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Calcium in PDB 1lbz: Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate

Enzymatic activity of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate

All present enzymatic activity of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate:
3.1.3.11; 3.1.3.25;

Protein crystallography data

The structure of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate, PDB code: 1lbz was solved by K.A.Stieglitz, K.A.Johnson, H.Yang, M.F.Roberts, B.A.Seaton, J.F.Head, B.Stec, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 89.610, 89.610, 102.940, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 25

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate (pdb code 1lbz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate, PDB code: 1lbz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1lbz

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Calcium binding site 1 out of 6 in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate


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 Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca290

b:15.8
occ:1.00
 OD2 A:ASP85 2.3 11.3 1.0
OD1 A:ASP200 2.8 25.9 1.0
O1P A:FBP295 2.8 32.5 1.0
O1 A:FBP295 2.8 27.1 1.0
OD2 A:ASP82 2.8 27.6 1.0
OE2 A:GLU67 2.9 86.3 1.0
OE1 A:GLU67 3.0 98.1 1.0
P1 A:FBP295 3.3 32.6 1.0
OD2 A:ASP200 3.3 41.5 1.0
CD A:GLU67 3.4 72.4 1.0
CG A:ASP200 3.4 27.8 1.0
CG A:ASP85 3.4 28.0 1.0
O2P A:FBP295 3.6 18.7 1.0
CA A:CA291 3.8 10.0 1.0
C1 A:FBP295 3.9 23.6 1.0
CG A:ASP82 4.0 41.5 1.0
CB A:ASP85 4.0 25.9 1.0
O A:HOH1124 4.1 25.4 1.0
CE1 A:TYR199 4.3 20.4 1.0
CD1 A:TYR199 4.5 26.3 1.0
OD1 A:ASP85 4.5 30.9 1.0
O A:HOH1052 4.5 23.1 1.0
NH1 A:ARG197 4.6 56.8 1.0
CA A:ASP85 4.6 32.6 1.0
O3P A:FBP295 4.6 31.7 1.0
OD1 A:ASP82 4.6 46.4 1.0
C2 A:FBP295 4.8 34.4 1.0
C3 A:FBP295 4.8 32.2 1.0
CG A:GLU67 4.9 63.7 1.0
CB A:ASP200 4.9 12.2 1.0
O3 A:FBP295 4.9 20.9 1.0

Calcium binding site 2 out of 6 in 1lbz

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Calcium binding site 2 out of 6 in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate


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 Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca291

b:10.0
occ:1.00
 OD1 A:ASP82 2.8 46.4 1.0
O1P A:FBP295 2.8 32.5 1.0
O A:LEU84 2.8 45.6 1.0
OE1 A:GLU67 2.8 98.1 1.0
O A:HOH1052 2.8 23.1 1.0
OD2 A:ASP82 3.2 27.6 1.0
CD A:GLU67 3.3 72.4 1.0
CG A:ASP82 3.3 41.5 1.0
C A:LEU84 3.4 40.1 1.0
OE2 A:GLU67 3.8 86.3 1.0
CA A:CA290 3.8 15.8 1.0
N A:ASP85 4.0 36.7 1.0
O A:HOH1139 4.0 31.7 1.0
CA A:ASP85 4.1 32.6 1.0
P1 A:FBP295 4.1 32.6 1.0
CG A:GLU67 4.1 63.7 1.0
OG1 A:THR87 4.2 34.2 1.0
O2P A:FBP295 4.2 18.7 1.0
O A:HOH1124 4.2 25.4 1.0
N A:LEU84 4.2 16.4 1.0
CB A:GLU67 4.3 56.1 1.0
CA A:LEU84 4.4 27.1 1.0
OD1 A:ASP46 4.5 33.0 1.0
CB A:ASP85 4.6 25.9 1.0
CB A:ASP82 4.7 28.7 1.0
OD2 A:ASP85 4.8 11.3 1.0
O3P A:FBP295 4.8 31.7 1.0
OE1 A:GLU68 4.9 51.5 1.0
CB A:LEU84 5.0 24.1 1.0
O1 A:FBP295 5.0 27.1 1.0

Calcium binding site 3 out of 6 in 1lbz

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Calcium binding site 3 out of 6 in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate


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 Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca292

b:10.3
occ:1.00
 O A:HOH1117 2.8 32.9 1.0
O A:HOH1139 2.8 31.7 1.0
O A:HOH1025 2.8 10.2 1.0
O A:PRO41 2.8 40.4 1.0
OG1 A:THR40 2.8 68.1 1.0
O A:HOH1124 2.8 25.4 1.0
O A:HOH1138 2.8 61.3 1.0
CB A:THR40 3.3 41.5 1.0
C A:PRO41 3.8 38.4 1.0
C A:THR40 3.8 38.4 1.0
N A:PRO41 4.0 36.9 1.0
O A:THR40 4.0 39.9 1.0
O A:HOH1052 4.0 23.1 1.0
OD2 A:ASP46 4.1 19.4 1.0
CA A:THR40 4.2 42.1 1.0
OE2 A:GLU68 4.4 55.1 1.0
CD A:PRO41 4.4 41.3 1.0
CG2 A:THR40 4.5 10.3 1.0
CA A:PRO41 4.5 36.0 1.0
OD2 A:ASP38 4.6 25.1 1.0
OE2 A:GLU67 4.6 86.3 1.0
OE1 A:GLU68 4.7 51.5 1.0
N A:THR42 4.7 32.9 1.0
O2P A:FBP295 4.8 18.7 1.0
OD1 A:ASP38 4.8 35.6 1.0
CG A:GLU67 4.8 63.7 1.0
CA A:THR42 5.0 22.1 1.0

