Calcium in PDB 5m6c: Crystal Structure of T71N Mutant of Human Hippocalcin

The structure of Crystal Structure of T71N Mutant of Human Hippocalcin, PDB code: 5m6c was solved by N.Helassa, S.V.Antonyuk, L.Y.Lian, L.P.Haynes, R.D.Burgoyne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.30 / 3.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	51.160, 51.160, 284.061, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 28.3

The binding sites of Calcium atom in the Crystal Structure of T71N Mutant of Human Hippocalcin (pdb code 5m6c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of T71N Mutant of Human Hippocalcin, PDB code: 5m6c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of T71N Mutant of Human Hippocalcin


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 T71N Mutant of Human Hippocalcin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:76.6 occ:1.00 OE1 A:GLU84 2.2 56.6 1.0 OD1 A:ASP77 2.3 66.9 1.0 O A:THR79 2.3 58.4 1.0 OD1 A:ASP73 2.4 60.6 1.0 OD1 A:ASN75 2.4 65.7 1.0 CD A:GLU84 3.3 56.5 1.0 CG A:ASP77 3.4 68.0 1.0 C A:THR79 3.5 60.0 1.0 CG A:ASP73 3.5 60.5 1.0 CG A:ASN75 3.6 63.7 1.0 OE2 A:GLU84 3.6 57.4 1.0 OD2 A:ASP77 3.9 67.8 1.0 ND2 A:ASN75 4.1 62.4 1.0 OD2 A:ASP73 4.2 59.5 1.0 CA A:ILE80 4.3 58.0 1.0 N A:ILE80 4.3 59.5 1.0 OG1 A:THR79 4.4 65.7 1.0 N A:THR79 4.4 64.5 1.0 CA A:THR79 4.5 62.8 1.0 CB A:ASP73 4.5 59.3 1.0 CG A:GLU84 4.6 54.5 1.0 CA A:ASP73 4.6 59.9 1.0 CB A:ASP77 4.6 67.3 1.0 N A:ASP77 4.6 70.4 1.0 OD2 A:ASP81 4.6 66.6 1.0 N A:ASP81 4.6 58.0 1.0 CB A:ASN75 4.9 63.9 1.0 N A:ASN75 4.9 65.1 1.0 C A:ILE80 4.9 58.1 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of T71N Mutant of Human Hippocalcin


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 T71N Mutant of Human Hippocalcin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:86.3 occ:1.00 OD1 A:ASP157 2.4 0.3 1.0 O A:LYS163 2.4 0.1 1.0 OD1 A:ASP161 2.6 1.0 1.0 OE2 A:GLU168 2.8 98.7 1.0 OE1 A:GLU168 2.8 0.8 1.0 OD1 A:ASN159 2.9 1.0 1.0 CD A:GLU168 3.2 0.9 1.0 CG A:ASP157 3.6 99.5 1.0 C A:LYS163 3.6 0.8 1.0 CG A:ASP161 3.6 0.1 1.0 CG A:ASN159 3.7 0.0 1.0 ND2 A:ASN159 3.9 0.1 1.0 OD2 A:ASP161 4.1 0.4 1.0 CA A:ASP157 4.2 0.6 1.0 N A:THR158 4.3 0.2 1.0 OD2 A:ASP157 4.3 95.9 1.0 N A:ASN159 4.4 0.6 1.0 CA A:LEU164 4.4 0.0 1.0 N A:LEU164 4.4 0.0 1.0 N A:ASP161 4.4 0.1 1.0 CB A:ASP157 4.5 0.9 1.0 N A:ASN160 4.5 0.7 1.0 N A:LYS163 4.5 0.3 1.0 CA A:LYS163 4.6 0.8 1.0 C A:ASP157 4.6 0.7 1.0 N A:SER165 4.7 0.3 1.0 CG A:GLU168 4.7 0.3 1.0 CB A:ASP161 4.8 0.5 1.0 CB A:ASN159 4.9 0.8 1.0 CA A:ASN159 4.9 0.2 1.0 C A:ASN159 5.0 0.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of T71N Mutant of Human Hippocalcin


