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Calcium in PDB 6oec: Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I

Protein crystallography data

The structure of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I, PDB code: 6oec was solved by A.C.Drennan, K.Shivaani, M.A.Seeger, M.P.Andreas, J.M.Gardner, E.K.R.Sether, S.L.Jasperson, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.14 / 2.51
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.197, 169.723, 122.028, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I (pdb code 6oec). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I, PDB code: 6oec:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6oec

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Calcium binding site 1 out of 7 in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:68.6
occ:1.00
 O B:GLU59 2.3 37.8 1.0
OD1 B:ASP13 2.6 40.9 1.0
OD2 B:ASP57 2.8 33.0 1.0
C B:GLU59 3.4 38.4 1.0
CG B:ASP57 3.4 32.4 1.0
CG B:ASP13 3.6 38.9 1.0
OE2 B:GLU12 3.7 40.8 1.0
OD1 B:ASP57 3.9 32.6 1.0
OD2 B:ASP13 3.9 42.0 1.0
N B:LEU60 4.2 40.5 1.0
CB B:GLU59 4.2 44.8 1.0
NZ B:LYS107 4.2 24.7 1.0
OE1 B:GLU12 4.2 29.9 1.0
CA B:GLU59 4.3 39.4 1.0
CB B:ASP57 4.3 27.1 1.0
CD B:GLU12 4.4 36.0 1.0
CA B:LEU60 4.4 44.3 1.0
N B:ASP13 4.6 30.4 1.0
N B:GLU59 4.7 41.0 1.0
CB B:ASP13 4.9 32.2 1.0
N B:SER14 4.9 32.1 1.0
CD2 B:LEU60 5.0 35.3 1.0
N B:GLY61 5.0 40.4 1.0

Calcium binding site 2 out of 7 in 6oec

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Calcium binding site 2 out of 7 in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:72.2
occ:1.00
 OD1 C:ASP13 2.7 51.3 1.0
OE2 C:GLU12 3.1 48.8 1.0
OD2 C:ASP57 3.2 47.3 1.0
OD2 C:ASP13 3.3 41.5 1.0
O C:GLU59 3.3 52.7 1.0
CG C:ASP13 3.4 50.8 1.0
NZ C:LYS107 3.9 41.9 1.0
CG C:ASP57 4.1 46.0 1.0
CB C:GLU59 4.2 57.2 1.0
C C:GLU59 4.2 49.6 1.0
CD C:GLU12 4.3 47.4 1.0
OE1 C:GLN17 4.4 45.4 1.0
OD1 C:ASP57 4.6 39.9 1.0
N C:SER14 4.6 47.1 1.0
CB C:SER14 4.7 40.3 1.0
OE1 C:GLU12 4.8 42.5 1.0
CE C:LYS107 4.8 43.3 1.0
CA C:GLU59 4.8 52.5 1.0
CB C:ASP13 4.8 41.5 1.0
N C:ASP13 4.9 46.6 1.0

Calcium binding site 3 out of 7 in 6oec

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Calcium binding site 3 out of 7 in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:71.6
occ:1.00
 OD1 E:ASP13 2.7 42.0 1.0
OE2 E:GLU12 2.9 41.3 1.0
OD2 E:ASP57 3.0 34.9 1.0
O E:GLU59 3.2 42.2 1.0
CG E:ASP13 3.6 43.0 1.0
CG E:ASP57 3.7 34.8 1.0
CD E:GLU12 3.8 34.2 1.0
NZ E:LYS107 3.8 30.6 1.0
OD2 E:ASP13 3.8 45.8 1.0
OE1 E:GLU12 3.9 34.3 1.0
OD1 E:ASP57 4.2 29.6 1.0
C E:GLU59 4.4 41.1 1.0
OE1 E:GLN17 4.4 41.0 1.0
N E:SER14 4.6 33.6 1.0
CB E:ASP57 4.6 27.3 1.0
N E:ASP13 4.7 33.0 1.0
CB E:SER14 4.8 32.5 1.0
NE2 E:GLN17 4.9 37.3 1.0
CB E:ASP13 4.9 37.7 1.0
CD E:GLN17 5.0 35.5 1.0

Calcium binding site 4 out of 7 in 6oec

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Calcium binding site 4 out of 7 in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:70.3
occ:1.00
 OD2 F:ASP57 2.7 41.4 1.0
OD1 F:ASP13 2.7 45.1 1.0
O F:GLU59 2.7 43.5 1.0
OE2 F:GLU12 3.2 43.3 1.0
CG F:ASP13 3.5 44.5 1.0
OD2 F:ASP13 3.5 48.8 1.0
C F:GLU59 3.6 44.1 1.0
CG F:ASP57 3.6 41.3 1.0
NZ F:LYS107 3.7 48.5 1.0
CB F:GLU59 3.7 43.2 1.0
CD F:GLU12 4.1 43.8 1.0
CA F:GLU59 4.2 42.3 1.0
OD1 F:ASP57 4.2 40.4 1.0
OE1 F:GLU12 4.3 42.0 1.0
N F:LEU60 4.4 43.6 1.0
CB F:ASP57 4.6 42.8 1.0
CA F:LEU60 4.6 41.0 1.0
CE F:LYS107 4.6 42.9 1.0
CG F:GLU59 4.8 57.2 1.0
N F:GLU59 4.8 47.8 1.0
OE1 F:GLN17 4.8 40.0 1.0
N F:ASP13 4.9 39.1 1.0
CB F:ASP13 4.9 38.1 1.0

