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Calcium in PDB 2p1r: Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.

Protein crystallography data

The structure of Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases., PDB code: 2p1r was solved by C.E.Nichols, H.K.Lamb, M.Lockyer, I.G.Charles, S.Pyne, A.R.Hawkins, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.000, 70.990, 102.160, 90.00, 118.51, 90.00
R / Rfree (%) 20.6 / 25.5

Other elements in 2p1r:

The structure of Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. (pdb code 2p1r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases., PDB code: 2p1r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 1 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:39.3
occ:1.00
 O A:LEU220 2.6 20.5 1.0
O A:LEU215 2.7 26.3 1.0
OD1 A:ASN200 2.7 24.8 1.0
OD1 A:ASP125 2.9 43.8 1.0
OD1 A:ASP218 2.9 32.0 1.0
CG A:ASP218 3.7 37.9 1.0
C A:LEU220 3.8 23.8 1.0
CG A:ASP125 3.8 49.6 1.0
CB A:ASP125 3.8 36.6 1.0
N A:LEU220 3.9 12.0 1.0
C A:LEU215 3.9 32.9 1.0
CG A:ASN200 3.9 31.8 1.0
CA A:ILE216 4.0 35.6 1.0
OD2 A:ASP218 4.0 38.6 1.0
C A:ILE216 4.1 37.1 1.0
N A:GLY219 4.2 31.9 1.0
N A:ASP218 4.2 33.3 1.0
N A:ASN217 4.4 35.5 1.0
O A:ASN200 4.4 25.1 1.0
N A:ILE216 4.4 31.1 1.0
CA A:LEU220 4.4 24.6 1.0
O A:ILE216 4.4 49.6 1.0
CA A:ASN200 4.5 20.4 1.0
CG2 A:VAL282 4.7 35.2 1.0
CB A:ASN200 4.7 20.8 1.0
C A:GLY219 4.8 22.9 1.0
CA A:GLY219 4.8 15.8 1.0
N A:LEU221 4.8 16.0 1.0
CB A:ASP218 4.8 32.0 1.0
CA A:ASP218 4.8 31.5 1.0
C A:ASP218 4.9 32.9 1.0
C A:ASN200 4.9 19.1 1.0
ND2 A:ASN200 4.9 22.3 1.0
CD2 A:LEU221 4.9 37.5 1.0
OD2 A:ASP125 5.0 54.7 1.0

Calcium binding site 2 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 2 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:48.7
occ:1.00
 O A:ASN245 2.7 37.8 1.0
O A:ILE248 2.8 33.6 1.0
O A:SER242 2.9 57.0 1.0
O A:ASP243 3.0 51.2 1.0
C A:ASP243 3.3 48.5 1.0
O A:HOH364 3.4 44.1 1.0
C A:ASN245 3.6 26.9 1.0
N A:ASN245 3.7 41.8 1.0
CA A:ASP243 3.8 52.4 1.0
C A:ILE248 3.9 27.3 1.0
C A:SER242 4.0 60.0 1.0
O A:HOH362 4.0 55.1 1.0
N A:ASP244 4.0 43.5 1.0
O A:HOH372 4.1 46.8 1.0
CB A:ILE248 4.2 11.7 1.0
CA A:ASN245 4.2 37.6 1.0
C A:ASP244 4.2 46.2 1.0
O C:HOH320 4.3 44.9 1.0
N A:ASP243 4.4 57.3 1.0
O A:HOH331 4.4 25.7 1.0
CA A:ASP244 4.5 42.9 1.0
CA A:ILE248 4.5 15.3 1.0
CG2 A:ILE248 4.5 14.2 1.0
N A:ILE248 4.6 11.0 1.0
CB A:ASN245 4.6 32.7 1.0
N A:PRO246 4.6 20.9 1.0
O A:ASP244 4.9 46.1 1.0
CA A:PRO246 4.9 19.7 1.0
N A:ILE249 4.9 31.4 1.0