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 T71N Mutant of Human Hippocalcin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:99.2 occ:1.00 O A:TYR115 2.3 82.9 1.0 OD1 A:ASP109 2.4 85.0 1.0 OD1 A:ASN113 2.4 0.7 1.0 OD1 A:ASP111 2.5 88.6 1.0 OE1 A:GLU120 2.8 87.1 1.0 OE2 A:GLU120 2.9 83.8 1.0 CD A:GLU120 3.2 86.8 1.0 CG A:ASP111 3.4 88.6 1.0 CG A:ASN113 3.4 0.5 1.0 C A:TYR115 3.5 86.3 1.0 CG A:ASP109 3.6 83.5 1.0 OD2 A:ASP111 3.7 88.5 1.0 ND2 A:ASN113 4.0 0.6 1.0 N A:TYR115 4.0 89.7 1.0 CA A:ASP109 4.1 79.5 1.0 N A:LEU110 4.2 81.4 1.0 N A:ASP111 4.2 87.1 1.0 N A:ASN113 4.2 92.0 1.0 N A:GLY112 4.2 89.8 1.0 CA A:TYR115 4.3 88.9 1.0 C A:ASP109 4.4 80.7 1.0 CB A:ASP109 4.4 81.5 1.0 OD2 A:ASP109 4.4 84.1 1.0 N A:ILE116 4.5 85.0 1.0 CB A:ASN113 4.6 96.8 1.0 CB A:ASP111 4.7 88.7 1.0 N A:GLY114 4.7 92.2 1.0 CA A:ILE116 4.7 87.1 1.0 CG A:GLU120 4.7 87.1 1.0 CB A:TYR115 4.8 92.5 1.0 CA A:ASP111 4.8 89.7 1.0 CA A:ASN113 4.9 93.9 1.0 C A:ASP111 5.0 90.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of T71N Mutant of Human Hippocalcin


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 T71N Mutant of Human Hippocalcin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:90.8 occ:1.00 O E:THR79 2.3 88.7 1.0 OE1 E:GLU84 2.3 79.8 1.0 OD1 E:ASN75 2.4 83.2 1.0 OD1 E:ASP77 2.4 91.5 1.0 OD1 E:ASP73 2.4 83.8 1.0 CD E:GLU84 3.3 79.2 1.0 CG E:ASP77 3.4 90.3 1.0 CG E:ASP73 3.4 87.5 1.0 C E:THR79 3.5 89.4 1.0 CG E:ASN75 3.5 84.2 1.0 OE2 E:GLU84 3.6 79.7 1.0 OD2 E:ASP77 3.8 89.9 1.0 ND2 E:ASN75 4.0 84.1 1.0 OD2 E:ASP73 4.1 89.1 1.0 CA E:ILE80 4.3 85.4 1.0 N E:ILE80 4.3 87.9 1.0 N E:THR79 4.4 90.0 1.0 N E:ASP77 4.4 86.5 1.0 CB E:ASP73 4.4 86.8 1.0 CA E:THR79 4.5 89.9 1.0 OG1 E:THR79 4.5 90.8 1.0 CA E:ASP73 4.5 85.2 1.0 N E:SER76 4.5 87.1 1.0 OD2 E:ASP81 4.6 81.4 1.0 CG E:GLU84 4.6 77.1 1.0 CB E:ASP77 4.7 88.7 1.0 CB E:ASN75 4.7 85.4 1.0 N E:ASP81 4.7 81.1 1.0 N E:ASN75 4.9 88.3 1.0 N E:THR74 5.0 88.3 1.0 C E:ILE80 5.0 83.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of T71N Mutant of Human Hippocalcin


