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Strontium in PDB 4ds7: Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110

Protein crystallography data

The structure of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110, PDB code: 4ds7 was solved by V.A.Klenchin, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.670, 145.444, 49.837, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 (pdb code 4ds7). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 8 binding sites of Strontium where determined in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110, PDB code: 4ds7:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 4ds7

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Strontium binding site 1 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:24.0
occ:1.00
 OD1 A:ASP23 2.5 28.0 1.0
O A:SER27 2.5 21.7 1.0
OD1 A:ASP21 2.6 25.1 1.0
OE1 A:GLU32 2.6 21.4 1.0
OG A:SER25 2.6 24.5 1.0
O A:HOH340 2.6 20.8 1.0
O A:HOH339 2.6 21.4 1.0
OE2 A:GLU32 2.7 23.3 1.0
CD A:GLU32 3.0 21.8 1.0
CG A:ASP23 3.6 27.5 1.0
CG A:ASP21 3.7 26.5 1.0
C A:SER27 3.7 22.2 1.0
CB A:SER25 3.8 26.4 1.0
OD2 A:ASP23 3.9 29.1 1.0
N A:SER25 4.2 27.4 1.0
CA A:ASP21 4.3 27.6 1.0
N A:SER29 4.4 19.5 1.0
N A:SER27 4.4 26.6 1.0
CB A:ASP21 4.5 28.4 1.0
CG A:GLU32 4.5 17.4 1.0
CA A:SER25 4.5 28.8 1.0
OG A:SER27 4.5 28.5 1.0
OD2 A:ASP21 4.5 26.0 1.0
CA A:ILE28 4.5 20.4 1.0
N A:ILE28 4.5 21.6 1.0
CA A:SER27 4.6 25.5 1.0
N A:ASP23 4.6 30.8 1.0
C A:ASP21 4.7 30.7 1.0
N A:LYS22 4.8 32.6 1.0
CB A:ASP23 4.9 25.3 1.0
C A:ILE28 4.9 21.3 1.0
N A:ASN24 4.9 31.2 1.0
N A:GLY26 5.0 27.6 1.0
CB A:SER29 5.0 23.7 1.0

Strontium binding site 2 out of 8 in 4ds7

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Strontium binding site 2 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr202

b:48.9
occ:1.00
 OD1 A:ASP94 2.3 30.3 1.0
O A:LEU100 2.4 30.6 1.0
OD1 A:ASN96 2.4 43.9 1.0
OE2 A:GLU105 2.5 30.4 1.0
OD1 A:ASP98 2.5 36.0 1.0
O A:HOH341 2.6 37.9 1.0
OE1 A:GLU105 2.6 29.3 1.0
CD A:GLU105 2.9 27.4 1.0
CG A:ASP98 3.4 39.6 1.0
CG A:ASP94 3.4 32.1 1.0
CG A:ASN96 3.4 46.8 1.0
C A:LEU100 3.5 28.3 1.0
OD2 A:ASP98 3.7 41.1 1.0
CA A:ASP94 4.0 28.9 1.0
ND2 A:ASN96 4.0 48.8 1.0
CB A:ASP94 4.2 30.6 1.0
N A:LEU100 4.2 28.7 1.0
OD2 A:ASP94 4.3 32.8 1.0
N A:ASP98 4.3 42.4 1.0
CA A:LEU100 4.3 27.9 1.0
C A:ASP94 4.4 31.2 1.0
CG A:GLU105 4.4 27.5 1.0
N A:ASN96 4.4 38.8 1.0
OE2 A:GLU135 4.5 48.0 1.0
N A:ILE101 4.5 27.8 1.0
N A:GLY97 4.5 45.6 1.0
CA A:ILE101 4.6 25.0 1.0
N A:LYS95 4.6 35.2 1.0
CB A:ASN96 4.6 45.2 1.0
CB A:LEU100 4.6 28.4 1.0
CB A:ASP98 4.6 41.1 1.0
O C:HOH338 4.8 34.7 1.0
N A:SER102 4.8 27.9 1.0
CA A:ASN96 4.9 43.6 1.0
CA A:ASP98 4.9 41.4 1.0
O A:ASP94 4.9 29.8 1.0
C A:ASN96 5.0 46.6 1.0

