Calcium in PDB 5g4p: Crystal Structure of Human Hippocalcin at 2.4 A Resolution

The structure of Crystal Structure of Human Hippocalcin at 2.4 A Resolution, PDB code: 5g4p was solved by S.V.Antonyuk, N.Helassa, 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)	47.43 / 2.42
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	50.970, 50.970, 284.582, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 27.7

The binding sites of Calcium atom in the Crystal Structure of Human Hippocalcin at 2.4 A Resolution (pdb code 5g4p). 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 Human Hippocalcin at 2.4 A Resolution, PDB code: 5g4p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Human Hippocalcin at 2.4 A Resolution


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 Human Hippocalcin at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:57.6 occ:1.00 O A:THR79 2.2 73.0 1.0 O A:HOH301 2.2 57.9 1.0 OD1 A:ASP73 2.3 81.1 1.0 OD1 A:ASP77 2.3 82.7 1.0 OE1 A:GLU84 2.4 72.5 1.0 OD1 A:ASN75 2.4 89.8 1.0 OE2 A:GLU84 2.8 74.6 1.0 CD A:GLU84 3.0 67.4 1.0 CG A:ASP77 3.1 78.6 1.0 CG A:ASP73 3.3 75.7 1.0 C A:THR79 3.4 68.6 1.0 CG A:ASN75 3.4 87.8 1.0 OD2 A:ASP77 3.4 76.4 1.0 ND2 A:ASN75 3.8 90.6 1.0 OD2 A:ASP73 3.9 74.8 1.0 N A:ASP77 4.2 82.6 1.0 N A:THR79 4.2 72.4 1.0 N A:ILE80 4.3 66.1 1.0 CB A:ASP73 4.3 72.1 1.0 CA A:ASP73 4.3 69.7 1.0 CB A:ASP77 4.3 80.7 1.0 CA A:THR79 4.4 70.2 1.0 CA A:ILE80 4.4 62.4 1.0 CG A:GLU84 4.6 62.5 1.0 N A:SER76 4.6 82.8 1.0 N A:ASN75 4.6 79.8 1.0 OG1 A:THR79 4.6 70.8 1.0 C A:ASP73 4.6 72.2 1.0 CA A:ASP77 4.7 81.2 1.0 CB A:ASN75 4.7 85.6 1.0 N A:ASP81 4.8 61.3 1.0 N A:GLY78 4.8 77.7 1.0 N A:THR74 4.8 72.8 1.0 CA A:ASN75 5.0 83.0 1.0 C A:ASN75 5.0 83.9 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human Hippocalcin at 2.4 A Resolution


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 Human Hippocalcin at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:83.8 occ:1.00 OD1 A:ASP157 2.3 0.7 1.0 O A:LYS163 2.3 0.1 1.0 OD1 A:ASP161 2.4 0.0 1.0 OD1 A:ASN159 2.5 0.4 1.0 OE1 A:GLU168 2.5 0.1 1.0 OE2 A:GLU168 2.8 0.2 1.0 CD A:GLU168 2.9 0.2 1.0 CG A:ASN159 3.5 0.5 1.0 C A:LYS163 3.5 1.0 1.0 CG A:ASP161 3.5 0.4 1.0 CG A:ASP157 3.6 0.4 1.0 ND2 A:ASN159 3.9 0.2 1.0 N A:ASP161 4.1 0.5 1.0 CA A:ASP157 4.1 0.5 1.0 C A:ASP157 4.1 0.1 1.0 N A:THR158 4.2 0.2 1.0 O A:HOH304 4.2 70.7 1.0 N A:ASN159 4.2 0.1 1.0 CA A:LEU164 4.2 0.1 1.0 CG A:GLU168 4.3 0.5 1.0 N A:LEU164 4.3 0.5 1.0 OD2 A:ASP161 4.3 0.4 1.0 N A:ASN160 4.3 0.3 1.0 CB A:ASP161 4.4 0.9 1.0 CB A:ASP157 4.4 0.6 1.0 OD2 A:ASP157 4.5 0.1 1.0 N A:LYS163 4.5 0.5 1.0 CA A:LYS163 4.5 0.9 1.0 O A:ASP157 4.7 0.2 1.0 CD2 A:LEU164 4.7 99.2 1.0 CA A:ASP161 4.7 0.5 1.0 N A:SER165 4.7 94.9 1.0 CB A:ASN159 4.8 0.9 1.0 CA A:ASN160 4.9 0.0 1.0 CB A:LYS163 4.9 0.4 1.0 CA A:ASN159 4.9 0.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human Hippocalcin at 2.4 A Resolution


