Calcium in PDB 8a45: Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate

Enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate

All present enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate:
2.2.1.7;

Protein crystallography data

The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate, PDB code: 8a45 was solved by R.Hamid, A.Hirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.12, 138.013, 231.626, 90, 90, 90
R / Rfree (%) 18.3 / 21.7

Other elements in 8a45:

The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate (pdb code 8a45). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate, PDB code: 8a45:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 8a45

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Calcium binding site 1 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:53.5
occ:1.00
 O A:HOH840 2.5 36.4 1.0
OD2 A:ASP526 2.7 40.5 1.0
O A:HOH1120 2.8 47.6 1.0
OD1 A:ASP526 2.8 33.3 1.0
O A:HOH1127 2.8 44.7 1.0
O A:HOH1192 2.9 49.7 1.0
CG A:ASP526 3.1 36.5 1.0
HH22 A:ARG501 3.9 42.7 1.0
HA2 A:GLY503 4.1 37.9 1.0
HH12 A:ARG501 4.4 33.1 1.0
CB A:ASP526 4.6 29.6 1.0
NH2 A:ARG501 4.7 35.6 1.0
O A:ARG502 4.7 29.8 1.0
HB2 A:ASP526 4.9 35.5 1.0
O A:HOH852 4.9 37.5 1.0

Calcium binding site 2 out of 12 in 8a45

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Calcium binding site 2 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:38.3
occ:1.00
 O A:TYR465 2.1 22.7 1.0
OD1 A:ASP413 2.3 27.6 1.0
O A:PHE467 2.5 25.6 1.0
OD2 A:ASP413 2.6 29.3 1.0
O A:HOH1030 2.6 38.2 1.0
CG A:ASP413 2.8 27.6 1.0
O A:HOH1007 2.8 32.0 1.0
C A:TYR465 3.3 25.0 1.0
HA A:ASP468 3.5 32.9 1.0
O A:HOH857 3.5 23.9 1.0
C A:PHE467 3.6 27.0 1.0
HD2 A:LYS386 3.6 36.7 1.0
HA A:TYR465 3.7 27.9 1.0
H A:GLY469 3.9 32.0 1.0
O A:GLY464 4.0 20.7 1.0
CA A:TYR465 4.1 23.2 1.0
C A:LEU466 4.1 26.6 1.0
HA A:LEU466 4.1 31.6 1.0
O A:LEU466 4.2 24.9 1.0
HZ3 A:LYS386 4.2 40.8 1.0
N A:LEU466 4.2 25.5 1.0
O A:HOH861 4.2 23.0 1.0
CB A:ASP413 4.3 21.8 1.0
N A:PHE467 4.3 25.2 1.0
CA A:ASP468 4.3 27.3 1.0
N A:ASP468 4.4 24.8 1.0
CA A:LEU466 4.4 26.3 1.0
CD A:LYS386 4.5 30.5 1.0
CA A:PHE467 4.5 26.8 1.0
H A:PHE467 4.6 30.3 1.0
N A:GLY469 4.6 26.6 1.0
HB3 A:ASP413 4.7 26.2 1.0
HB2 A:ASP413 4.7 26.2 1.0
O A:HOH1124 4.7 42.8 1.0
HA A:ASP413 4.8 27.8 1.0
HE3 A:LYS386 4.8 37.2 1.0
HB3 A:LYS386 4.9 28.6 1.0
O A:GLY469 4.9 22.1 1.0
CG A:TYR465 4.9 23.8 1.0
CD1 A:TYR465 4.9 23.8 1.0
HB3 A:PHE467 4.9 29.5 1.0
C A:GLY464 4.9 22.9 1.0
CA A:ASP413 4.9 23.1 1.0
NZ A:LYS386 5.0 34.0 1.0
HD1 A:TYR465 5.0 28.6 1.0

