 1.0 CA B:VAL38 4.5 31.9 1.0 N B:ARG33 4.5 48.7 1.0 N B:ASP40 4.6 35.0 1.0 C B:ASP32 4.6 46.5 1.0 N B:GLY35 4.7 50.7 1.0 CB B:ASN34 4.7 53.9 1.0 CG B:ASP40 4.8 54.2 1.0 CA B:ASP36 4.8 43.6 1.0 C B:VAL39 4.9 32.6 1.0 CA B:ASN34 5.0 56.3 1.0 CB B:GLU43 5.0 36.2 1.0

Calcium binding site 5 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:31.1 occ:1.00 O B:LYS74 2.2 25.4 1.0 OD1 B:ASN70 2.3 43.6 1.0 OE1 B:GLU79 2.3 30.9 1.0 OD1 B:ASP68 2.3 44.5 1.0 O B:HOH1106 2.4 26.9 1.0 OD1 B:ASP72 2.4 42.2 1.0 OE2 B:GLU79 2.4 34.8 1.0 CD B:GLU79 2.7 32.9 1.0 CG B:ASP72 3.3 33.1 1.0 C B:LYS74 3.3 23.7 1.0 CG B:ASN70 3.3 36.3 1.0 CG B:ASP68 3.5 38.9 1.0 OD2 B:ASP72 3.6 32.4 1.0 ND2 B:ASN70 3.7 32.7 1.0 N B:LYS74 4.2 30.3 1.0 CA B:ASP68 4.2 30.7 1.0 CG B:GLU79 4.2 33.8 1.0 CA B:LYS74 4.2 20.9 1.0 N B:LEU75 4.2 30.3 1.0 OD2 B:ASP76 4.3 46.0 1.0 CA B:LEU75 4.3 32.9 1.0 CB B:ASP68 4.3 30.2 1.0 OD2 B:ASP68 4.4 45.4 1.0 N B:ASP76 4.4 20.3 1.0 N B:ASP72 4.4 36.2 1.0 CB B:ASP72 4.6 32.1 1.0 N B:ASN70 4.6 31.7 1.0 CB B:LYS74 4.6 35.3 1.0 C B:ASP68 4.6 34.5 1.0 N B:VAL69 4.7 36.1 1.0 CB B:ASN70 4.7 33.7 1.0 N B:LYS71 4.8 38.2 1.0 C B:LEU75 4.8 32.3 1.0 CG B:ASP76 4.8 38.1 1.0 CA B:ASP72 5.0 35.4 1.0 CB B:GLU79 5.0 31.6 1.0

Calcium binding site 6 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:54.1 occ:1.00 O B:LYS105 2.2 68.8 1.0 OD1 B:ASP103 2.3 1.0 1.0 OD1 B:ASN101 2.3 80.0 1.0 OE1 B:GLU110 2.4 52.6 1.0 OE2 B:GLU110 2.4 66.9 1.0 OD2 B:ASP103 2.4 0.2 1.0 O B:HOH1104 2.4 55.2 1.0 OD1 B:ASP99 2.5 69.1 1.0 CG B:ASP103 2.6 0.6 1.0 CD B:GLU110 2.7 56.3 1.0 CG B:ASN101 3.1 74.5 1.0 ND2 B:ASN101 3.3 68.5 1.0 C B:LYS105 3.3 66.3 1.0 CG B:ASP99 3.7 62.0 1.0 CB B:ASP103 4.0 94.6 1.0 N B:ILE106 4.1 52.0 1.0 CA B:ILE106 4.1 48.8 1.0 CG B:GLU110 4.2 51.3 1.0 N B:LYS105 4.2 72.8 1.0 CA B:LYS105 4.3 67.8 1.0 N B:GLU107 4.4 62.6 1.0 OD2 B:ASP99 4.4 62.5 1.0 N B:ASP103 4.5 84.2 1.0 CB B:ASN101 4.6 76.0 1.0 CA B:ASP99 4.6 64.8 1.0 CB B:ASP99 4.6 60.9 1.0 N B:ASN101 4.7 69.3 1.0 C B:ILE106 4.7 50.9 1.0 CB B:LYS105 4.8 76.0 1.0 CA B:ASP103 4.8 88.2 1.0 N B:LYS100 4.8 62.4 1.0 N B:GLY104 4.8 66.0 1.0 N B:ASN102 4.9 80.6 1.0 CB B:GLU110 5.0 49.9 1.0 C B:ASP99 5.0 70.9 1.0

