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Calcium in PDB 3r8y: Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase

Enzymatic activity of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase

All present enzymatic activity of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase:
2.3.1.89;

Protein crystallography data

The structure of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase, PDB code: 3r8y was solved by S.M.Anderson, Z.Wawrzak, O.Onopriyenko, S.N.Peterson, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.41 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.421, 52.219, 134.550, 97.41, 93.19, 115.71
R / Rfree (%) 18.6 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase (pdb code 3r8y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase, PDB code: 3r8y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3r8y

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Calcium binding site 1 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca241

b:21.4
occ:1.00
 O B:HOH1195 3.1 39.8 1.0
O B:HOH452 3.1 23.6 1.0
O B:HOH265 3.1 21.3 1.0
N A:GLY138 3.1 12.1 1.0
ND2 A:ASN119 3.1 16.7 1.0
CA A:GLY137 3.7 8.2 1.0
CA A:GLY156 3.8 12.3 1.0
C A:GLY137 3.9 12.5 1.0
CE B:MET132 3.9 13.6 1.0
CA A:GLY138 4.1 14.5 1.0
CD1 A:ILE158 4.2 39.1 1.0
CG1 A:ILE158 4.2 37.3 1.0
CG A:ASN119 4.2 18.1 1.0
N A:GLY156 4.4 13.4 1.0
O A:HOH252 4.4 19.0 1.0
CB A:ASN119 4.5 13.8 1.0
C A:GLY156 4.6 17.4 1.0
O B:HOH257 4.6 23.1 1.0
O B:HOH1504 4.7 29.6 1.0
O A:HOH279 4.8 25.1 1.0

Calcium binding site 2 out of 9 in 3r8y

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Calcium binding site 2 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca242

b:23.1
occ:1.00
 O A:HOH1300 2.3 21.4 1.0
O C:HOH255 2.3 17.2 1.0
O B:HOH258 2.4 18.0 1.0
OD1 A:ASN115 2.5 18.7 1.0
OD1 B:ASN115 2.5 19.2 1.0
OD1 C:ASN115 2.5 20.5 1.0
CG A:ASN115 3.5 18.0 1.0
CG B:ASN115 3.6 18.0 1.0
CG C:ASN115 3.7 13.2 1.0
O A:GLY97 4.0 15.1 1.0
O B:GLY97 4.1 19.1 1.0
O C:GLY97 4.1 17.0 1.0
ND2 A:ASN115 4.2 12.3 1.0
ND2 B:ASN115 4.2 14.3 1.0
O A:HOH944 4.3 37.3 1.0
ND2 C:ASN115 4.4 11.0 1.0
O B:HOH781 4.5 38.6 1.0
O C:HOH959 4.6 31.9 1.0
CB A:ASN115 4.6 12.9 1.0
CB B:ASN115 4.7 13.4 1.0
CA A:GLY97 4.7 16.5 1.0
CA A:ASN115 4.8 11.6 1.0
CB C:ASN115 4.8 12.2 1.0
C A:GLY97 4.8 12.0 1.0
CA B:GLY97 4.9 16.5 1.0
CA B:ASN115 4.9 11.8 1.0
C B:GLY97 4.9 16.2 1.0
CA C:ASN115 4.9 11.3 1.0

Calcium binding site 3 out of 9 in 3r8y

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Calcium binding site 3 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca241

b:68.5
occ:1.00
 NZ B:LYS88 3.0 23.7 1.0
O B:HOH1407 3.5 47.0 1.0
O A:HOH1565 3.6 42.7 1.0
CE B:LYS88 3.7 21.6 1.0
O A:HOH1566 3.9 43.6 1.0
OD2 B:ASP86 4.2 27.1 1.0
CB A:VAL73 4.2 30.8 1.0
O B:HOH1440 4.2 48.6 1.0
CG2 A:VAL73 4.3 33.8 1.0
O B:HOH402 4.4 34.6 1.0
O B:HOH559 4.6 43.0 1.0
CG1 A:VAL73 4.9 28.6 1.0
CG B:ASP86 5.0 28.1 1.0

