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Sodium in PDB 3fyp: Crystal Structure of the Quadruple Mutant (N23C/C246S/D247E/P249A) of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of the Quadruple Mutant (N23C/C246S/D247E/P249A) of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of the Quadruple Mutant (N23C/C246S/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 Quadruple Mutant (N23C/C246S/D247E/P249A) of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3fyp 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) 37.96 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.781, 85.679, 163.828, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.7

Other elements in 3fyp:

The structure of Crystal Structure of the Quadruple Mutant (N23C/C246S/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 Quadruple Mutant (N23C/C246S/D247E/P249A) of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 3fyp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Quadruple Mutant (N23C/C246S/D247E/P249A) of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3fyp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3fyp

Go back to Sodium Binding Sites List in 3fyp
Sodium binding site 1 out of 2 in the Crystal Structure of the Quadruple Mutant (N23C/C246S/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 Quadruple Mutant (N23C/C246S/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:Na281

b:22.6
occ:1.00
 O C:HOH569 2.2 28.2 1.0
O C:ALA103 2.2 12.8 1.0
O C:HOH568 2.3 22.9 1.0
OD1 C:ASN130 2.4 17.1 1.0
O C:CYS106 2.5 18.9 1.0
O C:HOH544 3.2 33.6 1.0
C C:CYS106 3.3 14.4 1.0
C C:ALA103 3.4 16.9 1.0
CG C:ASN130 3.5 18.9 1.0
ND2 C:ASN130 3.9 20.8 1.0
CA C:ASP107 4.0 14.0 1.0
N C:ASP107 4.0 11.2 1.0
N C:CYS106 4.0 14.3 1.0
CA C:ALA103 4.1 10.7 1.0
CA C:CYS106 4.3 14.8 1.0
O C:HOH405 4.3 19.1 1.0
C C:VAL105 4.4 15.7 1.0
C C:GLU104 4.4 16.6 1.0
N C:GLU104 4.5 13.7 1.0
C C:ASP107 4.5 18.7 1.0
N C:VAL105 4.6 12.6 1.0
O C:ASP107 4.6 16.2 1.0
CA C:GLU104 4.6 17.3 1.0
O C:GLU104 4.7 15.6 1.0
CB C:ALA103 4.7 14.8 1.0
O C:VAL105 4.8 16.9 1.0
O C:HOH643 4.8 22.4 1.0
CB C:ASN130 4.8 12.0 1.0

Sodium binding site 2 out of 2 in 3fyp

Go back to Sodium Binding Sites List in 3fyp
Sodium binding site 2 out of 2 in the Crystal Structure of the Quadruple Mutant (N23C/C246S/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 2 of Crystal Structure of the Quadruple Mutant (N23C/C246S/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
D:Na283

b:46.1
occ:1.00
 O D:HOH478 1.9 23.5 1.0
O D:HOH454 2.2 19.6 1.0
O B:SER168 2.5 15.0 1.0
OG D:SER168 2.6 17.4 0.5
O D:GLY170 3.1 21.3 1.0
N D:GLY170 3.3 14.4 1.0
C B:SER168 3.4 15.5 1.0
CB D:SER168 3.7 16.6 0.5
CE1 A:PHE169 3.7 17.8 1.0
O D:SER168 3.8 14.3 1.0
C D:SER168 3.8 13.8 1.0
C D:GLY170 3.8 17.2 1.0
CB D:SER168 3.8 12.2 0.5
CA D:GLY170 3.8 14.6 1.0
CB B:SER168 3.8 15.5 1.0
N D:PHE169 3.9 11.6 1.0
CZ A:PHE169 3.9 13.5 1.0
C D:PHE169 4.1 9.2 1.0
CA B:SER168 4.1 11.7 1.0
CA D:PHE169 4.2 11.0 1.0
O A:HOH714 4.3 37.6 1.0
N B:PHE169 4.3 11.5 1.0
CA D:SER168 4.4 11.6 0.5
CA D:SER168 4.4 8.9 0.5
O B:HOH659 4.5 24.1 1.0
N B:SER168 4.5 14.0 1.0
O D:HOH420 4.5 22.9 1.0
CA B:PHE169 4.5 7.8 1.0
O B:HOH349 4.6 20.9 1.0
CD1 A:PHE169 4.7 17.7 1.0
N B:GLY170 4.9 14.4 1.0
CE2 A:PHE169 5.0 17.4 1.0
N D:TYR171 5.0 14.7 1.0
OG D:SER168 5.0 8.4 0.5

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: Tue Dec 15 06:11:15 2020

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