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Calcium in PDB 8a29: Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa

Enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa:
2.2.1.7;

Protein crystallography data

The structure of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29 was solved by R.Hamid, S.Adam, A.Lacour, L.Monjas, A.Hirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.444, 137.631, 232.082, 90, 90, 90
R / Rfree (%) 17.1 / 22.4

Other elements in 8a29:

The structure of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Magnesium (Mg) 13 atoms
Sodium (Na) 5 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa (pdb code 8a29). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 8a29

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Calcium binding site 1 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:61.8
occ:1.00
HH12 A:ARG145 2.2 33.4 1.0
NH1 A:ARG145 3.0 27.8 1.0
HA A:THR152 3.1 27.1 1.0
HH11 A:ARG145 3.3 33.4 1.0
HG22 A:THR152 3.4 34.0 1.0
HH22 A:ARG145 3.7 32.7 1.0
HD2 A:ARG108 3.8 27.6 1.0
HB3 E:CYS382 3.9 27.1 1.0
HB A:THR152 3.9 35.3 1.0
CA A:THR152 4.0 22.5 1.0
CZ A:ARG145 4.0 24.0 1.0
NE A:ARG108 4.1 27.1 1.0
CZ A:ARG108 4.1 28.9 1.0
HE A:ARG108 4.2 32.5 1.0
CG2 A:THR152 4.2 28.3 1.0
NH2 A:ARG145 4.2 27.3 1.0
O A:THR152 4.2 19.0 1.0
CB A:THR152 4.2 29.4 1.0
O E:CYS382 4.3 26.3 1.0
NH2 A:ARG108 4.4 23.6 1.0
HH21 A:ARG108 4.4 28.4 1.0
OE2 E:GLU383 4.4 31.8 1.0
HE2 A:MET168 4.5 25.6 1.0
CD A:ARG108 4.5 23.0 1.0
NH1 A:ARG108 4.6 24.1 1.0
C A:THR152 4.6 22.6 1.0
O A:HOH939 4.6 27.9 1.0
O A:HOH841 4.7 27.9 1.0
HG21 A:THR152 4.7 34.0 1.0
HH22 A:ARG108 4.7 28.4 1.0
HH11 A:ARG108 4.7 28.9 1.0
HG23 A:THR152 4.8 34.0 1.0
O A:ASP151 4.8 25.6 1.0
CB E:CYS382 4.8 22.6 1.0
HG2 A:ARG145 4.9 24.4 1.0
HH12 A:ARG108 4.9 28.9 1.0

Calcium binding site 2 out of 12 in 8a29

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Calcium binding site 2 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca707

b:66.2
occ:1.00
O A:HOH1024 2.8 41.2 1.0
HE22 A:GLN327 2.8 38.4 1.0
HH12 A:ARG358 2.9 48.6 1.0
HH22 A:ARG358 3.0 53.4 1.0
O B:HOH1161 3.2 37.8 1.0
NE2 A:GLN327 3.6 32.0 1.0
NH1 A:ARG358 3.7 40.5 1.0
NH2 A:ARG358 3.7 44.5 1.0
HE21 A:GLN327 4.1 38.4 1.0
CZ A:ARG358 4.2 48.2 1.0
OE1 A:GLN327 4.2 30.5 1.0
HH11 A:ARG358 4.3 48.6 1.0
CD A:GLN327 4.3 32.5 1.0
HH21 A:ARG358 4.4 53.4 1.0
O A:HOH982 4.6 27.4 1.0
OD1 A:ASP331 4.9 21.6 1.0

Calcium binding site 3 out of 12 in 8a29

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Calcium binding site 3 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:63.3
occ:1.00
O B:HOH1172 2.7 43.3 1.0
OD1 B:ASP526 2.8 31.0 1.0
O B:HOH1109 2.9 44.9 1.0
OD2 B:ASP526 2.9 40.2 1.0
CG B:ASP526 3.2 33.1 1.0
HA2 B:GLY503 3.9 32.4 1.0
HH22 B:ARG501 4.0 40.0 1.0
O B:HOH1097 4.3 45.1 1.0
HH12 B:ARG501 4.3 39.1 1.0
O B:ARG502 4.5 31.0 1.0
CB B:ASP526 4.7 31.3 1.0
NH2 B:ARG501 4.7 33.4 1.0
CA B:GLY503 4.9 27.0 1.0