Calcium binding site 3 out of 12 in 8a45

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Calcium binding site 3 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:56.6
occ:1.00
 O A:HOH1172 2.4 31.4 1.0
O A:HOH832 2.7 29.6 1.0
OE1 A:GLU558 2.8 25.1 1.0
HD11 A:LEU601 2.9 33.8 1.0
HG21 A:VAL513 2.9 27.3 1.0
O A:HOH1154 2.9 26.3 1.0
O A:HOH912 3.2 25.9 1.0
HD21 A:LEU601 3.4 36.3 1.0
OE2 A:GLU558 3.5 25.9 1.0
CD A:GLU558 3.5 26.0 1.0
CG2 A:VAL513 3.8 22.7 1.0
CD1 A:LEU601 3.8 28.1 1.0
HG23 A:VAL513 3.9 27.3 1.0
HG3 A:PRO476 3.9 24.7 1.0
NE2 A:GLN514 3.9 24.4 1.0
HB3 A:PRO476 4.0 24.1 1.0
HD13 A:LEU601 4.0 33.8 1.0
HB2 A:PRO476 4.0 24.1 1.0
HG22 A:VAL513 4.1 27.3 1.0
CD2 A:LEU601 4.2 30.2 1.0
O A:HOH1180 4.2 34.9 1.0
HD22 A:LEU601 4.3 36.3 1.0
CB A:PRO476 4.3 20.0 1.0
O A:HOH1186 4.4 37.6 1.0
HD12 A:LEU601 4.5 33.8 1.0
CG A:PRO476 4.5 20.6 1.0
O A:HOH850 4.6 23.3 1.0
CG A:LEU601 4.6 30.0 1.0
O A:HOH833 4.6 24.3 1.0
HB A:VAL513 4.8 29.1 1.0
HG A:LEU601 4.8 36.0 1.0
HG2 A:PRO476 4.9 24.7 1.0
CG A:GLU558 4.9 23.5 1.0
CB A:VAL513 4.9 24.2 1.0
HD23 A:LEU601 5.0 36.3 1.0

Calcium binding site 4 out of 12 in 8a45

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Calcium binding site 4 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:47.6
occ:1.00
 O D:ALA302 2.3 36.7 1.0
O D:GLY299 2.4 37.7 1.0
O D:HOH1074 2.4 43.8 1.0
O D:HOH1071 2.5 45.5 1.0
O D:HOH1019 2.6 36.7 1.0
O D:HOH1095 2.9 44.4 1.0
O D:HOH1001 2.9 46.8 1.0
HA D:ILE303 3.5 49.4 1.0
C D:ALA302 3.5 38.4 1.0
C D:GLY299 3.5 36.6 1.0
H D:ALA302 3.6 40.1 1.0
HA2 D:GLY299 3.8 43.0 1.0
HG22 D:ILE303 4.0 44.3 1.0
HA D:TYR300 4.1 44.0 1.0
CA D:GLY299 4.2 35.8 1.0
N D:ALA302 4.3 33.3 1.0
CA D:ILE303 4.3 41.1 1.0
O D:HOH1115 4.4 55.1 1.0
N D:ILE303 4.4 36.7 1.0
CA D:ALA302 4.5 36.2 1.0
HB3 D:ALA302 4.5 38.9 1.0
N D:TYR300 4.5 35.5 1.0
HA3 D:GLY299 4.6 43.0 1.0
O D:HOH975 4.7 42.6 1.0
CA D:TYR300 4.7 36.7 1.0
H D:HIS301 4.8 40.7 1.0
CG2 D:ILE303 4.9 36.9 1.0
O D:ILE298 5.0 36.4 1.0

Calcium binding site 5 out of 12 in 8a45

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Calcium binding site 5 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca704

b:39.3
occ:1.00
 OD2 D:ASP488 2.4 31.8 1.0
OD2 D:ASP486 2.4 28.1 1.0
O D:HOH851 2.6 49.6 1.0
OD1 D:ASP486 3.1 29.6 1.0
CG D:ASP486 3.1 29.6 1.0
CG D:ASP488 3.4 31.9 1.0
CB D:ASP488 3.8 28.2 1.0
OD1 D:ASP488 4.5 34.0 1.0
CB D:ASP486 4.6 28.5 1.0
HB2 D:ASP486 4.8 34.3 1.0
NE2 D:GLN490 4.8 43.0 1.0
HB3 D:ASP486 4.9 34.3 1.0

