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Calcium in PDB 5g58: Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 A Resolution

Protein crystallography data

The structure of Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 A Resolution, PDB code: 5g58 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) 43.87 / 2.54
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 50.660, 50.660, 283.460, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 A Resolution (pdb code 5g58). 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 A190T Mutant of Human Hippocalcin at 2.5 A Resolution, PDB code: 5g58:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5g58

Go back to Calcium Binding Sites List in 5g58
Calcium binding site 1 out of 6 in the Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 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 A190T Mutant of Human Hippocalcin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:71.8
occ:1.00
 OD1 A:ASN75 2.1 96.0 1.0
O A:THR79 2.2 61.9 1.0
OD1 A:ASP77 2.3 80.5 1.0
OD1 A:ASP73 2.4 67.9 1.0
OE1 A:GLU84 2.6 55.5 1.0
OE2 A:GLU84 3.0 57.6 1.0
CG A:ASP77 3.2 81.6 1.0
CD A:GLU84 3.2 54.5 1.0
CG A:ASN75 3.2 94.8 1.0
C A:THR79 3.3 62.6 1.0
OD2 A:ASP77 3.4 80.7 1.0
CG A:ASP73 3.5 67.8 1.0
ND2 A:ASN75 3.7 96.5 1.0
N A:ILE80 4.1 58.2 1.0
CA A:ILE80 4.1 54.9 1.0
OD2 A:ASP73 4.2 65.4 1.0
OG1 A:THR79 4.2 73.1 1.0
N A:THR79 4.3 70.3 1.0
CA A:THR79 4.4 67.8 1.0
N A:ASP77 4.4 80.8 1.0
CB A:ASP77 4.5 82.8 1.0
CB A:ASP73 4.5 64.2 1.0
CB A:ASN75 4.5 92.4 1.0
CA A:ASP73 4.5 62.6 1.0
N A:ASP81 4.6 53.2 1.0
N A:SER76 4.6 84.2 1.0
CG A:GLU84 4.7 50.9 1.0
N A:ASN75 4.8 88.7 1.0
C A:ILE80 4.9 54.0 1.0
N A:GLY78 4.9 77.7 1.0
CB A:THR79 4.9 69.8 1.0
CA A:ASP77 4.9 81.8 1.0
C A:ASP73 5.0 65.0 1.0
CA A:ASN75 5.0 90.2 1.0

Calcium binding site 2 out of 6 in 5g58

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Calcium binding site 2 out of 6 in the Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 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 A190T Mutant of Human Hippocalcin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:73.4
occ:1.00
 OD1 A:ASP161 2.4 0.9 1.0
O A:LYS163 2.4 95.5 1.0
OD1 A:ASP157 2.5 0.0 1.0
OE2 A:GLU168 2.6 88.0 1.0
OE1 A:GLU168 2.6 86.5 1.0
CD A:GLU168 2.9 88.5 1.0
OD1 A:ASN159 3.0 0.1 1.0
CG A:ASP161 3.2 0.3 1.0
ND2 A:ASN159 3.2 0.7 1.0
CG A:ASN159 3.4 0.5 1.0
OD2 A:ASP161 3.4 0.8 1.0
C A:LYS163 3.6 94.0 1.0
CG A:ASP157 3.7 0.1 1.0
N A:ASP161 4.1 0.4 1.0
OD2 A:ASP157 4.3 0.4 1.0
N A:ASN160 4.3 1.0 1.0
N A:LYS163 4.4 0.4 1.0
CA A:LEU164 4.4 86.4 1.0
CB A:ASP161 4.4 0.5 1.0
O A:HOH309 4.4 75.7 1.0
N A:LEU164 4.4 89.8 1.0
CG A:GLU168 4.5 88.0 1.0
N A:ASN159 4.5 0.5 1.0
CA A:LYS163 4.5 95.8 1.0
N A:SER165 4.5 83.3 1.0
CA A:ASP157 4.6 98.1 1.0
CB A:ASN159 4.7 0.5 1.0
CB A:LYS163 4.7 97.9 1.0
CB A:ASP157 4.7 98.0 1.0
N A:THR158 4.7 0.6 1.0
CA A:ASP161 4.7 0.1 1.0
C A:ASP157 4.8 0.8 1.0
CA A:ASN159 4.9 0.1 1.0
C A:LEU164 4.9 84.6 1.0
C A:ASN159 4.9 0.3 1.0
N A:GLY162 4.9 0.3 1.0