Calcium binding site 4 out of 6 in 1lbz

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Calcium binding site 4 out of 6 in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate


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 Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca590

b:10.0
occ:1.00
 OD2 B:ASP382 2.8 24.9 1.0
O1P B:FBP595 2.8 12.4 1.0
OD2 B:ASP500 2.8 70.2 1.0
OD1 B:ASP385 2.8 26.4 1.0
O1 B:FBP595 2.8 65.3 1.0
CG B:ASP500 3.3 68.4 1.0
P1 B:FBP595 3.5 49.4 1.0
OD1 B:ASP500 3.5 79.9 1.0
C1 B:FBP595 3.7 66.4 1.0
CA B:CA591 3.9 11.0 1.0
CG B:ASP385 3.9 13.3 1.0
CG B:ASP382 4.0 34.4 1.0
CB B:ASP385 4.3 15.2 1.0
CA B:ASP385 4.3 14.4 1.0
CB B:ASP500 4.4 63.8 1.0
O3P B:FBP595 4.4 41.3 1.0
CA B:ASP500 4.4 50.5 1.0
O3 B:FBP595 4.6 53.5 1.0
O2P B:FBP595 4.6 77.9 1.0
OE2 B:GLU367 4.7 29.7 1.0
OD1 B:ASP382 4.8 38.3 1.0
C2 B:FBP595 4.8 63.2 1.0
OE1 B:GLU367 4.8 19.4 1.0
CB B:ASP382 4.9 26.4 1.0
CD1 B:TYR499 4.9 27.6 1.0
CE1 B:TYR499 4.9 33.6 1.0
CD B:GLU367 4.9 41.4 1.0
OD2 B:ASP385 5.0 38.3 1.0
C3 B:FBP595 5.0 58.3 1.0

Calcium binding site 5 out of 6 in 1lbz

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Calcium binding site 5 out of 6 in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate


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 Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca591

b:11.0
occ:1.00
 O1P B:FBP595 2.8 12.4 1.0
O B:LEU384 2.8 46.6 1.0
O B:HOH1068 2.8 23.8 1.0
OE2 B:GLU367 2.8 29.7 1.0
O B:HOH1064 2.8 37.6 1.0
OD1 B:ASP382 2.8 38.3 1.0
OD2 B:ASP382 2.8 24.9 1.0
CG B:ASP382 3.3 34.4 1.0
C B:LEU384 3.5 31.2 1.0
CD B:GLU367 3.7 41.4 1.0
CA B:CA590 3.9 10.0 1.0
OE1 B:GLU367 3.9 19.4 1.0
N B:ASP385 4.1 18.6 1.0
CA B:ASP385 4.1 14.4 1.0
OG1 B:THR387 4.2 39.9 1.0
P1 B:FBP595 4.3 49.4 1.0
OD1 B:ASP346 4.4 42.0 1.0
CA B:LEU384 4.5 28.6 1.0
N B:LEU384 4.5 23.1 1.0
O3P B:FBP595 4.6 41.3 1.0
CB B:LEU384 4.8 26.1 1.0
CB B:ASP382 4.8 26.4 1.0
N B:GLY386 4.9 23.6 1.0
O2P B:FBP595 5.0 77.9 1.0
C B:ASP385 5.0 16.0 1.0

Calcium binding site 6 out of 6 in 1lbz

Go back to Calcium Binding Sites List in 1lbz
Calcium binding site 6 out of 6 in the Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate


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 Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Calcium Ions and Fructose-1,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca592

b:13.6
occ:1.00
 O B:HOH1140 2.7 21.9 1.0
O B:HOH1141 2.8 39.0 1.0
O B:HOH1113 2.8 27.8 1.0
O B:PRO341 2.8 39.2 1.0
OG1 B:THR340 2.8 14.4 1.0
OE1 B:GLU367 3.4 19.4 1.0
O B:HOH1064 3.8 37.6 1.0
OD1 B:ASP338 4.0 52.9 1.0
C B:PRO341 4.0 41.0 1.0
CB B:THR340 4.1 25.7 1.0
CD B:GLU367 4.2 41.4 1.0
O B:HOH1073 4.2 32.4 1.0
OD2 B:ASP346 4.3 39.3 1.0
OE1 B:GLU368 4.3 23.7 1.0
OE2 B:GLU368 4.4 28.2 1.0
C B:THR340 4.7 14.7 1.0
OE2 B:GLU367 4.7 29.7 1.0
CG B:ASP346 4.7 36.2 1.0
N B:PRO341 4.7 18.8 1.0
CG B:ASP338 4.7 35.9 1.0
CA B:THR342 4.8 32.0 1.0
CD B:GLU368 4.8 20.2 1.0
OD2 B:ASP338 4.8 28.8 1.0
O B:THR340 4.8 16.1 1.0
N B:THR342 4.8 40.0 1.0

Reference:

K.A.Stieglitz, K.A.Johnson, H.Yang, M.F.Roberts, B.A.Seaton, J.F.Head, B.Stec. Crystal Structure of A Dual Activity Impase/Fbpase (AF2372) From Archaeoglobus Fulgidus. the Story of A Mobile Loop. J.Biol.Chem. V. 277 22863 2002.
ISSN: ISSN 0021-9258
PubMed: 11940584
DOI: 10.1074/JBC.M201042200
Page generated: Thu Jul 11 11:50:23 2024

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