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 Human Hippocalcin at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:72.3 occ:1.00 OD1 A:ASP111 2.3 0.8 1.0 OD1 A:ASP109 2.3 0.7 1.0 OE1 A:GLU120 2.4 1.0 1.0 OD1 A:ASN113 2.5 0.4 1.0 O A:TYR115 2.6 0.8 1.0 OE2 A:GLU120 2.8 0.6 1.0 CD A:GLU120 2.9 0.9 1.0 CG A:ASN113 3.2 0.5 1.0 CG A:ASP111 3.3 1.0 1.0 ND2 A:ASN113 3.5 0.0 1.0 CG A:ASP109 3.6 0.4 1.0 C A:TYR115 3.8 0.0 1.0 OD2 A:ASP111 3.8 0.8 1.0 N A:ASP111 4.0 0.1 1.0 N A:ASN113 4.2 0.8 1.0 N A:GLY112 4.2 0.6 1.0 N A:LEU110 4.3 96.0 1.0 CB A:ASN113 4.3 0.9 1.0 N A:TYR115 4.3 0.2 1.0 CA A:ASP109 4.4 93.7 1.0 CG A:GLU120 4.4 0.8 1.0 CB A:ASP111 4.4 0.4 1.0 OD2 A:ASP109 4.4 0.8 1.0 C A:ASP109 4.4 93.8 1.0 CA A:ASP111 4.5 0.8 1.0 N A:SER117 4.5 0.7 1.0 CA A:TYR115 4.5 0.3 1.0 CB A:ASP109 4.6 98.2 1.0 C A:ASP111 4.7 1.0 1.0 CA A:ASN113 4.7 0.5 1.0 N A:ILE116 4.7 0.1 1.0 CA A:ILE116 4.8 0.6 1.0 N A:GLY114 4.9 0.2 1.0 CB A:TYR115 4.9 0.6 1.0 C A:LEU110 5.0 98.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human Hippocalcin at 2.4 A Resolution


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 Human Hippocalcin at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:66.6 occ:1.00 O E:THR79 2.2 92.5 1.0 OD1 E:ASP73 2.3 92.9 1.0 OE1 E:GLU84 2.4 96.3 1.0 OD1 E:ASN75 2.4 0.9 1.0 OE2 E:GLU84 2.8 97.2 1.0 CD E:GLU84 3.0 90.0 1.0 CG E:ASN75 3.1 0.9 1.0 ND2 E:ASN75 3.1 0.6 1.0 OD1 E:ASP77 3.2 89.2 1.0 C E:THR79 3.3 86.4 1.0 OD2 E:ASP77 3.3 90.7 1.0 CG E:ASP77 3.5 91.0 1.0 CG E:ASP73 3.5 87.8 1.0 OG1 E:THR79 3.9 86.2 1.0 N E:ILE80 4.1 84.9 1.0 OD2 E:ASP81 4.1 91.8 1.0 CA E:ILE80 4.2 83.4 1.0 CA E:THR79 4.2 85.9 1.0 N E:THR79 4.2 85.8 1.0 CB E:ASP73 4.3 86.3 1.0 CA E:ASP73 4.4 84.5 1.0 OD2 E:ASP73 4.5 87.1 1.0 CG E:GLU84 4.5 86.1 1.0 N E:ASP81 4.5 86.1 1.0 N E:ASP77 4.5 93.2 1.0 CB E:ASN75 4.5 0.5 1.0 CB E:THR79 4.6 85.5 1.0 N E:SER76 4.6 99.9 1.0 CB E:ASP77 4.7 93.6 1.0 CG E:ASP81 4.8 88.9 1.0 C E:ASP73 4.8 86.7 1.0 N E:THR74 4.9 89.2 1.0 C E:ILE80 4.9 84.1 1.0 N E:ASN75 4.9 97.0 1.0 C E:ASN75 5.0 0.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human Hippocalcin at 2.4 A Resolution