Calcium binding site 3 out of 6 in 5g58

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Calcium binding site 3 out of 6 in the Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 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 A190T Mutant of Human Hippocalcin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:74.8
occ:1.00
 O A:TYR115 2.4 75.3 1.0
OD1 A:ASN113 2.4 91.3 1.0
OE1 A:GLU120 2.4 79.0 1.0
OD1 A:ASP111 2.4 82.6 1.0
OD1 A:ASP109 2.4 75.1 1.0
OE2 A:GLU120 2.6 78.4 1.0
CD A:GLU120 2.8 79.1 1.0
CG A:ASN113 3.0 91.0 1.0
ND2 A:ASN113 3.2 92.7 1.0
CG A:ASP109 3.5 73.2 1.0
CG A:ASP111 3.6 87.5 1.0
C A:TYR115 3.6 77.0 1.0
CA A:ASP109 4.1 69.8 1.0
N A:ASP111 4.2 80.6 1.0
OD2 A:ASP111 4.2 86.8 1.0
N A:ASN113 4.2 85.6 1.0
N A:LEU110 4.2 73.0 1.0
C A:ASP109 4.3 70.7 1.0
CB A:ASP109 4.3 70.1 1.0
CG A:GLU120 4.3 79.4 1.0
CB A:ASN113 4.3 90.5 1.0
OD2 A:ASP109 4.4 74.3 1.0
N A:TYR115 4.4 78.5 1.0
N A:SER117 4.5 80.2 1.0
CA A:TYR115 4.5 79.8 1.0
N A:ILE116 4.5 75.4 1.0
CA A:ILE116 4.5 74.6 1.0
N A:GLY112 4.6 83.6 1.0
CB A:ASP111 4.7 87.3 1.0
CA A:ASP111 4.7 84.9 1.0
C A:ASP111 4.7 86.3 1.0
CA A:ASN113 4.8 87.4 1.0
CB A:TYR115 4.9 84.9 1.0
C A:ILE116 5.0 79.0 1.0
O A:ASP109 5.0 70.5 1.0

Calcium binding site 4 out of 6 in 5g58

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Calcium binding site 4 out of 6 in the Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 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 A190T Mutant of Human Hippocalcin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:75.9
occ:1.00
 O E:THR79 2.2 83.4 1.0
OD1 E:ASN75 2.3 86.3 1.0
OE1 E:GLU84 2.3 86.5 1.0
OD1 E:ASP77 2.4 88.0 1.0
OD1 E:ASP73 2.5 73.5 1.0
OE2 E:GLU84 3.0 86.0 1.0
CD E:GLU84 3.0 83.8 1.0
CG E:ASP77 3.2 87.7 1.0
C E:THR79 3.3 81.4 1.0
CG E:ASN75 3.3 89.6 1.0
OD2 E:ASP77 3.4 87.2 1.0
CG E:ASP73 3.6 75.0 1.0
ND2 E:ASN75 3.8 92.1 1.0
N E:ILE80 4.0 78.1 1.0
CA E:ILE80 4.1 74.1 1.0
OG1 E:THR79 4.2 86.3 1.0
OD2 E:ASP73 4.3 71.5 1.0
N E:THR79 4.3 84.3 1.0
CA E:THR79 4.3 82.5 1.0
N E:ASP81 4.4 74.3 1.0
CG E:GLU84 4.5 79.6 1.0
N E:ASP77 4.5 83.3 1.0
CB E:ASP77 4.6 89.7 1.0
CB E:ASP73 4.6 75.4 1.0
CB E:ASN75 4.6 90.2 1.0
CA E:ASP73 4.6 75.8 1.0
N E:SER76 4.7 88.9 1.0
C E:ILE80 4.7 72.5 1.0
CB E:THR79 4.9 83.7 1.0
OD2 E:ASP81 4.9 86.4 1.0
N E:ASN75 4.9 85.5 1.0
N E:GLY78 5.0 87.3 1.0

