Atomistry » Strontium » PDB 3ilg-4rne » 4ds7
Atomistry »
  Strontium »
    PDB 3ilg-4rne »
      4ds7 »

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

Go back to Strontium Binding Sites List in 4ds7
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

Go back to Strontium Binding Sites List in 4ds7
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

Go back to Strontium Binding Sites List in 4ds7
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

Go back to Strontium Binding Sites List in 4ds7
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

Go back to Strontium Binding Sites List in 4ds7
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

Go back to Strontium Binding Sites List in 4ds7
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: Wed Dec 16 02:23:57 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy