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

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

All present enzymatic activity of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion:
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 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion, PDB code: 1lby 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 / 2.25
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 89.250, 89.250, 102.970, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 21

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 1lby

Go back to Manganese Binding Sites List in 1lby
Manganese 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 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn290

b:15.3
occ:1.00
 O1 A:PO4293 2.0 26.8 1.0
OD2 A:ASP85 2.0 11.1 1.0
O A:HOH1158 2.2 40.2 1.0
OD1 A:ASP200 2.3 53.9 1.0
OD2 A:ASP82 2.7 42.5 1.0
CG A:ASP85 3.0 19.3 1.0
O1 A:F6P295 3.0 69.1 0.7
CG A:ASP200 3.2 20.9 1.0
C1 A:F6P295 3.2 49.6 0.7
O2 A:F6P295 3.2 39.4 0.7
MN A:MN291 3.3 10.6 1.0
P A:PO4293 3.4 32.9 1.0
CB A:ASP85 3.4 17.1 1.0
CG A:ASP82 3.5 26.4 1.0
OE1 A:GLU67 3.6 27.8 1.0
CB A:ASP200 3.7 15.6 1.0
OD1 A:ASP82 3.7 30.4 1.0
C2 A:F6P295 3.7 38.0 0.7
CA A:ASP85 3.7 16.1 1.0
O3 A:F6P295 3.9 11.5 0.7
OD1 A:ASP85 4.1 19.6 1.0
CD A:GLU67 4.1 18.7 1.0
O4 A:PO4293 4.1 23.0 1.0
O3 A:PO4293 4.1 24.3 1.0
OE2 A:GLU67 4.1 33.6 1.0
OD2 A:ASP200 4.2 20.0 1.0
C3 A:F6P295 4.3 26.8 0.7
CA A:ASP200 4.4 15.2 1.0
O2 A:PO4293 4.4 11.7 1.0
N A:ASP85 4.7 24.9 1.0
C A:ASP85 4.9 11.6 1.0
CB A:ASP82 4.9 26.4 1.0
N A:GLY86 4.9 9.7 1.0
O5 A:F6P295 5.0 42.5 0.7

Manganese binding site 2 out of 6 in 1lby

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Manganese 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 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn291

b:10.6
occ:1.00
 OE1 A:GLU67 1.8 27.8 1.0
O A:HOH1140 2.3 0.0 1.0
OD1 A:ASP82 2.6 30.4 1.0
O1 A:PO4293 2.6 26.8 1.0
O A:LEU84 2.7 31.3 1.0
CD A:GLU67 2.7 18.7 1.0
O2 A:PO4293 2.9 11.7 1.0
OE2 A:GLU67 3.0 33.6 1.0
C A:LEU84 3.0 23.4 1.0
P A:PO4293 3.2 32.9 1.0
N A:ASP85 3.3 24.9 1.0
MN A:MN290 3.3 15.3 1.0
CA A:ASP85 3.4 16.1 1.0
CG A:ASP82 3.5 26.4 1.0
OG1 A:THR87 3.6 30.4 1.0
OD2 A:ASP82 3.8 42.5 1.0
O A:HOH1158 3.8 40.2 1.0
O4 A:PO4293 3.8 23.0 1.0
N A:LEU84 3.9 22.1 1.0
CA A:LEU84 4.0 15.1 1.0
CG A:GLU67 4.1 16.4 1.0
CB A:ASP85 4.2 17.1 1.0
OD2 A:ASP85 4.5 11.1 1.0
OE2 A:GLU68 4.5 58.8 1.0
O3 A:PO4293 4.5 24.3 1.0
C A:ASP85 4.5 11.6 1.0
CB A:GLU67 4.6 12.5 1.0
CD A:PRO83 4.6 16.7 1.0
OD1 A:ASP46 4.7 23.8 1.0
CB A:LEU84 4.7 6.3 1.0
CG A:ASP85 4.8 19.3 1.0
N A:GLY86 4.9 9.7 1.0
CB A:ASP82 4.9 26.4 1.0
OD1 A:ASP200 4.9 53.9 1.0
N A:PRO83 4.9 27.2 1.0

Manganese binding site 3 out of 6 in 1lby

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Manganese 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 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn292

b:18.6
occ:1.00
 O A:HOH1159 2.1 86.7 1.0
O A:HOH1001 2.3 60.9 1.0
OG1 A:THR40 2.4 20.0 1.0
OD2 A:ASP38 2.6 84.6 1.0
OE2 A:GLU67 2.7 33.6 1.0
O A:HOH1003 3.0 34.0 1.0
CG A:ASP38 3.3 42.9 1.0
CD A:GLU67 3.6 18.7 1.0
CG A:GLU67 3.8 16.4 1.0
CB A:THR40 3.8 45.2 1.0
OD1 A:ASP38 3.9 32.5 1.0
O2 A:PO4293 4.0 11.7 1.0
CB A:ASP38 4.1 35.1 1.0
O A:HOH1150 4.1 29.0 1.0
O A:PRO41 4.3 28.0 1.0
O3 A:PO4293 4.4 24.3 1.0
O A:THR40 4.5 33.8 1.0
CG2 A:THR40 4.5 69.2 1.0
OE2 A:GLU68 4.5 58.8 1.0
OE1 A:GLU68 4.6 36.0 1.0
O A:HOH1158 4.7 40.2 1.0
C A:THR40 4.7 28.0 1.0
P A:PO4293 4.7 32.9 1.0
CA A:THR40 4.7 36.5 1.0
OE1 A:GLU67 4.8 27.8 1.0
O A:HOH1160 4.8 26.2 1.0
CD A:GLU68 5.0 27.1 1.0