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 Human Hippocalcin at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca202 b:69.8 occ:1.00 OD1 E:ASP157 2.3 97.7 1.0 OD1 E:ASP161 2.3 0.2 1.0 O E:LYS163 2.4 0.4 1.0 OE1 E:GLU168 2.4 97.7 1.0 OD1 E:ASN159 2.5 0.6 1.0 OE2 E:GLU168 2.8 0.5 1.0 CD E:GLU168 2.9 93.6 1.0 CG E:ASP161 3.0 0.1 1.0 OD2 E:ASP161 3.4 0.3 1.0 CG E:ASN159 3.4 95.7 1.0 CG E:ASP157 3.4 93.4 1.0 C E:LYS163 3.6 96.9 1.0 ND2 E:ASN159 3.7 93.6 1.0 OD2 E:ASP157 4.0 95.9 1.0 N E:ASP161 4.1 0.5 1.0 CB E:ASP161 4.2 0.4 1.0 CA E:LEU164 4.4 86.7 1.0 N E:LYS163 4.4 99.3 1.0 CG E:GLU168 4.4 87.5 1.0 N E:LEU164 4.4 92.1 1.0 N E:ASN159 4.5 92.1 1.0 CA E:ASP161 4.5 0.9 1.0 N E:SER165 4.6 84.8 1.0 CA E:ASP157 4.6 86.3 1.0 CB E:ASP157 4.6 90.1 1.0 CA E:LYS163 4.6 99.3 1.0 CB E:ASN159 4.7 95.6 1.0 N E:THR158 4.8 86.5 1.0 N E:ASN160 4.8 94.6 1.0 N E:GLY162 4.8 0.1 1.0 C E:ASP161 4.9 0.7 1.0 C E:ASP157 4.9 87.5 1.0 C E:LEU164 4.9 85.4 1.0 CG E:LYS163 4.9 0.5 1.0 CA E:ASN159 5.0 94.1 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human Hippocalcin at 2.4 A Resolution


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 Human Hippocalcin at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca203 b:77.4 occ:1.00 OD1 E:ASP111 2.3 0.6 1.0 OD1 E:ASP109 2.3 0.4 1.0 OE1 E:GLU120 2.4 0.7 1.0 OD1 E:ASN113 2.5 0.2 1.0 O E:TYR115 2.6 0.5 1.0 OE2 E:GLU120 2.8 0.1 1.0 CD E:GLU120 2.9 0.4 1.0 CG E:ASN113 3.0 0.2 1.0 ND2 E:ASN113 3.1 0.6 1.0 CG E:ASP111 3.3 0.7 1.0 CG E:ASP109 3.4 92.3 1.0 OD2 E:ASP111 3.8 0.4 1.0 C E:TYR115 3.8 91.1 1.0 N E:ASN113 4.0 0.8 1.0 OD2 E:ASP109 4.2 92.5 1.0 N E:ASP111 4.2 0.4 1.0 N E:GLY112 4.2 0.1 1.0 CB E:ASN113 4.2 0.7 1.0 CA E:ASP109 4.3 87.6 1.0 CB E:ASP109 4.4 88.8 1.0 CG E:GLU120 4.4 0.4 1.0 CB E:ASP111 4.4 0.2 1.0 C E:ASP109 4.4 89.3 1.0 N E:TYR115 4.5 90.2 1.0 N E:LEU110 4.5 91.5 1.0 CA E:ASN113 4.6 0.7 1.0 CA E:ILE116 4.6 90.3 1.0 CA E:ASP111 4.6 0.2 1.0 N E:SER117 4.6 93.0 1.0 C E:ASP111 4.7 0.8 1.0 N E:ILE116 4.7 90.5 1.0 N E:GLY114 4.7 98.8 1.0 CA E:TYR115 4.7 88.9 1.0 C E:GLY112 4.9 0.6 1.0 O E:ASP109 5.0 86.8 1.0 CA E:GLY112 5.0 0.5 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