Strontium binding site 3 out of 8 in 4ds7

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Strontium binding site 3 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr201

b:50.6
occ:1.00
 O B:HOH323 2.2 49.8 1.0
OD1 B:ASP23 2.5 63.2 1.0
OG B:SER25 2.6 54.2 1.0
OD1 B:ASP21 2.6 50.7 1.0
OE1 B:GLU32 2.7 47.7 1.0
O B:SER27 2.7 42.3 1.0
OE2 B:GLU32 2.8 50.5 1.0
O B:HOH324 2.9 52.0 1.0
CD B:GLU32 3.1 47.7 1.0
CG B:ASP23 3.5 65.3 1.0
OD2 B:ASP23 3.7 70.0 1.0
CB B:SER25 3.7 57.4 1.0
C B:SER27 3.8 42.1 1.0
CG B:ASP21 3.8 45.8 1.0
N B:SER25 4.2 55.3 1.0
OG B:SER27 4.3 51.8 1.0
CA B:ASP21 4.4 43.4 1.0
CA B:SER25 4.5 56.9 1.0
N B:SER27 4.5 47.4 1.0
CB B:ASP21 4.6 42.4 1.0
CA B:ILE28 4.6 38.5 1.0
CG B:GLU32 4.6 46.8 1.0
N B:SER29 4.6 40.4 1.0
N B:ILE28 4.6 39.9 1.0
OD2 B:ASP21 4.6 45.7 1.0
CA B:SER27 4.6 44.9 1.0
C B:ASP21 4.7 47.1 1.0
N B:ASP23 4.7 59.7 1.0
N B:LYS22 4.8 50.0 1.0
CB B:ASP23 4.8 63.8 1.0
OG B:SER29 4.9 47.2 1.0
C B:SER25 4.9 55.2 1.0
N B:GLY26 5.0 53.3 1.0

Strontium binding site 4 out of 8 in 4ds7

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Strontium binding site 4 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr202

b:53.9
occ:1.00
 O B:LEU100 2.3 39.4 1.0
OD1 B:ASP94 2.4 31.7 1.0
OD1 B:ASP98 2.5 39.4 1.0
OE2 B:GLU105 2.5 34.2 1.0
O B:HOH325 2.5 38.9 1.0
OD1 B:ASN96 2.6 43.8 1.0
OE1 B:GLU105 2.6 33.0 1.0
CD B:GLU105 2.9 35.0 1.0
CG B:ASP98 3.3 45.3 1.0
C B:LEU100 3.5 34.7 1.0
CG B:ASP94 3.5 35.8 1.0
CG B:ASN96 3.5 47.8 1.0
OD2 B:ASP98 3.7 45.1 1.0
O B:HOH339 4.0 52.8 1.0
ND2 B:ASN96 4.0 50.1 1.0
CA B:ASP94 4.1 31.9 1.0
N B:LEU100 4.2 34.8 1.0
N B:ASP98 4.2 46.3 1.0
CB B:ASP94 4.3 31.0 1.0
CA B:LEU100 4.3 34.9 1.0
CG B:GLU105 4.4 37.1 1.0
OD2 B:ASP94 4.4 36.5 1.0
N B:ILE101 4.4 29.8 1.0
C B:ASP94 4.5 33.8 1.0
CB B:ASP98 4.5 46.7 1.0
CA B:ILE101 4.5 29.9 1.0
N B:SER102 4.5 31.1 1.0
N B:GLY97 4.6 45.9 1.0
N B:ASN96 4.6 44.5 1.0
CB B:LEU100 4.7 36.7 1.0
N B:LYS95 4.7 37.1 1.0
CA B:ASP98 4.8 46.1 1.0
CB B:ASN96 4.8 47.8 1.0
O B:HOH318 4.9 46.8 1.0
O B:ASP94 5.0 34.4 1.0
N B:GLY99 5.0 42.5 1.0

