Calcium in PDB 4n5x: Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1

The structure of Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1, PDB code: 4n5x was solved by Q.Yang, S.Bruschweiler, J.Chou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.07 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.210, 51.210, 112.153, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 22.5

The binding sites of Calcium atom in the Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1 (pdb code 4n5x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1, PDB code: 4n5x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:23.4 occ:1.00 O A:VAL38 2.3 20.6 1.0 OD1 A:ASP32 2.3 27.1 1.0 OD1 A:ASP36 2.4 25.0 1.0 O A:HOH356 2.4 17.6 1.0 OE1 A:GLU43 2.6 19.9 1.0 OE2 A:GLU43 2.6 25.3 1.0 OD1 A:ASN34 2.6 26.6 1.0 CD A:GLU43 2.9 22.8 1.0 CG A:ASP36 3.2 29.9 1.0 CG A:ASP32 3.3 29.8 1.0 C A:VAL38 3.5 27.3 1.0 OD2 A:ASP36 3.5 27.6 1.0 CG A:ASN34 3.6 29.2 1.0 ND2 A:ASN34 4.0 27.1 1.0 CA A:ASP32 4.1 30.6 1.0 N A:ASP36 4.1 31.6 1.0 OD2 A:ASP32 4.1 29.6 1.0 CB A:ASP32 4.1 26.4 1.0 N A:VAL38 4.2 25.4 1.0 CA A:VAL39 4.3 18.7 1.0 N A:VAL39 4.3 21.2 1.0 CG A:GLU43 4.4 17.1 1.0 CA A:VAL38 4.4 20.7 1.0 C A:ASP32 4.4 29.4 1.0 CB A:ASP36 4.4 29.8 1.0 CG2 A:VAL38 4.4 21.0 1.0 OD2 A:ASP40 4.5 19.1 1.0 N A:ASP40 4.5 16.1 1.0 N A:ASN34 4.5 28.6 1.0 N A:GLY35 4.6 32.4 1.0 CA A:ASP36 4.6 24.2 1.0 N A:ARG33 4.7 28.8 1.0 N A:GLY37 4.7 24.8 1.0 CB A:ASN34 4.8 34.1 1.0 O A:HOH392 4.8 38.7 1.0 C A:ASP36 4.9 28.6 1.0 C A:VAL39 4.9 21.4 1.0 O A:ASP32 4.9 32.2 1.0 CA A:ASN34 5.0 30.1 1.0 C A:ASN34 5.0 33.7 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:17.1 occ:1.00 O A:GLN57 2.3 19.7 1.0 OE2 A:GLU60 2.4 16.4 1.0 OE2 A:GLU61 2.4 14.5 1.0 O A:HOH390 2.5 14.9 1.0 OE1 A:GLU61 2.7 17.1 1.0 CD A:GLU61 2.9 14.9 1.0 CD A:GLU60 3.3 19.1 1.0 C A:GLN57 3.5 19.1 1.0 OE1 A:GLU60 3.9 18.3 1.0 NE2 A:GLN45 4.0 15.7 1.0 O A:HOH332 4.1 19.0 1.0 CG A:GLU60 4.1 13.5 1.0 N A:ASP58 4.4 20.4 1.0 CA A:ASP58 4.4 18.5 1.0 CA A:GLN57 4.4 22.0 1.0 CG A:GLU61 4.5 17.7 1.0 O A:HOH369 4.5 23.0 1.0 CB A:GLN57 4.6 16.8 1.0 CD A:GLN45 4.9 16.3 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:19.5 occ:1.00 O A:LYS74 2.3 19.5 1.0 OD1 A:ASP68 2.3 20.6 1.0 OD1 A:ASP72 2.4 25.0 1.0 OD1 A:ASN70 2.4 21.9 1.0 O A:HOH324 2.4 20.3 1.0 OE1 A:GLU79 2.5 18.9 1.0 OE2 A:GLU79 2.6 19.5 1.0 CD A:GLU79 2.9 21.5 1.0 CG A:ASP72 3.2 26.1 1.0 CG A:ASN70 3.3 24.6 1.0 CG A:ASP68 3.4 22.0 1.0 C A:LYS74 3.4 22.0 1.0 OD2 A:ASP72 3.5 26.5 1.0 ND2 A:ASN70 3.8 22.4 1.0 N A:LYS74 4.1 18.7 1.0 OD2 A:ASP68 4.1 21.8 1.0 N A:ASP72 4.2 18.3 1.0 CA A:ASP68 4.2 19.6 1.0 CA A:LYS74 4.3 24.3 1.0 CB A:ASP68 4.3 21.8 1.0 N A:LEU75 4.4 22.6 1.0 CG A:GLU79 4.4 18.7 1.0 CB A:ASP72 4.4 24.8 1.0 N A:ASN70 4.4 20.9 1.0 CA A:LEU75 4.5 22.7 1.0 C A:ASP68 4.5 22.8 