Calcium in PDB 3kf9: Crystal Structure of the Sdcen/Skmlck Complex

The structure of Crystal Structure of the Sdcen/Skmlck Complex, PDB code: 3kf9 was solved by L.Radu, L.Assairi, Y.Blouquit, D.Durand, S.Miron, J.B.Charbonnier, C.T.Craescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.750, 67.750, 129.530, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 29

The binding sites of Calcium atom in the Crystal Structure of the Sdcen/Skmlck Complex (pdb code 3kf9). 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 Structure of the Sdcen/Skmlck Complex, PDB code: 3kf9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


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 the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:12.5 occ:1.00 OD1 A:ASP39 2.2 24.4 1.0 O A:HOH193 2.2 6.8 1.0 OD1 A:ASP37 2.3 22.6 1.0 OE1 A:GLU48 2.4 19.1 1.0 O A:THR43 2.5 14.7 1.0 OG A:SER41 2.5 16.6 1.0 OE2 A:GLU48 2.8 21.9 1.0 CD A:GLU48 2.9 18.8 1.0 CG A:ASP39 3.2 23.4 1.0 CG A:ASP37 3.4 21.3 1.0 OD2 A:ASP39 3.4 24.8 1.0 CB A:SER41 3.6 19.0 1.0 C A:THR43 3.7 13.9 1.0 N A:SER41 4.0 18.5 1.0 OG1 A:THR43 4.2 16.8 1.0 CB A:ASP37 4.2 18.7 1.0 OD2 A:ASP37 4.2 23.0 1.0 N A:THR43 4.2 15.9 1.0 CA A:SER41 4.3 18.7 1.0 CA A:ASP37 4.3 18.5 1.0 CG A:GLU48 4.3 16.4 1.0 CA A:THR43 4.4 14.9 1.0 CB A:ASP39 4.6 22.1 1.0 N A:ILE44 4.6 12.7 1.0 N A:ASP39 4.7 20.1 1.0 N A:GLY40 4.7 19.4 1.0 C A:ASP37 4.7 18.6 1.0 N A:ASP45 4.7 13.9 1.0 N A:GLY42 4.8 17.2 1.0 OD2 A:ASP45 4.8 21.6 1.0 CA A:ILE44 4.8 11.9 1.0 N A:THR38 4.9 18.5 1.0 C A:SER41 4.9 18.0 1.0 C A:ASP39 5.0 20.8 1.0 CA A:ASP39 5.0 21.3 1.0 CB A:THR43 5.0 15.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


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 the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:21.3 occ:1.00 OD1 A:ASP73 2.0 18.3 1.0 O A:THR79 2.3 12.8 1.0 OE2 A:GLU84 2.4 15.4 1.0 OD1 A:ASP75 2.4 19.3 1.0 OE1 A:GLU84 2.4 14.0 1.0 OG A:SER77 2.6 12.4 1.0 CD A:GLU84 2.7 14.4 1.0 CG A:ASP73 3.3 19.1 1.0 CG A:ASP75 3.3 18.4 1.0 C A:THR79 3.5 12.2 1.0 OD2 A:ASP81 3.6 19.3 1.0 CB A:SER77 3.6 13.7 1.0 OD2 A:ASP75 3.6 20.5 1.0 CB A:ASP73 4.0 19.2 1.0 OG1 A:THR79 4.0 14.5 1.0 OD2 A:ASP73 4.2 17.4 1.0 CA A:ASP73 4.3 19.0 1.0 CG A:GLU84 4.3 13.3 1.0 N A:SER77 4.3 14.8 1.0 N A:THR79 4.3 13.6 1.0 N A:ILE80 4.4 10.8 1.0 N A:ASP81 4.4 10.2 1.0 CA A:ILE80 4.4 9.4 1.0 CA A:THR79 4.5 13.1 1.0 N A:ASP75 4.5 17.1 1.0 CA A:SER77 4.5 14.7 1.0 CG A:ASP81 4.5 16.4 1.0 CB A:ASP75 4.6 17.8 1.0 N A:LYS74 4.6 18.4 1.0 C A:ASP73 4.7 19.5 1.0 CB A:THR79 4.8 13.2 1.0 C A:ILE80 4.9 9.2 1.0 CA A:ASP75 4.9 17.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


