Calcium in PDB 5d43: Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form

The structure of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form, PDB code: 5d43 was solved by J.H.Park, S.Y.Kim, D.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.89 / 2.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.750, 72.061, 62.248, 90.00, 97.26, 90.00
R / Rfree (%)	27.4 / 32.9

The binding sites of Calcium atom in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form (pdb code 5d43). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form, PDB code: 5d43:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:84.4 occ:1.00 O A:THR47 2.5 77.8 1.0 OG A:SER45 2.5 75.2 1.0 OD1 A:ASP41 2.7 85.5 1.0 OD1 A:ASP43 3.4 93.9 1.0 CG A:ASP43 3.7 94.6 1.0 C A:THR47 3.7 76.0 1.0 CB A:ASP43 3.8 93.6 1.0 CB A:SER45 3.9 76.7 1.0 CG A:ASP41 3.9 86.3 1.0 OG1 A:THR47 3.9 74.4 1.0 OE1 A:GLU52 4.3 83.5 1.0 OD2 A:ASP43 4.4 95.1 1.0 N A:ASP43 4.5 94.1 1.0 N A:THR47 4.5 72.9 1.0 CA A:THR47 4.5 74.9 1.0 N A:SER45 4.6 78.7 1.0 N A:ILE48 4.6 76.5 1.0 OD2 A:ASP41 4.6 84.7 1.0 CA A:ILE48 4.7 78.8 1.0 CB A:THR47 4.7 74.8 1.0 CA A:ASP43 4.8 93.0 1.0 CA A:SER45 4.8 77.7 1.0 CA A:ASP41 4.8 85.9 1.0 CB A:ASP41 4.9 86.8 1.0 N A:SER42 5.0 89.5 1.0

Calcium binding site 2 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1202 b:75.2 occ:1.00 O A:VAL76 2.4 96.8 1.0 OD2 A:ASP88 2.8 51.6 1.0 OD1 A:ASP88 3.4 54.0 1.0 CG A:ASP88 3.5 52.3 1.0 C A:VAL76 3.6 97.8 1.0 CA A:ASP77 4.2 0.4 1.0 N A:ASP77 4.3 0.2 1.0 CB A:ASP77 4.3 0.7 1.0 OD1 A:ASP77 4.5 0.3 1.0 CA A:VAL76 4.7 96.5 1.0 O A:LYS83 4.9 73.3 1.0 CG A:ASP77 4.9 0.5 1.0 CB A:ASP88 4.9 50.4 1.0

Calcium binding site 3 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1203 b:41.7 occ:1.00 O A:LYS120 2.3 37.9 1.0 OD1 A:ASP114 2.4 36.6 1.0 OG1 A:THR118 2.5 44.0 1.0 OD1 A:ASN125 2.5 49.2 1.0 OD1 A:ASP116 2.6 44.4 1.0 CG A:ASP116 3.4 43.3 1.0 OD2 A:ASP116 3.5 44.8 1.0 C A:LYS120 3.6 38.8 1.0 CG A:ASP114 3.6 35.7 1.0 CG A:ASN125 3.6 49.3 1.0 CB A:THR118 3.7 41.2 1.0 CG2 A:THR118 3.9 41.3 1.0 N A:THR118 4.1 39.8 1.0 ND2 A:ASN125 4.2 50.8 1.0 OE1 A:GLU156 4.3 55.8 1.0 N A:SER122 4.4 41.4 1.0 OD2 A:ASP114 4.4 34.9 1.0 N A:LYS120 4.4 39.7 1.0 CB A:ASP114 4.4 36.0 1.0 N A:ILE121 4.4 38.3 1.0 CA A:THR118 4.4 40.3 1.0 CA A:ILE121 4.4 39.3 1.0 CA A:ASP114 4.5 37.2 1.0 CA A:LYS120 4.5 40.0 1.0 OG A:SER122 4.7 41.0 1.0 CB A:ASN125 4.7 49.2 1.0 N A:GLU117 4.8 39.1 1.0 CB A:ASP116 4.9 41.6 1.0 C A:ILE121 4.9 40.1 1.0 CB A:SER122 4.9 41.8 1.0 N A:GLY119 5.0 39.9 1.0