Calcium binding site 4 out of 9 in 3r8y

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Calcium binding site 4 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca241

b:19.9
occ:1.00
 O A:HOH275 3.1 24.4 1.0
ND2 C:ASN119 3.1 15.0 1.0
N C:GLY138 3.1 11.3 1.0
O C:HOH476 3.2 32.7 1.0
O A:HOH259 3.2 16.8 1.0
CA C:GLY137 3.7 11.2 1.0
CA C:GLY156 3.8 11.4 1.0
CE A:MET132 3.9 8.1 1.0
C C:GLY137 3.9 13.0 1.0
CG1 C:ILE158 4.0 28.2 1.0
CA C:GLY138 4.1 10.9 1.0
CD1 C:ILE158 4.1 28.1 1.0
CG C:ASN119 4.2 15.0 1.0
N C:GLY156 4.4 11.7 1.0
O C:HOH1245 4.4 28.4 1.0
O A:HOH243 4.4 27.2 1.0
CB C:ASN119 4.5 14.0 1.0
C C:GLY156 4.5 14.5 1.0
O A:HOH272 4.8 25.6 1.0
O C:HOH261 4.8 20.9 1.0
O C:HOH288 4.9 23.4 1.0
OD1 A:ASP131 5.0 12.5 1.0
OD2 A:ASP131 5.0 15.8 1.0

Calcium binding site 5 out of 9 in 3r8y

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Calcium binding site 5 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca241

b:23.8
occ:1.00
 O D:HOH1549 2.3 22.8 1.0
O E:HOH257 2.4 19.4 1.0
O F:HOH276 2.4 21.0 1.0
OD1 E:ASN115 2.5 21.1 1.0
OD1 D:ASN115 2.5 18.1 1.0
OD1 F:ASN115 2.6 20.3 1.0
CG E:ASN115 3.5 19.3 1.0
CG D:ASN115 3.6 16.1 1.0
CG F:ASN115 3.7 14.5 1.0
O D:GLY97 3.9 15.1 1.0
O E:GLY97 4.1 19.1 1.0
O F:GLY97 4.1 18.4 1.0
O D:HOH1467 4.1 33.4 1.0
ND2 E:ASN115 4.1 13.7 1.0
ND2 D:ASN115 4.2 13.9 1.0
ND2 F:ASN115 4.4 13.4 1.0
CB E:ASN115 4.6 14.4 1.0
CB D:ASN115 4.6 11.9 1.0
O F:HOH895 4.6 36.2 1.0
O E:HOH989 4.6 37.2 1.0
CA D:GLY97 4.7 16.1 1.0
C D:GLY97 4.8 11.9 1.0
CA D:ASN115 4.8 11.2 1.0
CA E:GLY97 4.8 15.5 1.0
CA E:ASN115 4.9 11.6 1.0
CB F:ASN115 4.9 11.6 1.0
C E:GLY97 4.9 17.4 1.0

Calcium binding site 6 out of 9 in 3r8y

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Calcium binding site 6 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca242

b:23.3
occ:1.00
 O E:HOH305 3.0 21.7 1.0
O E:HOH268 3.1 19.6 1.0
N D:GLY138 3.1 12.8 1.0
ND2 D:ASN119 3.1 18.5 1.0
CA D:GLY137 3.7 9.3 1.0
CA D:GLY156 3.7 11.2 1.0
C D:GLY137 3.9 13.2 1.0
CE E:MET132 3.9 14.9 1.0
CD1 D:ILE158 4.1 38.5 1.0
CA D:GLY138 4.1 15.8 1.0
CG1 D:ILE158 4.2 36.9 1.0
CG D:ASN119 4.3 17.2 1.0
O D:HOH262 4.3 20.4 1.0
N D:GLY156 4.3 11.0 1.0
CB D:ASN119 4.5 14.3 1.0
C D:GLY156 4.6 18.4 1.0
O E:HOH945 4.7 21.9 1.0
O E:HOH274 4.8 27.7 1.0
O D:HOH389 4.8 22.5 1.0
O E:HOH1200 4.9 43.0 1.0
O D:HOH382 4.9 21.9 1.0