Strontium binding site 5 out of 8 in 4ds7

Go back to Strontium Binding Sites List in 4ds7
Strontium binding site 5 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr201

b:49.4
occ:1.00
 O C:HOH355 2.5 58.1 1.0
OD1 C:ASP21 2.5 44.7 1.0
OD1 C:ASP23 2.5 60.2 1.0
O C:SER27 2.7 40.3 1.0
OE1 C:GLU32 2.7 44.8 1.0
O C:HOH333 2.7 51.9 1.0
OG C:SER25 2.8 54.0 1.0
OE2 C:GLU32 2.8 51.1 1.0
CD C:GLU32 3.1 48.4 1.0
CG C:ASP23 3.6 64.7 1.0
CG C:ASP21 3.6 46.8 1.0
C C:SER27 3.8 41.8 1.0
OD2 C:ASP23 3.9 68.0 1.0
CB C:SER25 3.9 59.0 1.0
N C:SER25 4.3 61.3 1.0
CA C:ASP21 4.3 46.8 1.0
OG C:SER27 4.4 50.9 1.0
CB C:ASP21 4.4 44.5 1.0
OD2 C:ASP21 4.5 47.6 1.0
N C:SER27 4.5 46.6 1.0
CG C:GLU32 4.6 48.4 1.0
CA C:ILE28 4.6 37.9 1.0
N C:SER29 4.6 39.2 1.0
N C:ILE28 4.6 38.9 1.0
CA C:SER25 4.6 60.3 1.0
N C:ASP23 4.7 59.9 1.0
O C:HOH356 4.7 45.4 1.0
CA C:SER27 4.7 44.4 1.0
C C:ASP21 4.7 53.3 1.0
N C:LYS22 4.8 53.8 1.0
CB C:ASP23 4.8 64.3 1.0
O C:HOH352 4.9 47.4 1.0
N C:ASN24 4.9 62.9 1.0

Strontium binding site 6 out of 8 in 4ds7

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Strontium binding site 6 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr202

b:44.2
occ:1.00
 O C:LEU100 2.3 27.4 1.0
OD1 C:ASN96 2.4 30.6 1.0
OD1 C:ASP94 2.4 24.1 1.0
OD1 C:ASP98 2.5 25.0 1.0
O C:HOH334 2.5 30.3 1.0
OE1 C:GLU105 2.6 23.3 1.0
OE2 C:GLU105 2.6 25.6 1.0
CD C:GLU105 2.9 24.5 1.0
CG C:ASP98 3.2 30.2 1.0
CG C:ASN96 3.3 30.1 1.0
OD2 C:ASP98 3.5 29.9 1.0
C C:LEU100 3.5 25.9 1.0
CG C:ASP94 3.6 30.0 1.0
ND2 C:ASN96 3.7 33.5 1.0
N C:LEU100 4.1 26.0 1.0
CA C:ASP94 4.2 28.4 1.0
N C:ASP98 4.2 34.2 1.0
CA C:LEU100 4.3 25.6 1.0
CB C:ASP94 4.4 27.4 1.0
OD2 C:ASP94 4.4 28.9 1.0
CG C:GLU105 4.4 23.8 1.0
CB C:ASP98 4.5 30.8 1.0
N C:ILE101 4.5 24.3 1.0
N C:ASN96 4.5 32.1 1.0
C C:ASP94 4.5 29.9 1.0
CA C:ILE101 4.6 23.6 1.0
CB C:ASN96 4.6 33.8 1.0
N C:GLY97 4.6 32.6 1.0
N C:SER102 4.6 22.3 1.0
CB C:LEU100 4.7 28.2 1.0
CA C:ASP98 4.8 32.7 1.0
N C:LYS95 4.8 29.6 1.0
CA C:ASN96 4.9 33.4 1.0
N C:GLY99 4.9 29.5 1.0
O C:ASP94 4.9 30.5 1.0
C C:ASN96 4.9 33.9 1.0
C C:ASP98 5.0 32.5 1.0
OG C:SER102 5.0 20.2 1.0