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 the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:25.6 occ:1.00 OE2 A:GLU157 1.9 19.6 1.0 OD2 A:ASP150 2.2 21.7 1.0 O A:GLU152 2.3 17.3 1.0 OD1 A:ASP146 2.4 19.2 1.0 O A:HOH178 2.5 2.7 1.0 OD2 A:ASP148 2.8 24.8 1.0 CD A:GLU157 2.9 17.6 1.0 OD1 A:ASP148 2.9 24.4 1.0 CG A:ASP148 3.0 23.8 1.0 O A:ASP146 3.2 23.3 1.0 OE1 A:GLU157 3.2 15.6 1.0 CG A:ASP150 3.3 20.5 1.0 C A:GLU152 3.5 17.0 1.0 CG A:ASP146 3.6 20.8 1.0 OD1 A:ASP150 4.0 23.0 1.0 C A:ASP146 4.0 21.9 1.0 CA A:ASP146 4.2 20.9 1.0 CB A:ASP148 4.2 22.0 1.0 CG A:GLU157 4.3 16.9 1.0 N A:ASP148 4.3 22.0 1.0 N A:ASP150 4.3 21.4 1.0 N A:ASN154 4.3 14.2 1.0 CB A:ASP150 4.3 21.4 1.0 CA A:VAL153 4.4 14.2 1.0 N A:VAL153 4.4 15.5 1.0 OD2 A:ASP146 4.4 21.9 1.0 N A:GLU152 4.4 18.7 1.0 CB A:ASP146 4.5 21.3 1.0 CA A:GLU152 4.6 18.1 1.0 CA A:ASP148 4.6 22.7 1.0 CA A:ASP150 4.7 21.6 1.0 CG A:ASN154 4.8 15.2 1.0 C A:ASP148 4.8 23.2 1.0 ND2 A:ASN154 4.9 15.7 1.0 C A:VAL153 4.9 14.1 1.0 N A:GLY149 4.9 22.7 1.0 OD1 A:ASN154 5.0 14.4 1.0 N A:GLY151 5.0 21.2 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


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 the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:40.4 occ:1.00 O A:LYS116 2.3 13.6 1.0 OD1 A:ASP110 2.4 23.8 1.0 OD1 A:ASP112 2.5 19.7 1.0 ND2 A:ASN121 2.5 9.8 1.0 O A:HOH17 2.8 13.4 1.0 OG1 A:THR114 2.8 15.1 1.0 CG A:ASP112 3.4 18.6 1.0 CG A:ASP110 3.5 21.6 1.0 CG A:ASN121 3.5 11.4 1.0 C A:LYS116 3.5 12.9 1.0 OD1 A:ASN121 3.6 13.2 1.0 OD2 A:ASP112 3.7 17.0 1.0 CA A:ASP110 3.9 18.7 1.0 CB A:THR114 3.9 15.8 1.0 O A:HOH176 3.9 2.1 1.0 CG2 A:THR114 4.1 15.2 1.0 N A:THR114 4.1 17.0 1.0 CB A:ASP110 4.1 19.2 1.0 N A:LYS116 4.2 13.6 1.0 CA A:ILE117 4.4 11.3 1.0 N A:SER118 4.4 10.9 1.0 N A:ILE117 4.4 11.7 1.0 OD2 A:ASP110 4.4 23.7 1.0 CA A:THR114 4.5 16.2 1.0 CA A:LYS116 4.5 13.5 1.0 OG A:SER118 4.6 12.4 1.0 N A:ASP111 4.6 19.9 1.0 N A:ASP112 4.7 19.9 1.0 CB A:ASP112 4.8 19.6 1.0 N A:GLU113 4.8 18.9 1.0 N A:GLY115 4.8 14.6 1.0 C A:ASP110 4.8 19.4 1.0 CB A:ASN121 4.9 10.1 1.0 C A:ILE117 4.9 11.0 1.0 C A:THR114 4.9 15.5 1.0 N A:ASP110 4.9 17.8 1.0 CB A:SER118 4.9 11.8 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