Calcium binding site 3 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 3 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:39.2
occ:1.00
 OD1 B:ASN200 2.7 18.4 1.0
O B:LEU220 2.7 39.0 1.0
O B:LEU215 2.8 36.8 1.0
OD1 B:ASP218 2.8 28.0 1.0
OD1 B:ASP125 2.9 37.7 1.0
CG B:ASP125 3.7 42.9 1.0
CB B:ASP125 3.7 31.9 1.0
CG B:ASN200 3.8 27.6 1.0
C B:LEU220 3.8 27.8 1.0
CG B:ASP218 3.9 32.8 1.0
CA B:ILE216 3.9 33.9 1.0
C B:LEU215 3.9 35.4 1.0
N B:LEU220 4.0 32.5 1.0
C B:ILE216 4.0 33.4 1.0
OD2 B:ASP218 4.3 33.3 1.0
O B:ASN200 4.3 19.4 1.0
CA B:ASN200 4.3 20.6 1.0
N B:GLY219 4.4 31.0 1.0
N B:ASP218 4.4 32.9 1.0
N B:ASN217 4.4 26.9 1.0
N B:ILE216 4.4 33.7 1.0
O B:ILE216 4.4 44.7 1.0
CG2 B:VAL282 4.5 36.9 1.0
CB B:ASN200 4.6 17.2 1.0
CA B:LEU220 4.6 33.3 1.0
CD2 B:LEU221 4.8 41.6 1.0
C B:ASN200 4.8 18.3 1.0
ND2 B:ASN200 4.9 28.9 1.0
N B:LEU221 4.9 22.5 1.0
OD2 B:ASP125 4.9 50.0 1.0
C B:GLY219 4.9 39.3 1.0
CA B:GLY219 5.0 31.3 1.0

Calcium binding site 4 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 4 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:44.2
occ:1.00
 O B:ASN245 2.8 43.3 1.0
O B:ILE248 2.8 20.0 1.0
O B:SER242 2.9 46.5 1.0
O B:ASP243 3.0 52.3 1.0
C B:ASP243 3.3 49.9 1.0
O B:HOH361 3.3 45.7 1.0
C B:ASN245 3.7 38.0 1.0
CA B:ASP243 3.8 53.5 1.0
N B:ASN245 3.8 41.2 1.0
C B:ILE248 3.9 23.8 1.0
O D:HOH368 3.9 56.8 1.0
C B:SER242 4.0 51.4 1.0
N B:ASP244 4.1 43.2 1.0
O D:HOH319 4.2 48.8 1.0
CB B:ILE248 4.2 21.7 1.0
C B:ASP244 4.3 46.0 1.0
CA B:ASN245 4.3 36.9 1.0
N B:ASP243 4.4 53.4 1.0
O B:HOH334 4.4 33.1 1.0
CG2 B:ILE248 4.4 18.0 1.0
CA B:ILE248 4.5 19.5 1.0
CA B:ASP244 4.5 41.5 1.0
N B:ILE248 4.6 19.7 1.0
CB B:ASN245 4.7 30.8 1.0
N B:PRO246 4.7 36.5 1.0
O D:HOH375 4.8 53.1 1.0
O B:ASP244 4.9 47.8 1.0
N B:ILE249 4.9 22.3 1.0
O B:HOH321 5.0 36.6 1.0
CA B:PRO246 5.0 28.3 1.0

Calcium binding site 5 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 5 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca300

b:38.5
occ:1.00
 O C:LEU215 2.6 32.7 1.0
O C:LEU220 2.7 42.9 1.0
OD1 C:ASN200 2.7 24.4 1.0
OD1 C:ASP218 3.0 34.3 1.0
OD1 C:ASP125 3.3 32.8 1.0
O C:HOH333 3.6 37.4 1.0
C C:LEU215 3.7 38.8 1.0
C C:LEU220 3.8 32.4 1.0
CG C:ASN200 3.8 29.9 1.0
CA C:ILE216 3.9 45.9 1.0
CB C:ASP125 3.9 27.0 1.0
CG C:ASP218 4.0 39.8 1.0
O C:ASN200 4.0 28.6 1.0
CG C:ASP125 4.1 38.5 1.0
N C:LEU220 4.1 29.1 1.0
C C:ILE216 4.2 43.2 1.0
CA C:ASN200 4.3 33.6 1.0
N C:ILE216 4.3 42.9 1.0
OD2 C:ASP218 4.4 49.7 1.0
N C:ASN217 4.4 35.2 1.0
CA C:LEU220 4.5 29.6 1.0
N C:ASP218 4.5 34.9 1.0
N C:GLY219 4.6 33.1 1.0
C C:ASN200 4.6 31.4 1.0
CB C:ASN200 4.6 31.5 1.0
O C:ILE216 4.7 47.9 1.0
CD2 C:LEU221 4.7 36.2 1.0
CG2 C:VAL282 4.7 35.9 1.0
N C:LEU215 4.8 37.3 1.0
ND2 C:ASN200 4.8 29.0 1.0
N C:LEU221 4.8 35.2 1.0
CA C:LEU215 4.9 37.4 1.0
CA C:LEU221 5.0 30.6 1.0
C C:GLY219 5.0 35.2 1.0