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 T71N Mutant of Human Hippocalcin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca202 b:71.9 occ:1.00 O E:LYS163 2.4 79.8 1.0 OD1 E:ASP157 2.4 78.4 1.0 OD1 E:ASP161 2.4 74.0 1.0 OE1 E:GLU168 2.7 69.8 1.0 OD1 E:ASN159 2.9 75.3 1.0 OE2 E:GLU168 3.1 73.6 1.0 CD E:GLU168 3.3 72.5 1.0 CG E:ASP161 3.4 74.8 1.0 CG E:ASP157 3.6 78.1 1.0 C E:LYS163 3.6 76.1 1.0 CG E:ASN159 3.7 75.9 1.0 ND2 E:ASN159 3.9 75.8 1.0 OD2 E:ASP161 3.9 75.9 1.0 OD2 E:ASP157 4.3 78.2 1.0 CA E:LEU164 4.4 69.0 1.0 N E:ASP161 4.4 71.8 1.0 N E:LYS163 4.4 75.4 1.0 N E:LEU164 4.4 72.5 1.0 CA E:ASP157 4.5 74.1 1.0 CB E:ASP161 4.6 73.9 1.0 CA E:LYS163 4.6 75.5 1.0 CB E:ASP157 4.6 76.3 1.0 N E:SER165 4.6 69.5 1.0 N E:ASN159 4.7 76.7 1.0 CG E:GLU168 4.8 71.2 1.0 N E:ASN160 4.8 72.7 1.0 N E:THR158 4.8 73.9 1.0 N E:GLY162 4.8 74.0 1.0 C E:ASP157 4.9 74.3 1.0 CA E:ASP161 4.9 72.9 1.0 CD2 E:LEU164 4.9 66.9 1.0 CG E:LYS163 5.0 74.8 1.0 CB E:ASN159 5.0 76.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of T71N Mutant of Human Hippocalcin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of T71N Mutant of Human Hippocalcin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca203 b:78.6 occ:1.00 OD1 E:ASN113 2.3 73.2 1.0 OD1 E:ASP109 2.3 76.0 1.0 O E:TYR115 2.4 86.5 1.0 OE1 E:GLU120 2.7 75.4 1.0 OD1 E:ASP111 2.7 85.1 1.0 OE2 E:GLU120 2.8 79.8 1.0 CD E:GLU120 3.1 78.3 1.0 CG E:ASN113 3.4 78.7 1.0 CG E:ASP109 3.5 75.8 1.0 CG E:ASP111 3.5 84.5 1.0 C E:TYR115 3.6 84.9 1.0 OD2 E:ASP111 3.8 83.8 1.0 ND2 E:ASN113 4.0 79.8 1.0 N E:TYR115 4.1 86.0 1.0 N E:ASN113 4.2 86.3 1.0 CA E:ASP109 4.2 74.8 1.0 N E:GLY112 4.3 83.4 1.0 OD2 E:ASP109 4.3 78.2 1.0 N E:LEU110 4.4 77.9 1.0 CB E:ASP109 4.4 75.3 1.0 N E:ASP111 4.4 81.0 1.0 CA E:TYR115 4.4 85.4 1.0 C E:ASP109 4.5 77.8 1.0 CB E:ASN113 4.5 81.5 1.0 N E:ILE116 4.5 84.0 1.0 CG E:GLU120 4.6 78.6 1.0 N E:GLY114 4.6 84.7 1.0 CA E:ILE116 4.6 83.8 1.0 N E:SER117 4.8 84.3 1.0 CB E:ASP111 4.8 83.8 1.0 CA E:ASN113 4.8 84.4 1.0 CB E:TYR115 5.0 85.9 1.0 CA E:ASP111 5.0 82.7 1.0

N.Helassa, S.V.Antonyuk, L.Y.Lian, L.P.Haynes, R.D.Burgoyne. Biophysical and Functional Characterization of Hippocalcin Mutants Responsible For Human Dystonia. Hum. Mol. Genet. V. 26 2426 2017.
ISSN: ESSN 1460-2083
PubMed: 28398555
DOI: 10.1093/HMG/DDX133