Strontium binding site 7 out of 8 in 4ds7

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Strontium binding site 7 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr201

b:26.1
occ:1.00
 O D:SER27 2.5 24.9 1.0
OE1 D:GLU32 2.5 22.4 1.0
OD1 D:ASP23 2.5 31.0 1.0
OD1 D:ASP21 2.6 26.0 1.0
O D:HOH321 2.6 25.4 1.0
OG D:SER25 2.6 26.8 1.0
O D:HOH322 2.7 18.6 1.0
OE2 D:GLU32 2.8 23.0 1.0
CD D:GLU32 3.0 24.8 1.0
CG D:ASP23 3.6 35.2 1.0
C D:SER27 3.6 23.2 1.0
CG D:ASP21 3.7 31.7 1.0
CB D:SER25 3.8 29.4 1.0
OD2 D:ASP23 3.9 35.4 1.0
N D:SER25 4.2 33.0 1.0
CA D:ASP21 4.3 28.1 1.0
N D:SER29 4.4 22.6 1.0
N D:SER27 4.4 29.5 1.0
CA D:ILE28 4.5 22.8 1.0
CG D:GLU32 4.5 19.2 1.0
N D:ILE28 4.5 22.4 1.0
CB D:ASP21 4.5 31.2 1.0
OD2 D:ASP21 4.5 31.1 1.0
CA D:SER25 4.5 32.6 1.0
OG D:SER27 4.5 30.2 1.0
CA D:SER27 4.6 26.9 1.0
N D:ASP23 4.6 34.2 1.0
C D:ASP21 4.7 29.9 1.0
N D:LYS22 4.7 32.0 1.0
C D:ILE28 4.9 21.3 1.0
CB D:ASP23 4.9 32.9 1.0
N D:GLY26 4.9 32.6 1.0
N D:ASN24 4.9 31.6 1.0
C D:SER25 5.0 32.9 1.0

Strontium binding site 8 out of 8 in 4ds7

Go back to Strontium Binding Sites List in 4ds7
Strontium binding site 8 out of 8 in the Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of Yeast Calmodulin Bound to the C-Terminal Fragment of Spindle Pole Body Protein SPC110 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr202

b:67.6
occ:1.00
 O D:LEU100 2.3 46.1 1.0
OD1 D:ASP94 2.4 42.8 1.0
OD1 D:ASN96 2.5 62.0 1.0
OE2 D:GLU105 2.5 44.2 1.0
OD1 D:ASP98 2.5 45.2 1.0
OE1 D:GLU105 2.6 36.2 1.0
O D:HOH323 2.8 44.1 1.0
CD D:GLU105 2.9 41.5 1.0
CG D:ASN96 3.4 62.5 1.0
CG D:ASP98 3.5 50.8 1.0
C D:LEU100 3.5 42.8 1.0
CG D:ASP94 3.6 45.5 1.0
OD2 D:ASP98 3.8 56.7 1.0
ND2 D:ASN96 3.9 62.8 1.0
N D:LEU100 4.1 43.2 1.0
CA D:ASP94 4.2 43.6 1.0
CA D:LEU100 4.3 42.1 1.0
N D:ASP98 4.3 51.5 1.0
CG D:GLU105 4.4 41.9 1.0
CB D:ASP94 4.4 43.2 1.0
N D:GLY97 4.5 58.3 1.0
N D:ILE101 4.5 40.5 1.0
C D:ASP94 4.5 47.6 1.0
OD2 D:ASP94 4.5 46.4 1.0
N D:ASN96 4.5 61.1 1.0
CA D:ILE101 4.6 38.5 1.0
CB D:ASN96 4.6 64.3 1.0
N D:LYS95 4.7 50.5 1.0
N D:SER102 4.7 40.9 1.0
CB D:ASP98 4.7 52.2 1.0
CB D:LEU100 4.8 43.2 1.0
N D:GLY99 4.9 49.5 1.0
CA D:ASP98 4.9 52.3 1.0
CA D:ASN96 4.9 62.7 1.0

Reference:

S.Viswanath, M.Bonomi, S.J.Kim, V.A.Klenchin, K.C.Taylor, K.C.Yabut, N.T.Umbreit, H.A.Van Epps, J.Meehl, M.H.Jones, D.Russel, J.A.Velazquez-Muriel, M.Winey, I.Rayment, T.N.Davis, A.Sali, E.G.Muller. The Molecular Architecture of the Yeast Spindle Pole Body Core Determined By Bayesian Integrative Modeling. Mol. Biol. Cell 2017.
ISSN: ESSN 1939-4586
PubMed: 28814505
DOI: 10.1091/MBC.E17-06-0397
Page generated: Fri Oct 11 05:27:49 2024

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