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Calcium in PDB 2f59: Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione

Enzymatic activity of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione

All present enzymatic activity of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione:
2.5.1.78;

Protein crystallography data

The structure of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione, PDB code: 2f59 was solved by S.Klinke, V.Zylberman, H.R.Bonomi, I.Haase, B.G.Guimaraes, B.C.Braden, A.Bacher, M.Fischer, F.A.Goldbaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.50 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.317, 95.317, 171.743, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione (pdb code 2f59). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione, PDB code: 2f59:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2f59

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Calcium binding site 1 out of 6 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:63.5
occ:1.00
 O A:ALA67 2.8 41.6 1.0
OE1 A:GLU73 3.0 54.2 1.0
C A:ALA67 3.9 41.6 1.0
CD A:GLU73 4.2 53.4 1.0
CA A:ALA67 4.7 40.8 1.0
N A:ASP68 4.7 42.1 1.0
CA A:GLY70 4.7 40.9 1.0
CB A:ALA67 4.8 39.2 1.0
O A:GLY71 4.8 35.5 1.0
CA A:ASP68 4.8 43.6 1.0
N A:GLY70 4.8 41.0 1.0
CB A:GLU73 4.9 45.5 1.0
CG A:GLU73 4.9 51.2 1.0

Calcium binding site 2 out of 6 in 2f59

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Calcium binding site 2 out of 6 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:45.0
occ:1.00
 OE1 A:GLU124 2.8 32.9 1.0
OE2 A:GLU124 2.8 36.5 1.0
CD A:GLU124 3.2 34.5 1.0
O A:HOH342 4.6 30.5 1.0
O A:HOH356 4.6 20.8 1.0
CG A:GLU124 4.7 32.1 1.0
O A:HOH341 4.7 30.0 1.0

Calcium binding site 3 out of 6 in 2f59

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Calcium binding site 3 out of 6 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:63.1
occ:1.00
 OE1 B:GLU73 2.8 53.5 1.0
O B:ALA67 2.9 38.4 1.0
C B:ALA67 3.8 38.9 1.0
CD B:GLU73 4.0 52.5 1.0
N B:ASP68 4.6 40.8 1.0
CA B:ALA67 4.6 38.4 1.0
CA B:ASP68 4.7 44.0 1.0
CB B:GLU73 4.7 43.7 1.0
CB B:ALA67 4.7 35.5 1.0
CG B:GLU73 4.7 49.6 1.0
O B:GLY71 4.8 38.9 1.0
N B:GLY70 4.8 40.2 1.0
CA B:GLY70 4.8 38.8 1.0
OE2 B:GLU73 5.0 55.5 1.0

Calcium binding site 4 out of 6 in 2f59

Go back to Calcium Binding Sites List in 2f59
Calcium binding site 4 out of 6 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:39.5
occ:0.50
 O C:ALA67 2.8 37.2 1.0
OE1 C:GLU73 2.9 47.5 1.0
C C:ALA67 3.8 38.3 1.0
CD C:GLU73 4.1 48.0 1.0
CA C:ALA67 4.6 37.4 1.0
N C:ASP68 4.6 39.0 1.0
CB C:ALA67 4.7 35.0 1.0
CA C:ASP68 4.7 42.6 1.0
CB C:GLU73 4.7 40.2 1.0
CG C:GLU73 4.7 46.7 1.0
CA C:GLY70 4.7 38.5 1.0
O C:GLY71 4.7 36.0 1.0
N C:GLY70 4.8 40.1 1.0

Calcium binding site 5 out of 6 in 2f59

Go back to Calcium Binding Sites List in 2f59
Calcium binding site 5 out of 6 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:44.3
occ:1.00
 OE2 C:GLU124 2.7 29.4 1.0
OE1 C:GLU124 2.7 28.4 1.0
CD C:GLU124 3.1 30.0 1.0
O C:HOH348 4.5 23.9 1.0
O C:HOH336 4.5 24.9 1.0
CG C:GLU124 4.6 28.6 1.0

Calcium binding site 6 out of 6 in 2f59

Go back to Calcium Binding Sites List in 2f59
Calcium binding site 6 out of 6 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca306

b:58.1
occ:1.00
 OD2 D:ASP28 2.5 33.9 1.0
OD1 D:ASP25 3.1 27.5 1.0
CG D:ASP28 3.8 30.4 1.0
N D:ASP25 4.0 25.6 1.0
CG D:ASP25 4.0 29.8 1.0
CA D:ASP25 4.1 25.1 1.0
C D:ASP24 4.1 27.2 1.0
CB D:ASP24 4.1 30.3 1.0
O D:ASP24 4.2 26.0 1.0
OD2 D:ASP24 4.4 36.3 1.0
OD1 D:ASP28 4.5 33.9 1.0
CB D:ASP25 4.6 27.2 1.0
CG D:ASP24 4.7 36.2 1.0
CB D:ASP28 4.7 29.0 1.0
CA D:ASP24 4.8 28.6 1.0
NH1 D:ARG21 4.8 24.8 1.0
OD2 D:ASP25 4.9 35.1 1.0

Reference:

S.Klinke, V.Zylberman, H.R.Bonomi, I.Haase, B.G.Guimaraes, B.C.Braden, A.Bacher, M.Fischer, F.A.Goldbaum. Structural and Kinetic Properties of Lumazine Synthase Isoenzymes in the Order Rhizobiales J.Mol.Biol. V. 373 664 2007.
ISSN: ISSN 0022-2836
PubMed: 17854827
DOI: 10.1016/J.JMB.2007.08.021
Page generated: Tue Jul 8 05:28:38 2025

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