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Calcium in PDB 3k28: Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate

Enzymatic activity of Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate

All present enzymatic activity of Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate:
5.4.3.8;

Protein crystallography data

The structure of Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate, PDB code: 3k28 was solved by S.S.Sharma, J.S.Brunzelle, Z.Wawrzak, T.Skarina, A.Savchenko, W.F.Anderson, 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) 28.45 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 149.809, 113.688, 113.955, 90.00, 118.65, 90.00
R / Rfree (%) 14.7 / 18.5

Other elements in 3k28:

The structure of Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate (pdb code 3k28). 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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate, PDB code: 3k28:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3k28

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Calcium binding site 1 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca430

b:22.8
occ:0.80
 O A:ILE103 2.2 12.3 1.0
O A:HOH1265 2.3 26.0 1.0
O A:VAL106 2.3 13.1 1.0
O A:ILE109 2.4 14.1 1.0
O A:HOH517 2.6 20.8 1.0
O A:PRO107 3.0 19.5 1.0
C A:ILE103 3.3 13.7 1.0
C A:ILE109 3.4 15.0 1.0
C A:VAL106 3.4 15.4 1.0
C A:PRO107 3.5 18.9 1.0
N A:ILE109 3.6 12.6 1.0
CA A:PRO107 3.8 14.1 1.0
CA A:ILE109 3.9 10.8 1.0
CA A:ILE103 4.0 11.1 1.0
O A:HOH622 4.0 39.5 1.0
N A:PRO107 4.1 13.8 1.0
CG2 A:ILE103 4.2 12.5 1.0
CB A:ILE109 4.4 11.1 1.0
N A:GLU104 4.4 13.8 1.0
N A:SER108 4.4 15.1 1.0
C A:SER108 4.4 16.7 1.0
N A:GLU110 4.5 11.0 1.0
O A:HOH477 4.5 31.8 1.0
CA A:VAL106 4.5 11.2 1.0
N A:VAL106 4.5 12.5 1.0
O A:HOH589 4.6 29.2 1.0
CB A:ILE103 4.7 12.4 1.0
CA A:GLU104 4.8 14.8 1.0
C A:GLU104 4.8 18.1 1.0
O A:VAL102 4.9 13.3 1.0
CA A:GLU110 4.9 10.3 1.0
O A:GLU104 4.9 17.0 1.0
O A:HOH828 4.9 49.9 1.0
CA A:SER108 5.0 14.8 1.0
O A:HOH825 5.0 47.9 1.0

Calcium binding site 2 out of 10 in 3k28

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Calcium binding site 2 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca431

b:25.9
occ:0.80
 O A:HOH1433 2.3 38.5 1.0
O A:HOH1432 2.4 35.7 1.0
O A:HOH1248 2.4 25.5 1.0
O A:HOH1264 2.4 36.5 1.0
O A:HOH1431 2.4 38.7 1.0
O A:HOH1434 2.5 44.0 1.0
OE1 A:GLU284 4.4 22.2 1.0
OE2 A:GLU110 4.4 26.9 1.0
O A:HOH577 4.5 29.3 1.0
OE2 A:GLU284 4.5 25.9 1.0
OE1 A:GLU110 4.7 17.8 1.0
CE A:LYS282 4.8 36.2 1.0
O A:HOH662 4.8 24.1 1.0
CD A:GLU284 4.9 23.7 1.0

Calcium binding site 3 out of 10 in 3k28

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Calcium binding site 3 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca430

b:24.6
occ:0.80
 O B:ILE103 2.1 15.8 1.0
O B:HOH1262 2.3 23.2 1.0
O B:ILE109 2.3 17.8 1.0
O B:VAL106 2.4 21.7 1.0
O B:HOH507 2.6 23.3 1.0
O B:PRO107 3.1 23.9 1.0
C B:ILE103 3.3 17.8 1.0
C B:ILE109 3.4 17.0 1.0
C B:VAL106 3.4 21.1 1.0
C B:PRO107 3.6 22.8 1.0
N B:ILE109 3.7 15.9 1.0
CA B:PRO107 3.9 19.2 1.0
CA B:ILE109 3.9 14.4 1.0
CA B:ILE103 4.0 13.9 1.0
N B:PRO107 4.1 18.4 1.0
CG2 B:ILE103 4.2 16.3 1.0
CB B:ILE109 4.4 16.1 1.0
N B:GLU104 4.4 16.9 1.0
N B:GLU110 4.4 13.9 1.0
N B:SER108 4.5 17.4 1.0
C B:SER108 4.5 19.4 1.0
CA B:VAL106 4.5 14.6 1.0
N B:VAL106 4.6 15.5 1.0
O B:HOH447 4.6 35.3 1.0
CB B:ILE103 4.7 16.2 1.0
CA B:GLU104 4.7 18.1 1.0
C B:GLU104 4.8 21.8 1.0
O B:VAL102 4.8 15.3 1.0
O B:GLU104 4.9 20.8 1.0
CA B:GLU110 4.9 12.7 1.0

