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Calcium in PDB 2i0f: Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1)

Enzymatic activity of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1)

All present enzymatic activity of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1):
2.5.1.78;

Protein crystallography data

The structure of Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1), PDB code: 2i0f 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) 30.00 / 2.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.101, 68.521, 90.649, 90.00, 108.40, 90.00
R / Rfree (%) 24.2 / 28.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1) (pdb code 2i0f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1), PDB code: 2i0f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2i0f

Go back to Calcium Binding Sites List in 2i0f
Calcium binding site 1 out of 5 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:42.0
occ:1.00
 OE2 A:GLU124 2.7 26.8 1.0
OE1 A:GLU124 2.8 22.7 1.0
CD A:GLU124 3.1 25.1 1.0
O A:HOH433 4.4 28.0 1.0
CG A:GLU124 4.6 24.6 1.0

Calcium binding site 2 out of 5 in 2i0f

Go back to Calcium Binding Sites List in 2i0f
Calcium binding site 2 out of 5 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:54.7
occ:1.00
 OXT A:ALA157 2.8 35.0 1.0
OD1 B:ASP65 2.8 38.5 1.0
OD2 B:ASP65 2.9 39.0 1.0
CG B:ASP65 3.2 37.3 1.0
C A:ALA157 3.8 36.5 1.0
O B:HOH550 3.8 47.1 1.0
CA A:ALA157 4.2 36.0 1.0
NH2 A:ARG152 4.5 43.8 1.0
ND2 B:ASN69 4.6 47.4 1.0
CB A:ALA157 4.6 35.9 1.0
CB B:ASP65 4.7 34.3 1.0
O A:ALA157 4.8 37.3 1.0

Calcium binding site 3 out of 5 in 2i0f

Go back to Calcium Binding Sites List in 2i0f
Calcium binding site 3 out of 5 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:59.0
occ:1.00
 O B:ALA67 2.6 45.5 1.0
OE1 B:GLU73 3.2 50.0 1.0
C B:ALA67 3.5 45.5 1.0
O B:GLY71 4.2 43.5 1.0
N B:GLY70 4.2 48.8 1.0
CA B:ALA67 4.2 43.4 1.0
CA B:GLY70 4.3 48.4 1.0
N B:ASP68 4.4 46.3 1.0
CB B:ALA67 4.4 40.1 1.0
CD B:GLU73 4.4 49.2 1.0
CA B:ASP68 4.6 49.4 1.0
C B:GLY70 4.7 48.2 1.0
N B:GLY71 4.7 46.6 1.0
C B:ASP68 4.8 49.9 1.0

Calcium binding site 4 out of 5 in 2i0f

Go back to Calcium Binding Sites List in 2i0f
Calcium binding site 4 out of 5 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:71.5
occ:1.00
 O B:HOH546 2.6 29.8 1.0
O B:HOH547 3.0 49.2 1.0
OE2 B:GLU40 3.1 40.7 1.0
CD B:GLU40 4.3 41.0 1.0
OE1 B:GLU40 4.9 42.9 1.0

Calcium binding site 5 out of 5 in 2i0f

Go back to Calcium Binding Sites List in 2i0f
Calcium binding site 5 out of 5 in the Lumazine Synthase RIBH1 From Brucella Abortus (Gene BRUAB1_0785, Swiss-Prot Entry Q57DY1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca303

b:44.2
occ:1.00
 OE2 E:GLU124 2.7 27.3 1.0
OE1 E:GLU124 2.9 27.4 1.0
CD E:GLU124 3.1 24.0 1.0
CG E:GLU124 4.6 22.4 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 06:06:27 2025

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