Calcium binding site 6 out of 12 in 8a45

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Calcium binding site 6 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca705

b:48.0
occ:1.00
 OE2 D:GLU456 2.5 25.1 1.0
O D:HOH1029 2.6 27.1 1.0
OD2 D:ASP455 2.7 26.9 1.0
HG2 D:GLU456 3.0 23.9 1.0
O D:HOH832 3.0 24.4 1.0
HH22 D:ARG500 3.0 34.6 1.0
HZ2 D:LYS459 3.0 30.4 1.0
HB3 D:ASP455 3.3 30.3 1.0
CD D:GLU456 3.5 23.4 1.0
CG D:GLU456 3.7 19.8 1.0
NH2 D:ARG500 3.7 28.8 1.0
CG D:ASP455 3.7 26.3 1.0
HH21 D:ARG533 3.8 28.3 1.0
HD2 D:LYS459 3.8 32.6 1.0
HH12 D:ARG500 3.8 41.2 1.0
NZ D:LYS459 3.9 25.3 1.0
CB D:ASP455 4.0 25.2 1.0
HH21 D:ARG500 4.1 34.6 1.0
HZ1 D:LYS459 4.2 30.4 1.0
HG3 D:GLU456 4.2 23.9 1.0
HZ3 D:LYS459 4.3 30.4 1.0
HA D:GLU456 4.3 24.6 1.0
H D:GLU456 4.3 25.1 1.0
N D:GLU456 4.4 20.9 1.0
NH1 D:ARG500 4.4 34.3 1.0
CZ D:ARG500 4.5 31.3 1.0
O D:HOH953 4.5 30.9 1.0
OD1 D:ASP453 4.5 20.8 1.0
NH2 D:ARG533 4.5 23.6 1.0
CD D:LYS459 4.6 27.2 1.0
HB2 D:ASP455 4.6 30.3 1.0
OE1 D:GLU456 4.6 23.9 1.0
C D:ASP455 4.6 22.3 1.0
HH22 D:ARG533 4.7 28.3 1.0
CA D:GLU456 4.7 20.4 1.0
CE D:LYS459 4.7 27.4 1.0
OD2 D:ASP453 4.7 22.7 1.0
HD3 D:LYS459 4.7 32.6 1.0
CB D:GLU456 4.8 21.6 1.0
O D:HOH1120 4.8 33.3 1.0
HE3 D:LYS459 4.9 32.9 1.0
OD1 D:ASP455 4.9 31.5 1.0
CA D:ASP455 5.0 20.9 1.0

Calcium binding site 7 out of 12 in 8a45

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Calcium binding site 7 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca706

b:72.2
occ:1.00
 O D:HOH951 3.0 26.7 1.0
O D:HOH1043 3.6 24.7 1.0
O D:HOH1126 3.8 25.6 1.0
O D:HOH981 3.9 32.0 1.0
O D:HOH824 3.9 24.8 1.0
O D:HOH1014 4.2 21.6 1.0
O D:HOH1046 4.3 33.1 1.0
HG2 D:GLU517 4.3 29.0 1.0
O D:HOH855 4.4 29.2 1.0
O D:VAL513 4.5 21.4 1.0
O D:HOH1150 4.6 33.4 1.0
O D:HOH988 4.6 26.6 1.0
O D:HOH1121 4.7 34.6 1.0
HD13 D:LEU601 4.8 35.4 1.0
HB D:VAL513 4.9 23.9 1.0
HB3 D:ALA516 4.9 26.3 1.0