Calcium binding site 6 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 6 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:51.3
occ:1.00
 O C:ASN245 2.8 33.2 1.0
O C:ILE248 2.9 25.2 1.0
O C:ASP243 2.9 51.2 1.0
O C:SER242 3.0 61.5 1.0
C C:ASP243 3.3 51.3 1.0
CA C:ASP243 3.7 56.6 1.0
C C:ASN245 3.7 35.3 1.0
O C:HOH365 3.8 77.5 1.0
O C:HOH370 3.8 47.0 1.0
N C:ASN245 3.9 21.2 1.0
C C:ILE248 3.9 30.0 1.0
C C:SER242 4.0 55.0 1.0
CB C:ILE248 4.1 40.3 1.0
N C:ASP244 4.1 45.0 1.0
O C:HOH310 4.1 30.1 1.0
C C:ASP244 4.3 29.3 1.0
N C:ASP243 4.3 52.8 1.0
CA C:ASN245 4.4 30.5 1.0
CG2 C:ILE248 4.4 33.1 1.0
CA C:ILE248 4.4 30.6 1.0
O A:HOH362 4.5 55.1 1.0
CA C:ASP244 4.5 33.9 1.0
N C:ILE248 4.6 29.6 1.0
N C:PRO246 4.7 41.8 1.0
CB C:ASN245 4.8 28.8 1.0
OD1 C:ASP243 4.9 97.6 1.0
CA C:PRO246 4.9 31.7 1.0
CB C:ASP243 4.9 72.7 1.0

Calcium binding site 7 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 7 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:72.3
occ:1.00
 O C:ARG81 2.8 72.8 1.0
O C:GLY83 3.0 51.9 1.0
O C:HOH400 3.0 38.9 1.0
O B:GLY94 3.2 34.0 1.0
O B:HOH370 3.4 44.2 1.0
ND2 B:ASN97 3.7 49.6 1.0
C C:ARG81 3.7 67.8 1.0
O B:THR95 3.8 41.0 1.0
N C:GLY83 3.9 58.0 1.0
C C:GLY83 4.0 58.3 1.0
C B:GLY94 4.2 41.4 1.0
C C:ASP82 4.3 60.2 1.0
CA C:ASP82 4.3 61.6 1.0
CA B:THR95 4.4 42.3 1.0
N C:ASP82 4.4 59.8 1.0
C B:THR95 4.4 43.7 1.0
N C:ARG81 4.5 68.7 1.0
CA C:GLY83 4.5 57.9 1.0
CG B:ASN97 4.6 50.0 1.0
OD1 B:ASN97 4.7 49.3 1.0
CA C:ARG81 4.7 69.5 1.0
N B:THR95 4.7 40.5 1.0

Calcium binding site 8 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 8 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


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 Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca300

