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Sodium in PDB 4jtj: Crystal Structure of R117K Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of R117K Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of R117K Mutant 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 R117K Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 4jtj was solved by T.M.Allison, F.C.Cochrane, G.B.Jameson, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.55 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.468, 85.370, 163.023, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.6

Other elements in 4jtj:

The structure of Crystal Structure of R117K Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of R117K Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 4jtj). 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 R117K Mutant of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 4jtj:

Sodium binding site 1 out of 1 in 4jtj

Go back to Sodium Binding Sites List in 4jtj
Sodium binding site 1 out of 1 in the Crystal Structure of R117K Mutant 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 R117K Mutant 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:Na302

b:26.9
occ:1.00
 O C:ALA103 2.2 21.4 1.0
O C:HOH465 2.4 33.9 1.0
OD1 C:ASN130 2.4 26.1 1.0
O C:HOH441 2.4 37.1 1.0
O C:HOH484 2.5 37.5 1.0
O C:CYS106 2.5 26.6 1.0
C C:CYS106 3.4 26.1 1.0
C C:ALA103 3.4 21.5 1.0
CG C:ASN130 3.5 26.7 1.0
ND2 C:ASN130 3.9 26.6 1.0
CA C:ASP107 4.1 24.5 1.0
CA C:ALA103 4.1 23.6 1.0
N C:ASP107 4.1 22.7 1.0
N C:CYS106 4.2 23.0 1.0
O C:HOH414 4.3 30.8 1.0
C C:GLU104 4.4 26.4 1.0
CA C:CYS106 4.5 22.9 1.0
N C:GLU104 4.5 22.8 1.0
C C:VAL105 4.5 25.6 1.0
O C:HOH485 4.6 45.4 1.0
N C:VAL105 4.6 24.9 1.0
C C:ASP107 4.6 23.6 1.0
O C:ASP107 4.6 25.0 1.0
CA C:GLU104 4.6 26.1 1.0
O C:GLU104 4.6 24.4 1.0
CB C:ALA103 4.7 25.6 1.0
O C:VAL105 4.7 28.9 1.0
CB C:ASN130 4.8 23.6 1.0
O C:HOH422 4.8 36.7 1.0

Reference:

T.M.Allison, F.C.Cochrane, G.B.Jameson, E.J.Parker. Examining the Role of Intersubunit Contacts in Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase. Biochemistry V. 52 4676 2013.
ISSN: ISSN 0006-2960
PubMed: 23746359
DOI: 10.1021/BI400521F
Page generated: Mon Oct 7 16:22:40 2024

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