Calcium binding site 7 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:37.8 occ:1.00 OD1 C:ASP32 2.3 32.9 1.0 OD1 C:ASN34 2.3 46.9 1.0 ND2 C:ASN34 2.3 55.6 1.0 OE2 C:GLU43 2.3 45.2 1.0 OD1 C:ASP36 2.4 60.1 1.0 OE1 C:GLU43 2.4 46.3 1.0 O C:HOH1101 2.4 41.3 1.0 CG C:ASN34 2.5 46.2 1.0 O C:VAL38 2.6 30.9 1.0 CD C:GLU43 2.7 41.5 1.0 CG C:ASP36 3.2 53.0 1.0 OD2 C:ASP36 3.4 46.5 1.0 CG C:ASP32 3.5 35.6 1.0 C C:VAL38 3.8 33.3 1.0 OD2 C:ASP40 3.9 50.5 1.0 CB C:ASN34 4.0 39.5 1.0 N C:ASN34 4.2 37.8 1.0 CG C:GLU43 4.2 34.9 1.0 OD2 C:ASP32 4.3 43.8 1.0 CA C:ASP32 4.3 39.6 1.0 N C:ASP36 4.4 37.2 1.0 CB C:ASP32 4.4 29.8 1.0 CB C:ASP36 4.4 47.4 1.0 N C:ARG33 4.5 39.5 1.0 CG2 C:VAL38 4.5 31.8 1.0 CA C:ASN34 4.5 38.2 1.0 C C:ASP32 4.6 38.5 1.0 N C:GLY35 4.6 38.8 1.0 CA C:VAL39 4.6 24.8 1.0 N C:VAL38 4.6 31.8 1.0 N C:VAL39 4.7 31.1 1.0 CA C:VAL38 4.8 38.8 1.0 C C:ASN34 4.8 40.9 1.0 N C:ASP40 4.9 28.6 1.0 CA C:ASP36 4.9 38.6 1.0 CG C:ASP40 4.9 46.5 1.0

Calcium binding site 8 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1002 b:38.7 occ:1.00 O C:LYS74 2.3 38.2 1.0 OD1 C:ASP68 2.3 38.2 1.0 OD1 C:ASN70 2.3 48.8 1.0 OD1 C:ASP72 2.4 43.0 1.0 OE2 C:GLU79 2.4 34.3 1.0 O C:HOH1105 2.4 34.6 1.0 OE1 C:GLU79 2.5 32.2 1.0 CD C:GLU79 2.8 27.8 1.0 CG C:ASP72 3.3 44.3 1.0 CG C:ASN70 3.4 40.5 1.0 C C:LYS74 3.4 33.3 1.0 CG C:ASP68 3.4 33.3 1.0 OD2 C:ASP72 3.7 55.9 1.0 ND2 C:ASN70 3.8 42.0 1.0 CA C:ASP68 4.1 32.3 1.0 N C:LYS74 4.2 40.0 1.0 OD2 C:ASP76 4.2 46.8 1.0 CB C:ASP68 4.2 31.1 1.0 CG C:GLU79 4.3 28.4 1.0 OD2 C:ASP68 4.3 34.9 1.0 CA C:LYS74 4.3 35.5 1.0 N C:LEU75 4.3 29.3 1.0 N C:ASP72 4.4 40.5 1.0 CA C:LEU75 4.4 32.9 1.0 N C:ASN70 4.5 38.8 1.0 N C:ASP76 4.5 29.5 1.0 C C:ASP68 4.5 40.6 1.0 N C:VAL69 4.6 44.0 1.0 CB C:ASP72 4.6 42.2 1.0 CB C:ASN70 4.7 43.0 1.0 N C:LYS71 4.7 47.1 1.0 CB C:LYS74 4.7 41.4 1.0 CG C:ASP76 4.9 37.5 1.0 CA C:ASP72 4.9 41.8 1.0 CA C:ASN70 5.0 42.1 1.0 C C:LEU75 5.0 30.5 1.0

