Calcium in PDB 7clt: Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein

Protein crystallography data

The structure of Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein, PDB code: 7clt was solved by S.A.Mun, J.Park, K.R.Park, Y.Lee, J.Y.Kang, T.Park, M.Jin, J.Yang, C.D.Jun, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.60 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.77, 47.556, 87.199, 90, 90, 90
R / Rfree (%) 20.9 / 22.9

Other elements in 7clt:

The structure of Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein (pdb code 7clt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein, PDB code: 7clt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7clt

Go back to Calcium Binding Sites List in 7clt
Calcium binding site 1 out of 2 in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein


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 EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:21.9
occ:1.00
OD2 A:ASP104 2.2 28.5 1.0
O A:PHE110 2.2 27.4 1.0
O A:HOH404 2.2 22.9 1.0
OD2 A:ASP108 2.3 30.4 1.0
OE1 A:GLU115 2.3 33.4 1.0
O A:HOH418 2.5 34.5 1.0
OE2 A:GLU115 2.6 33.2 1.0
CD A:GLU115 2.8 32.9 1.0
CG A:ASP108 3.2 30.4 1.0
CG A:ASP104 3.2 32.9 1.0
C A:PHE110 3.3 25.6 1.0
OD1 A:ASP108 3.5 30.9 1.0
OD1 A:ASP104 4.0 32.0 1.0
N A:PHE110 4.1 26.2 1.0
CA A:ASP104 4.1 34.6 1.0
CA A:PHE110 4.1 24.9 1.0
CB A:ASP104 4.2 35.1 1.0
OD2 A:ASP112 4.2 33.0 1.0
N A:ILE111 4.2 22.2 1.0
CG A:GLU115 4.3 27.3 1.0
CA A:ILE111 4.3 23.1 1.0
N A:ASP108 4.3 37.1 1.0
N A:GLY106 4.4 42.3 1.0
C A:ASP104 4.4 38.2 1.0
CB A:PHE110 4.4 21.7 1.0
N A:ASP112 4.5 21.0 1.0
CB A:ASP108 4.5 30.8 1.0
N A:ARG107 4.6 38.1 1.0
N A:ALA105 4.6 37.1 1.0
CG A:ASP112 4.6 23.6 1.0
CA A:GLY106 4.8 39.1 1.0
C A:ILE111 4.9 21.7 1.0
CA A:ASP108 4.9 33.5 1.0
C A:GLY106 4.9 42.2 1.0
N A:GLY109 5.0 30.7 1.0
O A:ASP104 5.0 39.4 1.0

Calcium binding site 2 out of 2 in 7clt

Go back to Calcium Binding Sites List in 7clt
Calcium binding site 2 out of 2 in the Crystal Structure of the EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein


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 EFHD1/Swiprosin-2, A Mitochondrial Actin- Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:19.1
occ:1.00
OD2 A:ASP140 2.3 19.9 1.0
O A:LYS146 2.3 15.3 1.0
OE2 A:GLU151 2.4 17.5 1.0
OD2 A:ASP142 2.4 21.3 1.0
OD2 A:ASP144 2.5 17.0 1.0
OE1 A:GLU151 2.6 16.5 1.0
CD A:GLU151 2.9 16.4 1.0
O A:HOH420 3.0 12.7 1.0
CG A:ASP140 3.4 16.6 1.0
CG A:ASP144 3.5 20.9 1.0
CG A:ASP142 3.5 23.4 1.0
C A:LYS146 3.5 19.2 1.0
ZN A:ZN304 3.6 26.7 1.0
OD1 A:ASP144 3.8 20.7 1.0
OD1 A:ASP142 4.0 21.9 1.0
CA A:ASP140 4.2 16.0 1.0
N A:LYS146 4.2 16.9 1.0
OD1 A:ASP140 4.2 18.2 1.0
CB A:ASP140 4.3 17.7 1.0
CG A:GLU151 4.4 17.0 1.0
N A:ASP144 4.4 20.4 1.0
N A:LEU147 4.4 16.6 1.0
CA A:LEU147 4.4 16.7 1.0
N A:SER148 4.5 21.0 1.0
N A:ASP142 4.5 21.6 1.0
CA A:LYS146 4.5 17.2 1.0
C A:ASP140 4.5 19.8 1.0
O A:HOH413 4.5 25.2 1.0
N A:PHE143 4.6 22.8 1.0
CG A:LYS146 4.7 19.1 1.0
N A:GLU141 4.7 18.4 1.0
N A:GLY145 4.7 17.8 1.0
CB A:ASP142 4.8 18.6 1.0
CB A:ASP144 4.8 17.2 1.0
C A:ASP142 4.8 22.4 1.0
C A:LEU147 4.9 19.7 1.0
CA A:ASP142 4.9 20.0 1.0
CA A:ASP144 4.9 20.1 1.0

Reference:

S.A.Mun, J.Park, K.R.Park, Y.Lee, J.Y.Kang, T.Park, M.Jin, J.Yang, C.D.Jun, S.H.Eom. Structural and Biochemical Characterization of EFHD1/Swiprosin-2, An Actin-Binding Protein in Mitochondria Front Cell Dev Biol 2020.
ISSN: ESSN 2296-634X
DOI: 10.3389/FCELL.2020.628222
Page generated: Sun Jan 24 09:40:10 2021

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