Calcium binding site 8 out of 12 in 8a45

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Calcium binding site 8 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca703

b:30.4
occ:1.00
 OD2 E:ASP486 2.3 30.2 1.0
OD2 E:ASP488 2.4 21.2 1.0
O E:HOH1049 2.4 33.9 1.0
O E:HOH1047 2.6 31.0 1.0
O E:HOH1063 2.6 25.8 1.0
OD1 E:ASP486 2.8 25.6 1.0
CG E:ASP486 2.9 26.5 1.0
HB2 E:ASP488 3.2 29.9 1.0
CG E:ASP488 3.4 25.3 1.0
CB E:ASP488 3.8 24.8 1.0
H E:ASP488 4.1 22.2 1.0
HB3 E:ASP488 4.3 29.9 1.0
HD2 E:PRO487 4.4 32.4 1.0
CB E:ASP486 4.4 28.2 1.0
OD1 E:ASP488 4.5 26.2 1.0
O E:HOH912 4.6 24.6 1.0
HB2 E:ASP486 4.7 33.9 1.0
HB3 E:ASP486 4.8 33.9 1.0
N E:ASP488 4.8 18.5 1.0
CA E:ASP488 5.0 22.7 1.0

Calcium binding site 9 out of 12 in 8a45

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Calcium binding site 9 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca703

b:36.0
occ:1.00
 OD2 F:ASP488 2.4 23.9 1.0
OD2 F:ASP486 2.4 27.2 1.0
O F:HOH1087 2.6 29.5 1.0
OD1 F:ASP486 2.8 25.3 1.0
CG F:ASP486 2.9 27.1 1.0
HB2 F:ASP488 3.1 27.9 1.0
CG F:ASP488 3.4 25.0 1.0
CB F:ASP488 3.8 23.2 1.0
H F:ASP488 4.1 25.8 1.0
HB3 F:ASP488 4.3 27.9 1.0
O F:HOH810 4.3 25.2 1.0
CB F:ASP486 4.4 24.9 1.0
OD1 F:ASP488 4.5 25.2 1.0
HD2 F:PRO487 4.6 31.9 1.0
HB2 F:ASP486 4.7 30.0 1.0
HB3 F:ASP486 4.8 30.0 1.0
N F:ASP488 4.8 21.4 1.0
CA F:ASP488 4.9 25.0 1.0

Calcium binding site 10 out of 12 in 8a45

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Calcium binding site 10 out of 12 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca704

b:41.2
occ:1.00
 O F:ALA302 2.2 32.7 1.0
O F:HOH1075 2.5 39.9 1.0
O F:GLY299 2.5 30.1 1.0
O F:HOH1036 2.7 31.8 1.0
O F:HOH967 2.7 35.3 1.0
O F:HOH1097 2.7 47.8 1.0
O F:HOH1098 2.8 48.9 1.0
C F:ALA302 3.4 30.3 1.0
H F:ALA302 3.5 31.4 1.0
HA F:ILE303 3.5 36.9 1.0
C F:GLY299 3.6 32.2 1.0
HA2 F:GLY299 3.9 38.3 1.0
HG22 F:ILE303 3.9 37.9 1.0
HA F:TYR300 4.1 36.3 1.0
N F:ALA302 4.2 26.1 1.0
HB3 F:ALA302 4.3 36.4 1.0
N F:ILE303 4.3 31.2 1.0
CA F:ILE303 4.3 30.7 1.0
CA F:GLY299 4.3 31.9 1.0
CA F:ALA302 4.3 29.9 1.0
O F:HOH1102 4.4 39.8 1.0
O F:HOH941 4.5 32.6 1.0
N F:TYR300 4.6 30.3 1.0
CG2 F:ILE303 4.7 31.5 1.0
HG23 F:ILE303 4.7 37.9 1.0
HA3 F:GLY299 4.8 38.3 1.0
CA F:TYR300 4.8 30.2 1.0
H F:HIS301 4.8 35.8 1.0
CB F:ALA302 4.8 30.2 1.0
O F:ILE298 5.0 30.5 1.0

Reference:

R.Hamid, A.Hirsch. Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate To Be Published.
Page generated: Wed Jul 26 12:54:43 2023

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