Calcium binding site 4 out of 10 in 3k28

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Calcium binding site 4 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca431

b:30.8
occ:0.90
 O B:HOH996 2.3 32.3 1.0
O B:HOH1429 2.4 44.8 1.0
O B:HOH1427 2.4 22.1 0.5
O B:HOH1239 2.5 23.4 1.0
O B:HOH1427 4.1 20.5 0.5
OE2 B:GLU110 4.2 42.3 1.0
OE1 B:GLU284 4.5 16.2 1.0
OE2 B:GLU284 4.6 21.7 1.0
O B:HOH764 4.6 31.7 1.0
OE2 C:GLU12 4.6 40.8 0.5
CE B:LYS282 4.6 32.8 1.0
OE1 B:GLU110 4.7 19.7 1.0
O B:HOH1256 4.9 34.6 1.0
CD B:GLU110 4.9 39.6 1.0
CG B:LYS282 4.9 19.6 1.0
CD B:GLU284 5.0 30.0 1.0

Calcium binding site 5 out of 10 in 3k28

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Calcium binding site 5 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca432

b:54.0
occ:1.00
 O B:HOH1244 3.3 29.3 1.0
OG B:SER24 3.4 19.1 1.0
O B:HOH1437 3.4 25.5 1.0
CG2 B:VAL26 3.7 22.5 1.0
O A:HOH1393 3.7 49.6 1.0
OG1 A:THR300 4.1 15.3 1.0
CA A:THR300 4.2 11.3 1.0
N A:THR300 4.3 11.7 1.0
C A:GLY299 4.3 15.7 1.0
CB B:SER24 4.4 12.0 1.0
O A:GLY299 4.4 14.7 1.0
O B:HOH1240 4.5 22.4 1.0
CB A:ALA298 4.6 11.0 1.0
CB A:THR300 4.7 15.6 1.0
CG1 B:VAL26 4.8 25.2 1.0
N A:GLY299 4.8 13.7 1.0
CB B:VAL26 4.9 23.8 1.0
CA A:GLY299 5.0 13.7 1.0

Calcium binding site 6 out of 10 in 3k28

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Calcium binding site 6 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca430

b:38.9
occ:1.00
 O C:ILE103 2.2 21.0 1.0
O C:VAL106 2.2 17.7 1.0
O C:ILE109 2.4 17.0 1.0
O C:HOH492 2.4 34.0 1.0
O C:HOH1026 2.6 31.7 1.0
O C:PRO107 2.7 27.0 1.0
C C:VAL106 3.3 20.3 1.0
C C:ILE103 3.3 21.6 1.0
C C:PRO107 3.3 24.8 1.0
C C:ILE109 3.4 18.0 1.0
N C:ILE109 3.6 16.8 1.0
CA C:PRO107 3.7 20.8 1.0
CA C:ILE109 3.9 15.2 1.0
N C:PRO107 4.0 20.3 1.0
CA C:ILE103 4.0 17.6 1.0
CG2 C:ILE103 4.2 20.6 1.0
N C:SER108 4.3 19.6 1.0
C C:SER108 4.3 20.6 1.0
CB C:ILE109 4.4 17.2 1.0
CA C:VAL106 4.4 17.0 1.0
N C:GLU104 4.5 20.8 1.0
N C:VAL106 4.5 19.1 1.0
N C:GLU110 4.5 15.4 1.0
O C:HOH1088 4.5 33.5 1.0
CB C:ILE103 4.7 19.6 1.0
O C:HOH910 4.7 34.8 1.0
CA C:GLU104 4.8 22.2 1.0
CA C:SER108 4.8 18.3 1.0
C C:GLU104 4.9 24.3 1.0
O C:VAL102 4.9 20.2 1.0
O C:GLU104 4.9 24.1 1.0
CA C:GLU110 5.0 16.1 1.0

Calcium binding site 7 out of 10 in 3k28

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Calcium binding site 7 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca431

b:30.4
occ:1.00
 O C:HOH433 2.0 11.1 0.5
OD1 C:ASN233 2.4 18.9 1.0
O C:HOH849 2.6 42.2 1.0
O C:HOH857 2.8 45.5 1.0
O C:PHE194 3.0 20.6 1.0
CG C:ASN233 3.5 24.5 1.0
C C:PHE194 3.9 19.1 1.0
ND2 C:ASN233 3.9 16.1 1.0
CA C:GLU195 4.4 16.1 1.0
N C:GLU195 4.4 17.0 1.0
CA C:GLY198 4.4 20.7 1.0
O C:HOH452 4.6 24.3 1.0
O C:HOH845 4.6 46.6 1.0
CB C:PHE194 4.7 15.2 1.0
CB C:ASN233 4.8 10.8 1.0
CA C:PHE194 4.8 14.3 1.0
O C:GLU195 4.9 19.1 1.0
N C:GLY198 4.9 20.3 1.0