Calcium binding site 7 out of 9 in 3r8y

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Calcium binding site 7 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca241

b:19.6
occ:1.00
 ND2 F:ASN119 3.1 16.2 1.0
O D:HOH271 3.1 21.6 1.0
N F:GLY138 3.1 10.6 1.0
O F:HOH960 3.2 38.0 1.0
O D:HOH272 3.3 17.1 1.0
CA F:GLY137 3.7 10.3 1.0
CA F:GLY156 3.7 8.4 1.0
CE D:MET132 3.9 10.2 1.0
O D:HOH971 3.9 49.1 1.0
C F:GLY137 3.9 10.5 1.0
CG1 F:ILE158 4.0 27.2 1.0
CA F:GLY138 4.1 12.4 1.0
CD1 F:ILE158 4.1 27.7 1.0
CG F:ASN119 4.2 16.1 1.0
N F:GLY156 4.4 12.0 1.0
O F:HOH286 4.4 21.8 1.0
C F:GLY156 4.5 14.9 1.0
CB F:ASN119 4.5 13.1 1.0
O D:HOH573 4.6 25.0 1.0
O D:HOH268 4.7 26.8 1.0
O F:HOH257 4.9 23.0 1.0
O F:GLY156 5.0 18.1 1.0

Calcium binding site 8 out of 9 in 3r8y

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Calcium binding site 8 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca242

b:54.7
occ:1.00
 O F:LYS164 2.8 16.7 1.0
O F:HOH758 3.0 40.1 1.0
O F:HOH594 3.0 39.9 1.0
N F:LYS164 3.5 21.9 1.0
C F:LYS164 3.8 15.6 1.0
O F:HOH677 3.8 40.1 1.0
O F:HOH1059 3.9 42.8 1.0
CA F:GLY183 4.0 12.7 1.0
CA F:LYS164 4.0 17.5 1.0
C F:ALA163 4.1 22.9 1.0
CB F:ALA163 4.1 19.7 1.0
CB F:LYS164 4.3 16.5 1.0
CA F:ALA163 4.3 21.0 1.0
N F:GLY183 4.4 13.1 1.0
CG2 F:VAL157 4.4 27.5 1.0
CG1 F:VAL157 4.5 31.7 1.0
C F:GLU182 4.8 15.3 1.0
O F:ALA163 4.9 23.5 1.0
N F:PRO165 5.0 13.8 1.0
O F:HOH1251 5.0 36.7 1.0

Calcium binding site 9 out of 9 in 3r8y

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Calcium binding site 9 out of 9 in the Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca243

b:59.4
occ:1.00
 O F:HOH274 2.7 21.9 1.0
OE1 F:GLU182 3.0 46.6 1.0
O F:HOH600 3.1 38.1 1.0
O F:HOH286 3.1 21.8 1.0
O D:HOH630 3.4 41.5 1.0
O F:GLY156 3.5 18.1 1.0
CD F:GLU182 3.6 41.8 1.0
CB F:GLU182 3.7 18.4 1.0
CB F:ALA155 3.8 15.5 1.0
CG F:GLU182 4.1 28.6 1.0
O F:HOH684 4.1 32.1 1.0
O F:HOH647 4.2 27.6 1.0
OE2 F:GLU182 4.3 43.1 1.0
N F:GLY156 4.5 12.0 1.0
C F:GLY156 4.7 14.9 1.0
N F:GLU182 4.7 12.3 1.0
O F:HOH296 4.7 21.8 1.0
CA F:GLU182 4.7 13.5 1.0
O D:HOH971 4.7 49.1 1.0
O D:HOH400 4.7 27.2 1.0
O F:HOH1606 4.8 48.2 1.0
CA F:ALA155 4.8 13.8 1.0
O F:HOH1411 4.9 39.0 1.0
C F:ALA155 4.9 15.8 1.0

Reference:

S.M.Anderson, Z.Wawrzak, O.Onopriyenko, S.N.Peterson, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases(Csgid). Structure of the Bacillus Anthracis Tetrahydropicolinate Succinyltransferase To Be Published.
Page generated: Sat Jul 13 17:53:05 2024

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