Calcium binding site 4 out of 12 in 8a29

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Calcium binding site 4 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:67.5
occ:1.00
HH12 C:ARG145 2.6 28.2 1.0
HH22 C:ARG145 3.1 40.0 1.0
O C:HOH1060 3.1 29.6 1.0
NH1 C:ARG145 3.4 23.5 1.0
NH2 C:ARG145 3.8 33.3 1.0
HH11 C:ARG145 4.0 28.2 1.0
HA C:THR152 4.0 28.1 1.0
CZ C:ARG108 4.0 30.9 1.0
CZ C:ARG145 4.0 22.7 1.0
HG22 C:THR152 4.1 31.3 1.0
NH2 C:ARG108 4.1 29.8 1.0
HH21 C:ARG108 4.3 35.8 1.0
HH22 C:ARG108 4.3 35.8 1.0
NH1 C:ARG108 4.3 25.1 1.0
NE C:ARG108 4.3 28.0 1.0
HD2 C:ARG108 4.4 28.0 1.0
HH12 C:ARG108 4.5 30.2 1.0
HE C:ARG108 4.5 33.6 1.0
HH21 C:ARG145 4.5 40.0 1.0
HH11 C:ARG108 4.6 30.2 1.0
O C:HOH930 4.8 33.6 1.0
HB C:THR152 4.9 28.6 1.0
O C:HOH943 4.9 23.4 1.0
O C:HOH1018 4.9 39.7 1.0
CA C:THR152 4.9 23.4 1.0
CD C:ARG108 4.9 23.3 1.0
CG2 C:THR152 5.0 26.1 1.0

Calcium binding site 5 out of 12 in 8a29

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Calcium binding site 5 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca704

b:54.1
occ:1.00
O D:HOH989 2.2 34.1 1.0
O D:PHE467 2.3 24.1 1.0
O D:HOH999 2.4 30.7 1.0
O D:GLY464 2.4 18.7 1.0
OD1 D:ASP413 2.4 27.1 1.0
O D:TYR465 2.6 23.3 1.0
O D:GLY469 3.3 20.9 1.0
HA D:TYR465 3.3 27.0 1.0
C D:TYR465 3.3 22.2 1.0
C D:PHE467 3.4 21.2 1.0
H D:GLY469 3.5 26.1 1.0
C D:GLY464 3.5 22.5 1.0
HB3 D:PHE467 3.5 24.7 1.0
CG D:ASP413 3.6 24.6 1.0
H D:PHE467 3.6 27.2 1.0
HZ2 D:LYS386 3.6 33.4 1.0
N D:PHE467 3.7 22.7 1.0
CA D:TYR465 3.7 22.5 1.0
HZ1 D:LYS386 3.8 33.4 1.0
HD2 D:PHE467 3.9 21.8 1.0
CA D:PHE467 4.0 21.4 1.0
N D:TYR465 4.1 20.8 1.0
OD2 D:ASP413 4.1 27.8 1.0
NZ D:LYS386 4.1 27.9 1.0
HA D:ASP413 4.2 24.9 1.0
CB D:PHE467 4.2 20.6 1.0
HB2 D:LEU415 4.2 24.0 1.0
C D:LEU466 4.2 22.4 1.0
HE3 D:LYS386 4.3 33.0 1.0
N D:LEU466 4.3 21.5 1.0
N D:GLY469 4.3 21.8 1.0
HB3 D:ALA471 4.3 21.8 1.0
HA D:ASP468 4.4 30.8 1.0
C D:GLY469 4.4 19.0 1.0
HB2 D:ALA471 4.4 21.8 1.0
N D:ASP468 4.5 22.7 1.0
O D:HOH846 4.5 23.9 1.0
H D:VAL414 4.6 26.5 1.0
CD2 D:PHE467 4.6 18.1 1.0
N D:VAL414 4.6 22.1 1.0
C D:ASP413 4.7 21.0 1.0
CA D:ASP413 4.7 20.7 1.0
CA D:LEU466 4.7 18.9 1.0
HA2 D:GLY464 4.7 25.4 1.0
CB D:ASP413 4.7 24.8 1.0
CE D:LYS386 4.8 27.5 1.0
O D:LEU466 4.8 21.3 1.0
CA D:GLY464 4.8 21.1 1.0
CB D:ALA471 4.8 18.2 1.0
HZ3 D:LYS386 4.9 33.4 1.0
CA D:ASP468 4.9 25.7 1.0
HA D:LEU466 4.9 22.7 1.0
H D:LEU466 4.9 25.8 1.0
C D:VAL414 4.9 23.1 1.0
HA D:PHE467 4.9 25.6 1.0
CG D:PHE467 4.9 19.2 1.0
H D:TYR465 4.9 24.9 1.0
O D:VAL414 5.0 16.9 1.0
HB2 D:PHE467 5.0 24.7 1.0
CA D:GLY469 5.0 21.1 1.0
HA D:LEU415 5.0 22.9 1.0

