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Sodium in PDB 2qkf: Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

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

All present enzymatic activity of Crystal Structure 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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 2qkf was solved by F.C.Cochrane, M.L.Patchett, 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) 40.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.515, 85.295, 162.686, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.5

Other elements in 2qkf:

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

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 2qkf). 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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 2qkf:

Sodium binding site 1 out of 1 in 2qkf

Go back to Sodium Binding Sites List in 2qkf
Sodium binding site 1 out of 1 in the Crystal Structure 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 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na283

b:24.5
occ:1.00
 O C:ALA103 2.2 23.5 1.0
O C:HOH408 2.3 34.9 1.0
OD1 C:ASN130 2.4 26.0 1.0
O C:HOH339 2.4 34.9 1.0
O C:CYS106 2.5 26.2 1.0
C C:ALA103 3.4 24.6 1.0
C C:CYS106 3.4 23.8 1.0
CG C:ASN130 3.5 25.2 1.0
ND2 C:ASN130 3.9 25.7 1.0
CA C:ALA103 4.1 23.7 1.0
N C:CYS106 4.1 24.4 1.0
N C:ASP107 4.1 24.1 1.0
CA C:ASP107 4.1 24.8 1.0
O C:HOH321 4.3 29.4 1.0
CA C:CYS106 4.4 24.4 1.0
C C:GLU104 4.4 27.5 1.0
N C:GLU104 4.4 24.6 1.0
C C:VAL105 4.4 26.0 1.0
O C:GLU104 4.6 28.3 1.0
N C:VAL105 4.6 23.9 1.0
CA C:GLU104 4.6 27.6 1.0
C C:ASP107 4.6 23.7 1.0
O C:ASP107 4.7 22.4 1.0
CB C:ALA103 4.7 23.1 1.0
CB C:ASN130 4.7 24.4 1.0
O C:VAL105 4.7 24.7 1.0
O C:HOH368 4.9 32.6 1.0

Reference:

F.C.Cochrane, M.L.Patchett, G.B.Jameson, E.J.Parker. Re-Establishing A Metal-Binding Scaffold with Full Activity in the Metal-Independent KDO8P Synthase From Neisseria Meningitidis To Be Published.
Page generated: Sun Aug 17 11:32:33 2025

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