Calcium binding site 5 out of 6 in 5g58

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Calcium binding site 5 out of 6 in the Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 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 A190T Mutant of Human Hippocalcin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:68.2
occ:1.00
 OD1 E:ASP161 2.2 69.9 1.0
O E:LYS163 2.3 73.7 1.0
OD1 E:ASP157 2.5 65.6 1.0
OE1 E:GLU168 2.6 66.9 1.0
OE2 E:GLU168 2.7 73.5 1.0
CG E:ASP161 3.0 72.4 1.0
CD E:GLU168 3.0 68.7 1.0
OD1 E:ASN159 3.1 79.4 1.0
OD2 E:ASP161 3.3 69.9 1.0
ND2 E:ASN159 3.4 75.7 1.0
C E:LYS163 3.5 72.2 1.0
CG E:ASN159 3.5 76.9 1.0
CG E:ASP157 3.6 68.7 1.0
N E:ASP161 4.1 74.5 1.0
N E:LYS163 4.2 72.7 1.0
OD2 E:ASP157 4.3 68.9 1.0
CB E:ASP161 4.3 75.7 1.0
CA E:LEU164 4.4 64.7 1.0
N E:LEU164 4.4 67.9 1.0
CA E:LYS163 4.5 73.5 1.0
N E:ASN160 4.5 75.0 1.0
CG E:GLU168 4.5 66.3 1.0
N E:SER165 4.6 69.0 1.0
CA E:ASP157 4.6 66.7 1.0
CA E:ASP161 4.6 76.0 1.0
CB E:ASP157 4.6 67.5 1.0
N E:ASN159 4.7 74.3 1.0
CG E:LYS163 4.7 80.4 1.0
N E:GLY162 4.8 73.9 1.0
CB E:ASN159 4.8 76.4 1.0
N E:THR158 4.8 69.3 1.0
C E:ASP157 4.9 70.3 1.0
C E:LEU164 4.9 67.1 1.0
C E:ASP161 4.9 75.7 1.0

Calcium binding site 6 out of 6 in 5g58

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Calcium binding site 6 out of 6 in the Crystal Structure of A190T Mutant of Human Hippocalcin at 2.5 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 A190T Mutant of Human Hippocalcin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:81.1
occ:1.00
 OD1 E:ASN113 2.3 83.3 1.0
O E:TYR115 2.3 74.7 1.0
OD1 E:ASP109 2.4 69.3 1.0
OD1 E:ASP111 2.4 75.8 1.0
OE1 E:GLU120 2.4 68.8 1.0
OE2 E:GLU120 2.6 73.7 1.0
CD E:GLU120 2.9 72.0 1.0
CG E:ASN113 3.0 84.5 1.0
ND2 E:ASN113 3.1 87.1 1.0
CG E:ASP109 3.4 68.8 1.0
C E:TYR115 3.6 75.3 1.0
CG E:ASP111 3.6 77.8 1.0
CA E:ASP109 4.1 65.8 1.0
N E:ASN113 4.1 79.7 1.0
N E:ASP111 4.2 72.1 1.0
OD2 E:ASP111 4.2 80.3 1.0
CB E:ASP109 4.2 66.5 1.0
N E:LEU110 4.2 67.4 1.0
C E:ASP109 4.3 66.8 1.0
OD2 E:ASP109 4.3 73.2 1.0
CB E:ASN113 4.3 85.1 1.0
N E:TYR115 4.3 74.8 1.0
CG E:GLU120 4.4 73.3 1.0
CA E:TYR115 4.4 74.9 1.0
N E:GLY112 4.5 72.0 1.0
N E:ILE116 4.5 74.6 1.0
N E:SER117 4.5 74.1 1.0
CA E:ILE116 4.6 74.6 1.0
CA E:ASN113 4.7 82.7 1.0
C E:ASP111 4.7 73.7 1.0
CB E:ASP111 4.7 76.4 1.0
CA E:ASP111 4.7 73.7 1.0
CB E:TYR115 4.8 78.6 1.0
N E:GLY114 4.9 80.0 1.0
O E:ASP109 4.9 65.5 1.0

Reference:

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
Page generated: Sun Jul 14 19:29:05 2024

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