Calcium binding site 6 out of 12 in 8a29

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Calcium binding site 6 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca705

b:49.6
occ:1.00
OE2 D:GLU456 2.4 21.1 1.0
OD2 D:ASP455 2.7 27.1 1.0
HG2 D:GLU456 2.8 26.0 1.0
HH22 D:ARG500 3.0 34.6 1.0
O D:HOH835 3.0 25.6 1.0
O D:HOH984 3.0 31.3 1.0
HB3 D:ASP455 3.2 32.8 1.0
CD D:GLU456 3.3 23.9 1.0
CG D:GLU456 3.5 21.7 1.0
CG D:ASP455 3.7 27.3 1.0
HD2 D:LYS459 3.7 27.8 1.0
NH2 D:ARG500 3.7 28.9 1.0
HZ3 D:LYS459 3.9 41.5 1.0
CB D:ASP455 3.9 27.3 1.0
HH21 D:ARG533 3.9 26.9 1.0
HH12 D:ARG500 3.9 34.5 1.0
H D:GLU456 4.0 23.7 1.0
HG3 D:GLU456 4.1 26.0 1.0
N D:GLU456 4.1 19.7 1.0
HA D:GLU456 4.1 29.0 1.0
HH21 D:ARG500 4.1 34.6 1.0
HE2 D:LYS459 4.2 39.6 1.0
OD1 D:ASP453 4.3 17.1 1.0
C D:ASP455 4.4 21.4 1.0
CD D:LYS459 4.4 23.2 1.0
CA D:GLU456 4.5 24.2 1.0
HD3 D:LYS459 4.5 27.8 1.0
OE1 D:GLU456 4.5 24.0 1.0
NH1 D:ARG500 4.5 28.7 1.0
CB D:GLU456 4.6 24.6 1.0
CZ D:ARG500 4.6 30.4 1.0
HB2 D:ASP455 4.6 32.8 1.0
NZ D:LYS459 4.6 34.5 1.0
O D:HOH871 4.6 28.0 1.0
CE D:LYS459 4.6 33.0 1.0
NH2 D:ARG533 4.7 22.4 1.0
OD2 D:ASP453 4.7 22.6 1.0
O D:HOH1043 4.7 32.1 1.0
HH22 D:ARG533 4.8 26.9 1.0
CA D:ASP455 4.8 20.0 1.0
O D:HOH1104 4.8 38.9 1.0
OD1 D:ASP455 4.8 24.8 1.0
O D:ASP455 4.9 19.9 1.0
CG D:ASP453 4.9 21.4 1.0

Calcium binding site 7 out of 12 in 8a29

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Calcium binding site 7 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca706

b:69.8
occ:1.00
O D:HOH1064 2.5 52.0 1.0
O D:HIS550 2.9 23.6 1.0
O D:HOH1112 2.9 40.7 1.0
O D:ALA547 3.0 32.1 1.0
HA2 D:GLY548 3.7 30.9 1.0
HG23 D:VAL580 3.8 40.1 1.0
HA D:GLU551 3.9 25.1 1.0
C D:HIS550 3.9 21.8 1.0
H D:HIS550 4.0 26.7 1.0
O D:GLY548 4.0 31.1 1.0
C D:GLY548 4.1 29.2 1.0
HB D:VAL580 4.1 31.4 1.0
C D:ALA547 4.1 24.4 1.0
CA D:GLY548 4.3 25.7 1.0
HG21 D:VAL580 4.3 40.1 1.0
N D:HIS550 4.4 22.2 1.0
CG2 D:VAL580 4.5 33.4 1.0
N D:SER549 4.5 26.3 1.0
OE2 D:GLU551 4.5 47.4 1.0
N D:GLY548 4.7 24.1 1.0
CB D:VAL580 4.8 26.2 1.0
CA D:GLU551 4.8 20.9 1.0
N D:GLU551 4.8 22.8 1.0
CA D:HIS550 4.8 21.0 1.0
HA D:VAL580 4.8 36.8 1.0
H D:SER549 4.8 31.5 1.0
OE1 D:GLU551 4.9 40.1 1.0
CD D:GLU551 4.9 34.0 1.0
C D:SER549 5.0 27.5 1.0
HA D:SER549 5.0 33.4 1.0

Calcium binding site 8 out of 12 in 8a29

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Calcium binding site 8 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca707

b:38.0
occ:1.00
O D:HOH1012 2.3 29.6 1.0
O D:ASP620 2.4 30.4 1.0
O D:HOH1128 2.6 39.3 1.0
O D:HOH1088 2.8 43.7 1.0
O D:HOH880 2.8 38.0 1.0
C D:ASP620 3.5 32.1 1.0
HA D:ASP620 3.8 32.2 1.0
HB3 D:ASP620 4.1 30.6 1.0
HA D:ARG621 4.1 43.9 1.0
CA D:ASP620 4.2 26.8 1.0
N D:ARG621 4.6 33.6 1.0
CB D:ASP620 4.6 25.5 1.0
O D:GLN622 4.7 45.7 1.0
CA D:ARG621 4.8 36.6 1.0
O D:HOH1101 4.9 36.6 1.0