Calcium binding site 9 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1003 b:92.0 occ:1.00 OD1 C:ASP103 2.3 0.4 1.0 OE2 C:GLU110 2.3 58.8 1.0 O C:LYS105 2.3 55.3 1.0 OE1 C:GLU110 2.4 63.4 1.0 OD2 C:ASP103 2.4 0.5 1.0 OD1 C:ASP99 2.4 74.0 1.0 OD1 C:ASN101 2.4 0.2 1.0 CG C:ASP103 2.6 0.2 1.0 CD C:GLU110 2.7 59.8 1.0 ND2 C:ASN101 2.9 0.6 1.0 CG C:ASN101 3.0 0.2 1.0 C C:LYS105 3.5 52.1 1.0 CG C:ASP99 3.6 66.5 1.0 CB C:ASP103 4.1 0.9 1.0 CG C:GLU110 4.1 55.3 1.0 CA C:ILE106 4.2 46.2 1.0 N C:LYS105 4.3 61.8 1.0 N C:ILE106 4.3 47.3 1.0 OD2 C:ASP99 4.4 63.9 1.0 CB C:ASN101 4.4 0.8 1.0 CA C:LYS105 4.5 58.0 1.0 CA C:ASP99 4.5 65.1 1.0 N C:ASN101 4.6 0.3 1.0 CB C:ASP99 4.6 64.2 1.0 N C:ASP103 4.6 96.8 1.0 CG C:LYS105 4.6 61.8 1.0 N C:LYS100 4.7 62.1 1.0 N C:GLU107 4.7 64.7 1.0 NZ C:LYS105 4.8 64.6 1.0 N C:GLY104 4.8 83.7 1.0 C C:ASP99 4.9 67.7 1.0 CA C:ASP103 4.9 98.7 1.0 N C:ASN102 4.9 97.3 1.0 CA C:ASN101 5.0 0.5 1.0 C C:ILE106 5.0 57.5 1.0

Calcium binding site 10 out of 13 in the Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Calcium-Bound Regulatory Domain of the Human Atp-Mg/Pi Carrier in the P212121 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1004 b:86.4 occ:1.00 OD1 C:ASP135 2.4 77.7 1.0 OE2 C:GLU146 2.4 59.1 1.0 O C:THR141 2.5 53.6 1.0 OG1 C:THR139 2.5 59.1 1.0 OE1 C:GLU146 2.5 48.0 1.0 OD2 C:ASP137 2.5 88.1 1.0 CD C:GLU146 2.8 50.8 1.0 CG C:ASP135 3.2 70.0 1.0 O C:HOH1117 3.3 40.4 1.0 CG C:ASP137 3.4 85.1 1.0 OD2 C:ASP135 3.6 72.4 1.0 C C:THR141 3.7 50.9 1.0 CB C:ASP137 3.8 80.6 1.0 CB C:THR139 3.8 65.7 1.0 N C:ASP137 4.2 67.7 1.0 CA C:VAL142 4.2 42.0 1.0 CB C:ASP135 4.2 59.7 1.0 CG2 C:THR139 4.2 69.0 1.0 CG C:GLU146 4.3 46.0 1.0 N C:VAL142 4.4 45.7 1.0 CA C:ASP135 4.5 52.8 1.0 OD1 C:ASP137 4.5 87.3 1.0 N C:VAL136 4.5 58.8 1.0 N C:THR139 4.6 68.6 1.0 CA C:ASP137 4.6 75.7 1.0 N C:THR141 4.7 62.8 1.0 OG1 C:THR141 4.7 71.7 1.0 CA C:THR139 4.7 67.4 1.0 CA C:THR141 4.8 60.6 1.0 N C:ASP143 4.8 43.5 1.0 CG1 C:VAL142 4.9 37.7 1.0 C C:ASP135 4.9 53.1 1.0 N C:GLY138 4.9 91.2 1.0

S.P.Harborne, J.J.Ruprecht, E.R.Kunji. Calcium-Induced Conformational Changes in the Regulatory Domain of the Human Mitochondrial Atp-Mg/Pi Carrier. Biochim.Biophys.Acta V.1847 1245 2015.
ISSN: ISSN 0006-3002
PubMed: 26164100
DOI: 10.1016/J.BBABIO.2015.07.002