1.0 OD2 A:ASP76 4.6 24.4 1.0 N A:ASP76 4.6 18.4 1.0 CB A:ASN70 4.6 22.1 1.0 N A:LYS71 4.7 19.6 1.0 N A:GLY73 4.7 20.1 1.0 CA A:ASP72 4.7 22.8 1.0 N A:VAL69 4.7 19.0 1.0 CB A:LYS74 4.8 23.1 1.0 CA A:ASN70 4.8 21.4 1.0 O A:HOH321 4.9 20.5 1.0 C A:ASP72 4.9 21.0 1.0 C A:ASN70 4.9 24.7 1.0 O A:ASP68 5.0 20.5 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:18.4 occ:1.00 OD1 A:ASP99 2.3 18.2 1.0 O A:LYS105 2.3 17.1 1.0 O A:HOH308 2.4 15.5 1.0 OE2 A:GLU110 2.4 17.6 1.0 OD1 A:ASN101 2.4 17.6 1.0 OE1 A:GLU110 2.5 13.2 1.0 OD1 A:ASP103 2.5 19.1 1.0 CD A:GLU110 2.8 17.2 1.0 CG A:ASP103 3.3 19.4 1.0 CG A:ASN101 3.4 20.1 1.0 CG A:ASP99 3.4 17.6 1.0 C A:LYS105 3.4 14.7 1.0 OD2 A:ASP103 3.5 18.1 1.0 ND2 A:ASN101 3.8 22.1 1.0 N A:LYS105 4.1 18.4 1.0 CA A:ASP99 4.1 17.2 1.0 OD2 A:ASP99 4.2 17.4 1.0 CA A:LYS105 4.2 16.5 1.0 CB A:ASP99 4.2 19.2 1.0 N A:ASP103 4.2 21.5 1.0 CG A:GLU110 4.2 15.0 1.0 N A:ASN101 4.3 19.0 1.0 N A:ILE106 4.4 17.6 1.0 C A:ASP99 4.4 17.3 1.0 CA A:ILE106 4.5 15.5 1.0 CB A:ASP103 4.5 21.7 1.0 CB A:LYS105 4.5 18.3 1.0 CB A:ASN101 4.6 17.7 1.0 N A:ASN102 4.6 21.9 1.0 N A:LYS100 4.6 17.6 1.0 OE2 A:GLU107 4.6 18.2 1.0 CA A:ASN101 4.7 19.8 1.0 CA A:ASP103 4.8 20.4 1.0 C A:ASN101 4.8 23.0 1.0 N A:GLU107 4.8 15.9 1.0 O A:ASP99 4.9 15.3 1.0 N A:GLY104 4.9 17.9 1.0 CG A:GLU107 5.0 22.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of N-Terminal Calmodulin-Like Calcium Sensor of Human Mitochondrial Atp-Mg/Pi Carrier SCAMC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:15.3 occ:1.00 OD1 A:ASP135 2.2 15.2 1.0 O A:THR141 2.4 16.9 1.0 OD1 A:ASP137 2.4 18.5 1.0 O A:HOH311 2.4 16.1 1.0 OG1 A:THR139 2.5 15.3 1.0 OE1 A:GLU146 2.5 14.5 1.0 OE2 A:GLU146 2.5 21.6 1.0 CD A:GLU146 2.8 19.9 1.0 CG A:ASP135 3.3 19.5 1.0 CG A:ASP137 3.4 20.6 1.0 C A:THR141 3.6 18.4 1.0 OD2 A:ASP137 3.7 20.9 1.0 CB A:THR139 3.8 15.9 1.0 OG1 A:THR141 4.0 18.0 1.0 N A:THR139 4.0 17.6 1.0 OD2 A:ASP135 4.1 16.7 1.0 CG2 A:THR139 4.2 20.6 1.0 CB A:ASP135 4.3 22.1 1.0 CA A:ASP135 4.3 20.1 1.0 N A:THR141 4.3 22.2 1.0 N A:ASP137 4.3 24.9 1.0 CG A:GLU146 4.3 21.8 1.0 CA A:VAL142 4.4 13.2 1.0 CA A:THR139 4.4 20.0 1.0 N A:VAL136 4.4 24.2 1.0 N A:VAL142 4.5 17.4 1.0 OD2 A:ASP143 4.5 22.6 1.0 CA A:THR141 4.5 17.9 1.0 N A:ASP143 4.6 13.2 1.0 CB A:ASP137 4.7 23.2 1.0 N A:GLY138 4.7 20.7 1.0 O A:HOH406 4.7 24.5 1.0 C A:ASP135 4.8 20.4 1.0 N A:MET140 4.8 19.9 1.0 CA A:ASP137 4.8 23.3 1.0 C A:THR139 4.9 18.7 1.0 C A:ASP137 4.9 23.1 1.0 CB A:THR141 4.9 18.0 1.0 C A:VAL142 5.0 15.6 1.0 CG A:ASP143 5.0 17.5 1.0 O A:HOH360 5.0 32.0 1.0

Q.Yang, S.Bruschweiler, J.J.Chou. A Self-Sequestered Calmodulin-Like Ca(2+) Sensor of Mitochondrial Scamc Carrier and Its Implication to Ca(2+)-Dependent Atp-Mg/Pi Transport. Structure V. 22 209 2014.
ISSN: ISSN 0969-2126
PubMed: 24332718
DOI: 10.1016/J.STR.2013.10.018