Calcium binding site 4 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1204 b:52.4 occ:1.00 O A:GLU156 2.4 45.7 1.0 OD1 A:ASP152 2.5 60.8 1.0 OD1 A:ASP150 2.5 53.1 1.0 OE1 A:GLU161 2.6 45.3 1.0 OE2 A:GLU161 2.8 46.6 1.0 CD A:GLU161 3.1 45.6 1.0 OD2 A:ASP154 3.1 58.3 1.0 OD1 A:ASP154 3.2 59.4 1.0 CG A:ASP152 3.4 60.0 1.0 CG A:ASP154 3.4 57.6 1.0 C A:GLU156 3.6 46.2 1.0 CG A:ASP150 3.6 52.7 1.0 ND2 A:ASN158 3.7 46.9 1.0 OD2 A:ASP152 3.7 59.8 1.0 CA A:ASP150 4.2 52.4 1.0 CA A:VAL157 4.3 43.2 1.0 N A:ASN158 4.3 43.2 1.0 CB A:ASP150 4.4 52.3 1.0 N A:VAL157 4.4 43.9 1.0 N A:GLU156 4.5 48.4 1.0 N A:ASP154 4.5 55.7 1.0 N A:ASP152 4.5 59.5 1.0 CG A:ASN158 4.5 45.2 1.0 OD2 A:ASP150 4.6 52.3 1.0 CG A:GLU161 4.6 44.2 1.0 CA A:GLU156 4.6 48.0 1.0 N A:GLY153 4.6 56.2 1.0 N A:ARG151 4.7 55.8 1.0 CB A:ASP152 4.7 59.7 1.0 CB A:ASP154 4.7 55.4 1.0 C A:ASP150 4.8 54.1 1.0 C A:VAL157 4.8 43.1 1.0 CA A:ASP152 5.0 59.0 1.0

Calcium binding site 5 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1201 b:69.6 occ:1.00 O B:THR47 2.4 51.2 1.0 OD1 B:ASP41 2.5 67.5 1.0 OG B:SER45 2.6 61.3 1.0 O B:HOH1303 2.6 37.6 1.0 O B:HOH1301 2.8 67.4 1.0 OD1 B:ASP43 2.9 76.1 1.0 C B:THR47 3.6 49.6 1.0 CG B:ASP43 3.6 74.8 1.0 CG B:ASP41 3.7 68.5 1.0 OD2 B:ASP43 3.7 74.6 1.0 CB B:SER45 4.0 60.3 1.0 OG1 B:THR47 4.1 52.6 1.0 OD2 B:ASP41 4.5 66.7 1.0 CA B:ASP41 4.5 74.9 1.0 N B:THR47 4.5 51.0 1.0 N B:ILE48 4.5 48.1 1.0 CA B:THR47 4.5 50.4 1.0 OE2 B:GLU52 4.5 59.4 1.0 N B:SER45 4.6 61.4 1.0 CA B:ILE48 4.6 46.6 1.0 CB B:ASP41 4.6 70.8 1.0 OE1 B:GLU52 4.7 60.9 1.0 CA B:SER45 4.8 59.5 1.0 N B:ASP43 4.8 76.5 1.0 N B:SER42 4.9 77.6 1.0 CB B:THR47 4.9 50.5 1.0 C B:ASP41 4.9 76.5 1.0 CG2 B:ILE48 5.0 45.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1202 b:37.1 occ:1.00 O B:VAL76 2.4 59.8 1.0 OD2 B:ASP88 2.7 35.9 1.0 OD1 B:ASP88 2.9 37.4 1.0 CG B:ASP88 3.2 36.2 1.0 C B:VAL76 3.5 57.8 1.0 CB B:ASP77 3.8 65.8 1.0 CA B:ASP77 4.0 65.7 1.0 N B:ASP77 4.1 61.6 1.0 OG B:SER85 4.6 44.4 1.0 CB B:ASP88 4.7 35.9 1.0 CA B:VAL76 4.7 54.9 1.0 CG1 B:VAL76 4.8 54.7 1.0