Calcium binding site 9 out of 12 in 8a29

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Calcium binding site 9 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca706

b:49.3
occ:1.00
HH E:TYR363 2.1 34.2 1.0
O E:HOH1095 2.6 43.3 1.0
OD2 E:ASP365 2.6 28.4 1.0
HE2 E:TYR363 2.8 31.0 1.0
HB2 E:ASP365 2.8 27.0 1.0
O E:HOH1149 2.9 36.6 1.0
OH E:TYR363 3.0 28.5 1.0
HD3 E:LYS347 3.1 43.7 1.0
HB3 E:ASP365 3.2 27.0 1.0
HZ3 E:LYS347 3.3 53.9 1.0
CB E:ASP365 3.3 22.5 1.0
CG E:ASP365 3.4 29.5 1.0
CE2 E:TYR363 3.5 25.9 1.0
HB2 E:LYS347 3.7 41.5 1.0
CZ E:TYR363 3.7 25.7 1.0
O E:HOH960 3.9 35.7 1.0
CD E:LYS347 4.1 36.4 1.0
NZ E:LYS347 4.1 44.9 1.0
HZ2 E:LYS347 4.3 53.9 1.0
O E:HOH947 4.4 45.4 1.0
HB3 E:LYS347 4.4 41.5 1.0
CB E:LYS347 4.5 34.6 1.0
HD2 E:LYS347 4.5 43.7 1.0
OD1 E:ASP365 4.6 27.3 1.0
CE E:LYS347 4.7 35.1 1.0
HZ1 E:LYS347 4.7 53.9 1.0
CA E:ASP365 4.8 18.7 1.0
CD2 E:TYR363 4.8 27.2 1.0
HE2 E:LYS347 4.8 42.1 1.0
CG E:LYS347 4.9 31.6 1.0

Calcium binding site 10 out of 12 in 8a29

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Calcium binding site 10 out of 12 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca707

b:47.8
occ:1.00
OD2 E:ASP455 2.5 24.4 1.0
O E:HOH1069 2.6 29.2 1.0
OE2 E:GLU456 2.7 22.4 1.0
O E:HOH844 2.9 20.4 1.0
HG2 E:GLU456 3.1 21.2 1.0
HB3 E:ASP455 3.2 29.0 1.0
HZ2 E:LYS459 3.2 32.6 1.0
HH22 E:ARG500 3.3 32.0 1.0
HZ3 E:LYS459 3.5 32.6 1.0
CG E:ASP455 3.5 25.1 1.0
CD E:GLU456 3.6 22.6 1.0
NZ E:LYS459 3.8 27.1 1.0
CG E:GLU456 3.8 17.7 1.0
CB E:ASP455 3.8 24.2 1.0
HD2 E:LYS459 3.8 25.7 1.0
HH21 E:ARG533 3.9 25.1 1.0
HH12 E:ARG500 3.9 30.4 1.0
NH2 E:ARG500 4.0 26.7 1.0
HZ1 E:LYS459 4.3 32.6 1.0
H E:GLU456 4.3 26.8 1.0
OD1 E:ASP453 4.3 20.4 1.0
HG3 E:GLU456 4.4 21.2 1.0
HA E:GLU456 4.4 26.2 1.0
N E:GLU456 4.4 22.3 1.0
HB2 E:ASP455 4.4 29.0 1.0
HH21 E:ARG500 4.5 32.0 1.0
O E:HOH850 4.5 20.4 1.0
NH1 E:ARG500 4.6 25.4 1.0
NH2 E:ARG533 4.6 20.9 1.0
C E:ASP455 4.6 18.1 1.0
CD E:LYS459 4.7 21.4 1.0
HH22 E:ARG533 4.7 25.1 1.0
OD2 E:ASP453 4.7 27.0 1.0
OD1 E:ASP455 4.7 26.6 1.0
CZ E:ARG500 4.7 33.5 1.0
O E:HOH1067 4.7 37.3 1.0
CA E:GLU456 4.8 21.9 1.0
OE1 E:GLU456 4.8 24.6 1.0
CE E:LYS459 4.9 24.4 1.0
HD3 E:LYS459 4.9 25.7 1.0
CB E:GLU456 4.9 19.7 1.0
CA E:ASP455 4.9 20.8 1.0
CG E:ASP453 5.0 27.5 1.0

Reference:

R.Hamid, S.Adam, A.Lacour, L.Monjas, A.Hirsch. Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding To Be Published.
Page generated: Fri Jul 19 06:44:24 2024

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