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Sodium in PDB 1xn1: Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)

Enzymatic activity of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)

All present enzymatic activity of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms):
2.5.1.78;

Protein crystallography data

The structure of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms), PDB code: 1xn1 was solved by S.Klinke, V.Zylberman, D.R.Vega, B.G.Guimaraes, B.C.Braden, F.A.Goldbaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.00 / 3.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.554, 120.238, 159.372, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) (pdb code 1xn1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms), PDB code: 1xn1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1xn1

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Sodium binding site 1 out of 7 in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na300

b:15.2
occ:1.00
 N E:SER113 3.1 9.9 1.0
OE2 A:GLU58 3.3 13.5 1.0
O E:SER113 3.6 6.5 1.0
OE1 A:GLU58 3.6 14.2 1.0
CD A:GLU58 3.9 14.3 1.0
CA E:LEU112 4.0 11.1 1.0
CA E:SER113 4.0 7.3 1.0
C E:LEU112 4.0 11.2 1.0
CB E:LEU112 4.0 11.0 1.0
C E:SER113 4.2 6.7 1.0
CG E:LEU112 4.2 11.8 1.0
CB A:TYR57 4.3 14.4 1.0
CB E:SER113 4.3 4.7 1.0
CD2 A:TYR57 4.4 16.1 1.0
CG A:TYR57 4.6 14.8 1.0
CD2 E:LEU112 5.0 12.2 1.0

Sodium binding site 2 out of 7 in 1xn1

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Sodium binding site 2 out of 7 in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:2.1
occ:1.00
 N A:SER113 3.0 9.1 1.0
O A:SER113 3.3 8.8 1.0
OE2 B:GLU58 3.3 17.0 1.0
CA A:SER113 3.8 9.6 1.0
C A:SER113 3.9 10.4 1.0
CA A:LEU112 3.9 9.6 1.0
C A:LEU112 3.9 9.1 1.0
CB A:LEU112 4.0 8.6 1.0
OE1 B:GLU58 4.0 15.1 1.0
CD B:GLU58 4.0 16.8 1.0
CB A:SER113 4.1 8.1 1.0
CD2 B:TYR57 4.2 8.7 1.0
CB B:TYR57 4.5 10.7 1.0
CG A:LEU112 4.6 7.5 1.0
CD2 A:LEU112 4.7 7.1 1.0
CG B:TYR57 4.8 6.7 1.0

Sodium binding site 3 out of 7 in 1xn1

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Sodium binding site 3 out of 7 in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:21.2
occ:1.00
 OD2 B:ASP52 2.9 29.9 1.0
CG2 B:ILE50 3.3 21.9 1.0
CG B:ASP52 3.9 26.5 1.0
O B:ILE50 3.9 25.2 1.0
OD1 B:ASP52 4.0 28.5 1.0
CB B:ILE50 4.1 21.8 1.0
C B:ILE50 4.4 24.3 1.0
NH1 A:ARG152 4.9 39.5 1.0
CA B:ILE50 4.9 23.9 1.0

Sodium binding site 4 out of 7 in 1xn1

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Sodium binding site 4 out of 7 in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:21.6
occ:1.00
 N D:SER113 3.3 9.3 1.0
OE2 E:GLU58 3.5 18.2 1.0
OE1 E:GLU58 3.5 18.1 1.0
O D:SER113 3.6 8.3 1.0
CD E:GLU58 3.9 18.1 1.0
CD2 E:TYR57 4.1 11.8 1.0
CA D:LEU112 4.1 11.6 1.0
CA D:SER113 4.1 7.8 1.0
CB D:LEU112 4.1 11.4 1.0
CB E:TYR57 4.1 12.2 1.0
C D:LEU112 4.2 11.4 1.0
C D:SER113 4.2 7.5 1.0
CB D:SER113 4.4 8.4 1.0
CG E:TYR57 4.5 12.3 1.0
CG D:LEU112 4.7 11.9 1.0
CD2 D:LEU112 4.9 12.2 1.0

Sodium binding site 5 out of 7 in 1xn1

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Sodium binding site 5 out of 7 in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:19.3
occ:1.00
 OE2 F:GLU58 3.2 21.6 1.0
N J:SER113 3.5 8.7 1.0
OE1 F:GLU58 3.6 17.4 1.0
O J:SER113 3.7 11.6 1.0
CD F:GLU58 3.8 18.8 1.0
CB J:LEU112 4.1 10.0 1.0
CA J:LEU112 4.2 11.3 1.0
C J:LEU112 4.3 10.2 1.0
CA J:SER113 4.3 7.8 1.0
C J:SER113 4.4 8.1 1.0
CG J:LEU112 4.4 9.3 1.0
CD2 F:TYR57 4.5 8.6 1.0
CB F:TYR57 4.6 9.8 1.0
CB J:SER113 4.7 5.6 1.0
CD2 J:LEU112 4.8 7.9 1.0
CG F:TYR57 5.0 8.7 1.0

Sodium binding site 6 out of 7 in 1xn1

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Sodium binding site 6 out of 7 in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na304

b:21.4
occ:1.00
 OE2 H:GLU58 2.9 20.9 1.0
N G:SER113 3.2 22.7 1.0
O G:SER113 3.7 19.3 1.0
CD H:GLU58 3.7 20.3 1.0
OE1 H:GLU58 3.8 19.7 1.0
CB G:LEU112 3.8 20.9 1.0
CA G:LEU112 3.9 22.7 1.0
C G:LEU112 4.0 23.8 1.0
CB H:TYR57 4.1 10.3 1.0
CD2 H:TYR57 4.1 11.2 1.0
CA G:SER113 4.2 20.3 1.0
C G:SER113 4.3 20.1 1.0
CG H:TYR57 4.5 9.7 1.0
CB G:SER113 4.5 20.2 1.0
CG G:LEU112 4.6 19.9 1.0
CD2 G:LEU112 5.0 20.4 1.0

Sodium binding site 7 out of 7 in 1xn1

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Sodium binding site 7 out of 7 in the Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Lumazine Synthase From Brucella Abortus (Orthorhombic Form at 3.05 Angstroms) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na305

b:18.6
occ:1.00
 OG J:SER113 3.1 5.4 1.0
O J:VAL115 3.1 6.7 1.0
CG2 F:VAL92 3.7 10.9 1.0
CG1 J:ILE97 3.7 5.2 1.0
C J:VAL115 3.8 7.4 1.0
CD1 J:LEU116 4.0 5.4 1.0
CD1 J:ILE97 4.1 5.0 1.0
CB J:SER113 4.2 5.6 1.0
N J:LEU116 4.3 9.2 1.0
N J:VAL115 4.4 8.6 1.0
CA J:LEU116 4.4 11.4 1.0
CA J:VAL115 4.6 7.0 1.0
CB J:VAL115 4.7 4.9 1.0
O J:SER113 4.7 11.6 1.0
C J:SER113 4.9 8.1 1.0

Reference:

S.Klinke, V.Zylberman, D.R.Vega, B.G.Guimaraes, B.C.Braden, F.A.Goldbaum. Crystallographic Studies on Decameric Brucella Spp. Lumazine Synthase: A Novel Quaternary Arrangement Evolved For A New Function? J.Mol.Biol. V. 353 124 2005.
ISSN: ISSN 0022-2836
PubMed: 16165152
DOI: 10.1016/J.JMB.2005.08.017
Page generated: Mon Oct 7 00:33:20 2024

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