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Calcium in PDB 2o6h: Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione

Enzymatic activity of Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione

All present enzymatic activity of Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione, PDB code: 2o6h 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) 48.80 / 2.70
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.649, 97.649, 175.400, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 27.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione (pdb code 2o6h). 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) Complexed with Inhibitor 5-Nitro-6-(D- Ribitylamino)-2,4(1H,3H) Pyrimidinedione, PDB code: 2o6h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2o6h

Go back to Calcium Binding Sites List in 2o6h
Calcium binding site 1 out of 6 in the Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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:68.9
occ:1.00
 OE1 A:GLU73 2.9 41.5 0.5
O A:ALA67 3.1 45.4 1.0
CD A:GLU73 3.2 40.6 0.5
OE2 A:GLU73 3.7 40.8 0.5
CG A:GLU73 3.8 38.4 1.0
C A:ALA67 4.1 44.7 1.0
CA A:ALA67 4.8 43.9 1.0
O A:GLY71 4.9 39.7 1.0
CA A:GLY70 4.9 45.9 1.0
CB A:ALA67 4.9 43.2 1.0
N A:GLY70 5.0 47.8 1.0
CB A:GLU73 5.0 37.7 1.0

Calcium binding site 2 out of 6 in 2o6h

Go back to Calcium Binding Sites List in 2o6h
Calcium binding site 2 out of 6 in the Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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:Ca302

b:44.9
occ:1.00
 OE1 A:GLU124 2.9 35.4 1.0
OE2 A:GLU124 3.0 36.6 1.0
CD A:GLU124 3.3 35.4 1.0
CG A:GLU124 4.9 34.9 1.0

Calcium binding site 3 out of 6 in 2o6h

Go back to Calcium Binding Sites List in 2o6h
Calcium binding site 3 out of 6 in the Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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:Ca303

b:50.1
occ:1.00
 OE1 B:GLU73 2.8 47.2 1.0
O B:ALA67 3.0 38.0 1.0
C B:ALA67 3.9 38.0 1.0
CD B:GLU73 4.0 45.1 1.0
CB B:ALA67 4.5 35.6 1.0
CA B:ALA67 4.5 37.4 1.0
OE2 B:GLU73 4.7 47.7 1.0
O B:GLY71 4.7 37.5 1.0
N B:ASP68 4.7 38.9 1.0
O B:HOH430 4.8 32.8 1.0
CA B:GLY70 4.9 41.1 1.0
N B:GLY70 4.9 40.6 1.0
CA B:ASP68 5.0 39.7 1.0
CB B:GLU73 5.0 37.2 1.0
OD1 B:ASP68 5.0 45.3 1.0

Calcium binding site 4 out of 6 in 2o6h

Go back to Calcium Binding Sites List in 2o6h
Calcium binding site 4 out of 6 in the Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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:Ca304

b:48.4
occ:0.50
 O C:ALA67 2.7 40.0 1.0
OE1 C:GLU73 3.1 46.5 1.0
C C:ALA67 3.6 39.5 1.0
O C:GLY71 3.9 45.4 1.0
CA C:GLY70 4.0 45.8 1.0
N C:GLY70 4.1 46.4 1.0
C C:GLY70 4.2 45.8 1.0
CA C:ALA67 4.2 36.3 1.0
CD C:GLU73 4.3 46.8 1.0
CB C:ALA67 4.5 33.6 1.0
N C:GLY71 4.5 45.8 1.0
N C:ASP68 4.5 41.5 1.0
O C:GLY70 4.7 46.0 1.0
CA C:ASP68 4.7 43.2 1.0
C C:ASP68 4.9 43.8 1.0
C C:GLY71 4.9 44.2 1.0
CB C:GLU73 4.9 40.4 1.0

Calcium binding site 5 out of 6 in 2o6h

Go back to Calcium Binding Sites List in 2o6h
Calcium binding site 5 out of 6 in the Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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:43.5
occ:1.00
 OE1 C:GLU124 2.8 36.4 1.0
OE2 C:GLU124 2.9 38.0 1.0
CD C:GLU124 3.3 35.5 1.0
CG C:GLU124 4.8 34.5 1.0

Calcium binding site 6 out of 6 in 2o6h

Go back to Calcium Binding Sites List in 2o6h
Calcium binding site 6 out of 6 in the Lumazine Synthase RIBH1 From Brucella Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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 Melitensis (Gene BMEI1187, Swiss-Prot Entry Q8YGH2) 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:56.1
occ:1.00
 OD1 D:ASP24 3.2 32.2 1.0
CB D:ASP24 3.4 31.1 1.0
CG D:ASP24 3.7 33.4 1.0
N D:ASP24 4.1 30.4 1.0
CA D:ASP24 4.4 30.4 1.0
O D:PHE22 4.7 28.3 1.0
OD2 D:ASP24 4.8 32.8 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 07:16:54 2025

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