Calcium binding site 8 out of 10 in 3k28

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Calcium binding site 8 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca430

b:29.4
occ:0.80
 O D:ILE109 2.3 16.0 1.0
O D:ILE103 2.3 15.2 1.0
O D:HOH471 2.4 26.2 1.0
O D:VAL106 2.4 17.4 1.0
O D:HOH543 2.5 26.1 1.0
O D:PRO107 3.0 21.9 1.0
C D:ILE109 3.3 18.4 1.0
C D:ILE103 3.5 16.3 1.0
C D:VAL106 3.5 18.5 1.0
C D:PRO107 3.5 20.7 1.0
N D:ILE109 3.7 15.1 1.0
CA D:PRO107 3.9 15.6 1.0
CA D:ILE109 3.9 14.8 1.0
CA D:ILE103 4.0 12.9 1.0
O D:HOH923 4.1 45.0 1.0
N D:PRO107 4.1 14.7 1.0
CG2 D:ILE103 4.2 15.9 1.0
C D:SER108 4.4 19.3 1.0
N D:GLU110 4.4 15.0 1.0
CB D:ILE109 4.4 16.1 1.0
N D:SER108 4.4 16.3 1.0
CA D:VAL106 4.6 15.5 1.0
N D:GLU104 4.6 16.6 1.0
N D:VAL106 4.6 15.8 1.0
O D:HOH1009 4.6 35.8 1.0
CB D:ILE103 4.7 14.6 1.0
O D:HOH736 4.8 33.9 1.0
CA D:GLU110 4.8 14.4 1.0
CA D:GLU104 4.9 17.2 1.0
C D:GLU104 4.9 20.6 1.0
CA D:SER108 4.9 15.4 1.0
O D:VAL102 5.0 16.3 1.0
O D:GLU104 5.0 20.9 1.0

Calcium binding site 9 out of 10 in 3k28

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Calcium binding site 9 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca431

b:32.3
occ:1.00
 O D:HOH1430 2.3 45.9 1.0
O D:HOH1425 2.4 21.9 1.0
O D:HOH1423 2.4 32.0 1.0
O D:HOH1424 2.4 44.4 1.0
O D:HOH1426 2.4 30.0 1.0
O D:HOH1261 2.5 48.9 1.0
O D:HOH1253 2.5 35.8 1.0
O D:HOH1251 4.1 38.8 1.0
OE2 D:GLU110 4.3 37.9 1.0
O A:HOH671 4.3 29.6 1.0
OE1 D:GLU284 4.5 17.7 1.0
O D:HOH568 4.6 29.0 1.0
OE2 D:GLU284 4.6 20.0 1.0
OE1 D:GLU110 4.7 17.8 1.0
CE D:LYS282 4.7 32.3 1.0
O D:HOH643 4.7 27.3 1.0
CD D:GLU110 4.9 36.5 1.0
CD D:GLU284 5.0 21.1 1.0

Calcium binding site 10 out of 10 in 3k28

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Calcium binding site 10 out of 10 in the Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate


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 A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca432

b:47.4
occ:1.00
 O C:HOH1450 2.2 43.4 1.0
O C:HOH1133 3.3 46.8 1.0
O C:HOH463 3.4 18.8 1.0
OG C:SER24 3.7 20.1 1.0
O C:HOH1438 3.7 25.9 1.0
OG1 D:THR300 4.0 17.6 1.0
CG1 C:VAL26 4.1 21.3 1.0
O C:HOH1044 4.4 39.5 1.0
CA D:THR300 4.4 14.2 1.0
N D:THR300 4.5 13.7 1.0
O C:HOH984 4.5 44.5 1.0
CB D:ALA298 4.6 16.5 1.0
O C:HOH527 4.6 28.0 1.0
C D:GLY299 4.6 17.5 1.0
CB C:SER24 4.7 17.2 1.0
CB D:THR300 4.7 17.5 1.0
O D:GLY299 4.8 16.9 1.0
N D:GLY299 5.0 15.3 1.0

Reference:

S.S.Sharma, J.S.Brunzelle, Z.Wawrzak, T.Skarina, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of A Glutamate-1-Semialdehyde Aminotransferase From Bacillus Anthracis with Bound Pyridoxal 5'Phosphate To Be Published.
Page generated: Sat Jul 13 11:55:56 2024

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