Atomistry » Calcium » PDB 2nce-2o86 » 2o6h
Atomistry »
  Calcium »
    PDB 2nce-2o86 »
      2o6h »

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: Sat Dec 12 03:48:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy