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Sodium in PDB 3fyo: Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis:
2.5.1.55;

Protein crystallography data

The structure of Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3fyo was solved by G.B.Jameson, E.J.Parker, F.P.Cochrane, M.L.Patchett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.94 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.740, 86.197, 163.891, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.7

Other elements in 3fyo:

The structure of Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 3fyo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3fyo:

Sodium binding site 1 out of 1 in 3fyo

Go back to Sodium Binding Sites List in 3fyo
Sodium binding site 1 out of 1 in the Crystal Structure of the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis


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 the Triple Mutant (N23C/D247E/P249A) of 3-Deoxy- D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na282

b:21.4
occ:1.00
 O C:ALA103 2.2 20.7 1.0
O C:HOH329 2.3 27.3 1.0
O C:HOH328 2.3 33.2 1.0
OD1 C:ASN130 2.4 23.6 1.0
O C:HOH607 2.4 28.6 1.0
O C:CYS106 2.5 23.7 1.0
C C:CYS106 3.3 22.1 1.0
C C:ALA103 3.4 21.4 1.0
CG C:ASN130 3.5 23.0 1.0
ND2 C:ASN130 3.9 24.5 1.0
CA C:ASP107 4.0 21.9 1.0
N C:ASP107 4.0 21.5 1.0
N C:CYS106 4.1 20.6 1.0
CA C:ALA103 4.1 20.0 1.0
CA C:CYS106 4.3 22.6 1.0
O C:HOH564 4.3 26.6 1.0
C C:GLU104 4.4 21.6 1.0
N C:GLU104 4.4 21.0 1.0
C C:VAL105 4.5 22.2 1.0
C C:ASP107 4.5 22.3 1.0
O C:ASP107 4.6 21.3 1.0
N C:VAL105 4.6 20.8 1.0
CA C:GLU104 4.6 22.1 1.0
O C:GLU104 4.7 19.8 1.0
CB C:ALA103 4.8 19.5 1.0
O C:HOH464 4.8 25.8 1.0
O C:VAL105 4.8 21.3 1.0
CB C:ASN130 4.8 16.2 1.0

Reference:

F.C.Cochrane, T.V.Cookson, G.B.Jameson, E.J.Parker. Reversing Evolution: Re-Establishing Obligate Metal Ion Dependence in A Metal-Independent KDO8P Synthase J.Mol.Biol. V. 390 646 2009.
ISSN: ISSN 0022-2836
PubMed: 19447118
DOI: 10.1016/J.JMB.2009.05.014
Page generated: Mon Oct 7 09:51:18 2024

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