b:41.2
occ:1.00
 O D:LEU215 2.6 29.4 1.0
O D:LEU220 2.6 29.6 1.0
OD1 D:ASN200 2.8 36.5 1.0
OD1 D:ASP125 3.2 42.9 1.0
OD1 D:ASP218 3.4 49.9 1.0
CG D:ASN200 3.7 30.0 1.0
C D:LEU215 3.8 39.8 1.0
C D:LEU220 3.8 29.9 1.0
CB D:ASP125 3.9 40.5 1.0
CA D:ILE216 4.0 44.8 1.0
CG D:ASP125 4.0 47.3 1.0
CG D:ASP218 4.0 45.9 1.0
N D:LEU220 4.0 25.7 1.0
O D:HOH360 4.0 30.7 1.0
O D:ASN200 4.1 32.5 1.0
OD2 D:ASP218 4.1 57.2 1.0
C D:ILE216 4.2 43.7 1.0
CA D:ASN200 4.3 26.7 1.0
N D:ILE216 4.4 41.0 1.0
N D:ASN217 4.4 40.5 1.0
ND2 D:ASN200 4.4 29.5 1.0
N D:GLY219 4.5 29.8 1.0
CA D:LEU220 4.5 28.5 1.0
N D:ASP218 4.5 32.7 1.0
CB D:ASN200 4.6 31.0 1.0
C D:ASN200 4.6 24.6 1.0
O D:ILE216 4.7 49.6 1.0
CG2 D:VAL282 4.7 31.0 1.0
CD2 D:LEU221 4.8 27.9 1.0
N D:LEU221 4.8 29.0 1.0
N D:LEU215 4.9 29.5 1.0
C D:GLY219 4.9 28.3 1.0
CA D:LEU215 5.0 37.9 1.0

Calcium binding site 9 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 9 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:49.6
occ:1.00
 O D:ASN245 2.8 32.5 1.0
O D:ILE248 2.8 33.1 1.0
O D:SER242 2.9 55.7 1.0
O D:ASP243 2.9 48.0 1.0
C D:ASP243 3.3 50.3 1.0
CA D:ASP243 3.6 54.4 1.0
O B:HOH320 3.7 46.5 1.0
C D:ASN245 3.7 30.8 1.0
C D:ILE248 3.9 22.9 1.0
N D:ASN245 3.9 31.6 1.0
CB D:ILE248 3.9 21.9 1.0
O D:HOH368 3.9 56.8 1.0
C D:SER242 3.9 52.1 1.0
N D:ASP244 4.1 43.7 1.0
CG2 D:ILE248 4.2 25.7 1.0
N D:ASP243 4.3 51.8 1.0
CA D:ASN245 4.3 29.5 1.0
CA D:ILE248 4.3 22.3 1.0
C D:ASP244 4.4 36.2 1.0
O D:HOH375 4.4 53.1 1.0
N D:ILE248 4.5 22.4 1.0
CA D:ASP244 4.6 39.3 1.0
CB D:ASN245 4.6 31.0 1.0
N D:PRO246 4.7 33.1 1.0
CB D:ASP243 4.9 65.5 1.0
OD1 D:ASP243 4.9 86.1 1.0
CA D:PRO246 5.0 31.5 1.0

Calcium binding site 10 out of 10 in 2p1r

Go back to Calcium Binding Sites List in 2p1r
Calcium binding site 10 out of 10 in the Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:79.5
occ:1.00
 O D:ARG81 2.9 72.6 1.0
O D:HOH382 3.0 39.1 1.0
O D:GLY83 3.1 47.5 1.0
O A:GLY94 3.3 39.7 1.0
O A:THR95 3.7 46.1 1.0
C D:ARG81 3.8 64.9 1.0
ND2 A:ASN97 3.9 38.8 1.0
N D:GLY83 4.0 62.3 1.0
C D:GLY83 4.1 56.2 1.0
O D:HOH397 4.1 57.5 1.0
C A:GLY94 4.3 42.6 1.0
CA A:THR95 4.3 48.0 1.0
C A:THR95 4.4 47.1 1.0
C D:ASP82 4.4 63.8 1.0
N D:ARG81 4.4 65.2 1.0
OD1 A:ASN97 4.5 39.2 1.0
CA D:ASP82 4.5 64.0 1.0
N D:ASP82 4.5 58.8 1.0
CG A:ASN97 4.6 39.6 1.0
O A:HOH403 4.6 54.5 1.0
CA D:GLY83 4.6 60.3 1.0
CA D:ARG81 4.7 65.0 1.0
N A:THR95 4.7 47.7 1.0

Reference:

C.E.Nichols, H.K.Lamb, M.Lockyer, I.G.Charles, S.Pyne, A.R.Hawkins, D.K.Stammers. Characterization of Salmonella Typhimurium Yegs, A Putative Lipid Kinase Homologous to Eukaryotic Sphingosine and Diacylglycerol Kinases Proteins: V. 68 13 2007STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 17393457
DOI: 10.1002/PROT.21386
Page generated: Fri Jul 12 14:56:07 2024

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