Calcium binding site 7 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1203 b:59.5 occ:1.00 O B:LYS120 2.4 69.1 1.0 OD1 B:ASN125 2.5 70.2 1.0 OD1 B:ASP114 2.5 63.9 1.0 OG1 B:THR118 2.6 55.7 1.0 OD1 B:ASP116 2.6 62.3 1.0 OD2 B:ASP116 3.3 65.0 1.0 CG B:ASP116 3.4 63.8 1.0 CG B:ASN125 3.5 70.3 1.0 C B:LYS120 3.6 67.5 1.0 CG B:ASP114 3.7 63.1 1.0 CB B:THR118 3.7 56.8 1.0 CG2 B:THR118 3.9 56.3 1.0 ND2 B:ASN125 4.0 70.8 1.0 N B:THR118 4.3 56.4 1.0 N B:SER122 4.4 71.4 1.0 CA B:ILE121 4.4 67.8 1.0 N B:ILE121 4.4 68.8 1.0 CB B:ASP114 4.5 63.8 1.0 N B:LYS120 4.5 63.5 1.0 CA B:ASP114 4.5 63.4 1.0 OG B:SER122 4.5 72.5 1.0 CA B:THR118 4.5 56.4 1.0 OD2 B:ASP114 4.5 63.4 1.0 CA B:LYS120 4.6 66.2 1.0 OE2 B:GLU156 4.7 79.3 1.0 CB B:ASN125 4.7 70.0 1.0 CB B:ASP116 4.8 62.7 1.0 C B:ILE121 4.8 68.8 1.0 CB B:SER122 4.9 72.8 1.0 N B:GLY119 5.0 58.4 1.0

Calcium binding site 8 out of 8 in the Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structrue of Mouse Centrin 1 in Calcium-Saturated Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1204 b:63.4 occ:1.00 O B:GLU156 2.2 64.5 1.0 OE1 B:GLU161 2.6 66.3 1.0 OD1 B:ASP150 2.7 80.3 1.0 OD1 B:ASP152 2.7 95.4 1.0 OD1 B:ASP154 3.0 73.5 1.0 OE2 B:GLU161 3.3 65.6 1.0 OD2 B:ASP154 3.3 73.4 1.0 CD B:GLU161 3.3 65.7 1.0 C B:GLU156 3.4 65.2 1.0 CG B:ASP154 3.5 74.4 1.0 CG B:ASP152 3.6 93.8 1.0 OD2 B:ASP152 3.7 93.2 1.0 CG B:ASP150 3.8 80.1 1.0 N B:ASN158 4.1 60.9 1.0 CA B:VAL157 4.1 62.6 1.0 N B:VAL157 4.2 62.8 1.0 CA B:ASP150 4.4 76.1 1.0 N B:GLU156 4.5 68.0 1.0 CB B:ASP150 4.5 78.3 1.0 CA B:GLU156 4.5 67.9 1.0 C B:VAL157 4.6 61.4 1.0 OD2 B:ASP150 4.6 81.7 1.0 N B:ASP154 4.7 79.8 1.0 OD1 B:ASN158 4.7 61.4 1.0 CG B:GLU161 4.8 65.2 1.0 N B:ARG151 4.8 79.4 1.0 CB B:ASP154 4.8 75.8 1.0 CB B:ASN158 4.8 60.2 1.0 N B:GLY153 4.9 87.7 1.0 N B:ASP152 4.9 88.8 1.0 C B:ASP150 5.0 77.2 1.0

S.Y.Kim, D.S.Kim, J.E.Hong, J.H.Park. Crystal Structure of Wild-Type Centrin 1 From Mus Musculus Occupied By CA2+ Biochemistry Mosc. V. 82 1129 2017.
ISSN: ISSN 0006-2979
DOI: 10.1134/S0006297917100054