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 the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:21.3 occ:1.00 O C:HOH12 1.9 9.2 1.0 OD1 C:ASP73 2.3 19.6 1.0 O C:THR79 2.4 12.1 1.0 OD2 C:ASP75 2.4 20.4 1.0 OG C:SER77 2.6 13.0 1.0 OE2 C:GLU84 2.6 13.1 1.0 OE1 C:GLU84 2.8 13.7 1.0 CD C:GLU84 3.1 14.3 1.0 CG C:ASP73 3.3 18.9 1.0 C C:THR79 3.5 11.4 1.0 CG C:ASP75 3.6 18.8 1.0 CB C:SER77 3.8 13.9 1.0 CB C:ASP73 3.8 18.1 1.0 CA C:ASP73 4.0 17.8 1.0 OD1 C:ASP75 4.1 20.0 1.0 N C:THR79 4.2 12.8 1.0 N C:SER77 4.2 14.9 1.0 CA C:ILE80 4.3 9.8 1.0 N C:ASP81 4.3 10.3 1.0 OD2 C:ASP73 4.3 19.4 1.0 N C:ILE80 4.4 10.3 1.0 OG1 C:THR79 4.4 12.8 1.0 CA C:THR79 4.5 11.9 1.0 N C:LYS74 4.5 16.6 1.0 N C:ASP75 4.5 15.9 1.0 CA C:SER77 4.5 14.8 1.0 CG C:GLU84 4.6 12.7 1.0 N C:GLY78 4.6 14.5 1.0 C C:ASP73 4.6 17.6 1.0 C C:ILE80 4.7 10.0 1.0 CB C:ASP75 4.8 17.1 1.0 CG C:ASP81 4.8 14.0 1.0 OD2 C:ASP81 4.9 15.9 1.0 C C:SER77 4.9 14.7 1.0 N C:GLY76 5.0 16.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