Calcium binding site 5 out of 7 in 6oec

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Calcium binding site 5 out of 7 in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca301

b:56.6
occ:1.00
 OD1 G:ASP13 2.7 28.2 1.0
OD2 G:ASP57 2.8 24.0 1.0
OE2 G:GLU12 2.9 30.3 1.0
O G:GLU59 3.0 29.6 1.0
CG G:ASP57 3.5 26.1 1.0
CG G:ASP13 3.7 29.6 1.0
NZ G:LYS107 3.7 25.8 1.0
OD2 G:ASP13 3.9 36.7 1.0
CD G:GLU12 3.9 31.7 1.0
OD1 G:ASP57 4.0 22.6 1.0
C G:GLU59 4.1 29.9 1.0
OE1 G:GLU12 4.2 28.4 1.0
CB G:ASP57 4.4 24.8 1.0
OE1 G:GLN17 4.5 34.5 1.0
N G:ASP13 4.7 23.4 1.0
CA G:LEU60 4.8 29.6 1.0
N G:LEU60 4.9 33.7 1.0
CE G:LYS107 4.9 22.7 1.0
N G:SER14 4.9 24.9 1.0
CB G:GLU59 5.0 36.1 1.0

Calcium binding site 6 out of 7 in 6oec

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Calcium binding site 6 out of 7 in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca301

b:61.8
occ:1.00
 OD1 I:ASP13 2.8 44.5 1.0
OD2 I:ASP57 3.2 34.0 1.0
O I:GLU59 3.2 37.5 1.0
OE2 I:GLU12 3.3 40.6 1.0
OD2 I:ASP13 3.4 49.4 1.0
CG I:ASP13 3.5 43.3 1.0
NZ I:LYS107 3.6 50.3 1.0
CG I:ASP57 3.8 36.1 1.0
OE2 I:GLU59 3.9 62.8 1.0
OD1 I:ASP57 4.0 36.1 1.0
CD I:GLU12 4.2 39.7 1.0
OE1 I:GLU12 4.3 41.8 1.0
C I:GLU59 4.4 44.7 1.0
CG I:GLU59 4.4 53.2 1.0
CD I:GLU59 4.6 69.3 1.0
OE1 I:GLN17 4.7 49.0 1.0
CB I:ASP57 4.8 30.6 1.0
N I:ASP13 4.9 38.6 1.0
CB I:ASP13 4.9 31.6 1.0
N I:SER14 5.0 38.4 1.0
CE I:LYS107 5.0 34.0 1.0

Calcium binding site 7 out of 7 in 6oec

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Calcium binding site 7 out of 7 in the Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Yeast SPC42 Trimeric Coiled-Coil Amino Acids 181-211 Fused to Pdb: 3H5I within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca301

b:72.9
occ:1.00
 OD1 L:ASP13 2.8 39.5 1.0
O L:GLU59 2.9 45.7 1.0
OD2 L:ASP57 3.4 36.5 1.0
OE2 L:GLU12 3.4 44.2 1.0
CG L:ASP13 3.7 39.9 1.0
OD2 L:ASP13 3.8 51.6 1.0
C L:GLU59 3.9 45.5 1.0
CG L:ASP57 4.0 36.4 1.0
CG L:GLU59 4.2 54.4 1.0
NZ L:LYS107 4.3 36.6 1.0
OD1 L:ASP57 4.4 37.7 1.0
CA L:LEU60 4.5 42.1 1.0
N L:LEU60 4.5 43.4 1.0
CD L:GLU12 4.6 38.8 1.0
CB L:GLU59 4.7 47.9 1.0
CA L:GLU59 4.8 44.5 1.0
CB L:ASP57 4.8 32.2 1.0
OE1 L:GLU12 4.9 36.5 1.0
C L:LEU60 5.0 46.4 1.0

Reference:

A.C.Drennan, S.Krishna, M.A.Seeger, M.P.Andreas, J.M.Gardner, E.K.R.Sether, S.L.Jaspersen, I.Rayment. Structure and Function of SPC42 Coiled-Coils in Yeast Centrosome Assembly and Duplication. Mol.Biol.Cell V. 30 1505 2019.
ISSN: ESSN 1939-4586
PubMed: 30969903
DOI: 10.1091/MBC.E19-03-0167
Page generated: Wed Jul 9 16:31:03 2025

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