Manganese binding site 4 out of 6 in 1lby

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Manganese 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 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn590

b:14.3
occ:1.00
 OD1 B:ASP500 1.9 18.1 1.0
O B:HOH1166 2.0 97.9 1.0
OD2 B:ASP382 2.1 2.6 1.0
OD1 B:ASP385 2.6 33.5 1.0
O1 B:PO4593 2.7 23.4 1.0
CG B:ASP500 3.1 13.2 1.0
O2 B:PO4593 3.3 11.6 1.0
C1 B:F6P595 3.3 38.1 0.6
CG B:ASP382 3.3 14.0 1.0
CG B:ASP385 3.5 32.9 1.0
P B:PO4593 3.5 16.9 1.0
OE1 B:GLU367 3.5 49.9 1.0
O2 B:F6P595 3.6 58.0 0.6
OD2 B:ASP500 3.7 28.6 1.0
O B:HOH1112 3.8 21.4 1.0
OD1 B:ASP382 3.9 5.4 1.0
MN B:MN591 3.9 6.8 1.0
O1 B:F6P595 3.9 74.1 0.6
C2 B:F6P595 3.9 36.5 0.6
CB B:ASP385 4.0 30.6 1.0
CA B:ASP385 4.2 31.7 1.0
CB B:ASP500 4.3 4.2 1.0
O4 B:PO4593 4.3 17.3 1.0
O3 B:F6P595 4.4 9.4 0.6
OD2 B:ASP385 4.4 41.0 1.0
CB B:ASP382 4.4 21.3 1.0
CA B:ASP500 4.5 14.6 1.0
CD1 B:TYR499 4.5 11.9 1.0
C3 B:F6P595 4.5 33.5 0.6
CD B:GLU367 4.6 34.1 1.0
CE1 B:TYR499 4.6 8.0 1.0
O B:HOH1180 4.8 97.9 1.0
O3 B:PO4593 4.8 61.9 1.0
O B:LEU384 4.8 12.8 1.0
OE2 B:GLU367 4.9 54.6 1.0

Manganese binding site 5 out of 6 in 1lby

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Manganese 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 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn591

b:6.8
occ:1.00
 O B:LEU384 1.9 12.8 1.0
O2 B:PO4593 1.9 11.6 1.0
OD1 B:ASP382 2.0 5.4 1.0
O B:HOH1005 2.5 26.0 1.0
OE1 B:GLU367 2.7 49.9 1.0
CG B:ASP382 2.9 14.0 1.0
C B:LEU384 2.9 12.0 1.0
OE2 B:GLU367 3.0 54.6 1.0
CD B:GLU367 3.1 34.1 1.0
P B:PO4593 3.2 16.9 1.0
OD2 B:ASP382 3.3 2.6 1.0
O3 B:PO4593 3.5 61.9 1.0
O B:HOH1166 3.6 97.9 1.0
N B:ASP385 3.7 23.8 1.0
O1 B:PO4593 3.8 23.4 1.0
N B:LEU384 3.8 23.7 1.0
MN B:MN590 3.9 14.3 1.0
CA B:LEU384 3.9 21.4 1.0
CA B:ASP385 4.0 31.7 1.0
CB B:ASP382 4.2 21.3 1.0
OE2 B:GLU368 4.2 11.8 1.0
CD B:PRO383 4.2 12.4 1.0
O4 B:PO4593 4.3 17.3 1.0
CG B:GLU367 4.4 16.1 1.0
CG B:PRO383 4.5 5.2 1.0
OG1 B:THR387 4.5 24.9 1.0
N B:PRO383 4.5 22.4 1.0
CA B:ASP382 4.5 17.3 1.0
CB B:LEU384 4.5 21.1 1.0
OD1 B:ASP346 4.6 26.0 1.0
C B:ASP382 4.6 23.0 1.0
CB B:GLU367 4.6 7.0 1.0
O B:HOH1165 4.6 99.5 1.0
CB B:ASP385 4.7 30.6 1.0
C B:PRO383 5.0 27.2 1.0

Manganese binding site 6 out of 6 in 1lby

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Manganese 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 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of A Complex (P32 Crystal Form) of Dual Activity Fbpase/Impase (AF2372) From Archaeoglobus Fulgidus with 3 Manganese Ions, Fructose-6-Phosphate, and Phosphate Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn592

b:23.1
occ:1.00
 O B:HOH1180 2.1 97.9 1.0
O B:HOH1165 2.2 99.5 1.0
OE2 B:GLU367 2.6 54.6 1.0
O B:HOH1108 2.6 20.2 1.0
OG1 B:THR340 2.6 58.6 1.0
OD2 B:ASP338 2.7 15.3 1.0
CB B:THR340 3.3 23.5 1.0
CD B:GLU367 3.5 34.1 1.0
CG B:ASP338 3.7 15.1 1.0
O3 B:PO4593 3.7 61.9 1.0
CG2 B:THR340 3.7 10.8 1.0
OD1 B:ASP338 3.9 12.4 1.0
CG B:GLU367 4.1 16.1 1.0
O B:HOH1004 4.2 11.5 1.0
O B:HOH1166 4.2 97.9 1.0
O1 B:PO4593 4.3 23.4 1.0
O B:HOH1148 4.3 31.6 1.0
OE1 B:GLU367 4.3 49.9 1.0
O B:PRO341 4.4 25.9 1.0
OE2 B:GLU368 4.5 11.8 1.0
P B:PO4593 4.6 16.9 1.0
CA B:THR340 4.7 14.9 1.0
OE1 B:GLU368 4.8 2.8 1.0
C B:THR340 4.9 14.9 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: Sat Oct 5 11:25:56 2024

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