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 the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:33.3 occ:1.00 OE1 C:GLU157 2.1 28.6 1.0 OD1 C:ASP148 2.4 38.8 1.0 OD1 C:ASP150 2.4 30.5 1.0 O C:HOH19 2.5 13.5 1.0 O C:GLU152 2.5 26.7 1.0 OD1 C:ASP146 2.6 33.0 1.0 CD C:GLU157 3.0 28.7 1.0 CG C:ASP150 3.1 31.2 1.0 OE2 C:GLU157 3.2 31.7 1.0 CG C:ASP148 3.2 37.3 1.0 OD2 C:ASP150 3.4 33.2 1.0 OD2 C:ASP148 3.6 37.7 1.0 C C:GLU152 3.6 25.3 1.0 CG C:ASP146 3.7 33.9 1.0 N C:ASP150 4.2 34.6 1.0 CG C:GLU157 4.2 26.6 1.0 CB C:ASP150 4.3 32.9 1.0 N C:GLU152 4.4 27.9 1.0 N C:ASN154 4.4 22.5 1.0 N C:VAL153 4.5 23.1 1.0 OD2 C:ASP146 4.5 35.8 1.0 CA C:GLU152 4.5 26.3 1.0 CA C:ASP146 4.5 32.6 1.0 CA C:VAL153 4.5 22.2 1.0 CB C:ASP148 4.5 36.8 1.0 N C:GLY149 4.5 37.3 1.0 N C:ASP148 4.5 36.3 1.0 CB C:ASP146 4.6 32.9 1.0 ND2 C:ASN154 4.6 24.2 1.0 CA C:ASP150 4.7 33.7 1.0 CG C:ASN154 4.8 24.2 1.0 CA C:ASP148 4.9 37.6 1.0 N C:ARG147 4.9 34.1 1.0 C C:VAL153 4.9 21.6 1.0 C C:ASP146 4.9 34.4 1.0 N C:GLY151 4.9 32.5 1.0 CB C:GLU152 5.0 25.8 1.0 CD C:LYS116 5.0 25.1 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:22.8 occ:1.00 OG C:SER41 2.0 18.0 1.0 OD1 C:ASP37 2.0 24.3 1.0 OD2 C:ASP39 2.2 25.5 1.0 O C:THR43 2.2 15.5 1.0 OE2 C:GLU48 2.4 21.5 1.0 OE1 C:GLU48 2.5 20.7 1.0 O C:HOH177 2.6 2.0 1.0 CD C:GLU48 2.8 20.1 1.0 CB C:SER41 3.2 21.1 1.0 CG C:ASP37 3.2 22.0 1.0 CG C:ASP39 3.3 25.4 1.0 C C:THR43 3.5 15.8 1.0 OD1 C:ASP39 3.7 28.0 1.0 N C:SER41 4.0 21.9 1.0 OG1 C:THR43 4.0 18.2 1.0 OD2 C:ASP37 4.0 24.8 1.0 CB C:ASP37 4.1 19.7 1.0 CA C:ASP37 4.1 20.1 1.0 CA C:SER41 4.1 21.5 1.0 N C:THR43 4.3 17.9 1.0 CG C:GLU48 4.3 17.8 1.0 N C:ILE44 4.3 15.0 1.0 CA C:THR43 4.4 16.3 1.0 CA C:ILE44 4.4 14.2 1.0 C C:ASP37 4.4 21.3 1.0 N C:ASP39 4.4 23.5 1.0 N C:ASP45 4.5 15.2 1.0 N C:THR38 4.6 21.6 1.0 CB C:ASP39 4.6 25.5 1.0 OD2 C:ASP45 4.7 23.8 1.0 N C:GLY40 4.7 23.2 1.0 N C:GLY42 4.8 20.3 1.0 C C:SER41 4.8 21.2 1.0 CB C:THR43 4.9 17.4 1.0 CA C:ASP39 4.9 24.8 1.0 C C:ILE44 4.9 14.6 1.0 CG C:ASP45 4.9 19.7 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Sdcen/Skmlck Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Sdcen/Skmlck Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:42.5 occ:1.00 O C:LYS116 2.2 16.6 1.0 ND2 C:ASN121 2.2 11.9 1.0 OD1 C:ASP110 2.4 22.4 1.0 O C:HOH187 2.4 2.0 1.0 OD2 C:ASP112 2.6 19.1 1.0 OG1 C:THR114 2.7 17.4 1.0 CG C:ASN121 3.3 13.6 1.0 C C:LYS116 3.4 16.4 1.0 CG C:ASP112 3.4 19.4 1.0 CG C:ASP110 3.5 21.2 1.0 OD1 C:ASP112 3.5 21.1 1.0 OD1 C:ASN121 3.7 13.9 1.0 O C:HOH1 3.7 2.0 1.0 OG C:SER118 3.9 16.7 1.0 CB C:THR114 4.0 17.4 1.0 N C:SER118 4.0 15.7 1.0 CG2 C:THR114 4.2 17.8 1.0 CA C:ILE117 4.2 15.0 1.0 N C:ILE117 4.3 15.8 1.0 N C:LYS116 4.3 16.2 1.0 CB C:ASP110 4.3 19.7 1.0 CA C:ASP110 4.3 18.8 1.0 N C:THR114 4.3 16.6 1.0 CA C:LYS116 4.4 17.0 1.0 CB C:SER118 4.4 17.1 1.0 OD2 C:ASP110 4.4 23.4 1.0 C C:ILE117 4.5 15.9 1.0 CB C:ASN121 4.6 13.9 1.0 CA C:THR114 4.7 16.9 1.0 CB C:LYS116 4.8 18.3 1.0 CB C:ASP112 4.9 20.0 1.0 C C:ASP110 4.9 18.7 1.0 CA C:SER118 4.9 16.6 1.0 N C:GLU113 5.0 18.0 1.0

L.Radu, S.Miron, D.Durand, L.Assairi, Y.Blouquit, J.B.Charbonnier. Structural Features of the Complexes Formed By Scherffelia Dubia Centrin To Be Published.