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Sodium in PDB 3qq0: Crystal Structure of A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of A Deletion Mutant (N59) 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 A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3qq0 was solved by T.M.Allison, 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) 32.76 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.058, 85.744, 163.187, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.9

Other elements in 3qq0:

The structure of Crystal Structure of A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 3qq0). 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 A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3qq0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3qq0

Go back to Sodium Binding Sites List in 3qq0
Sodium binding site 1 out of 2 in the Crystal Structure of A Deletion Mutant (N59) 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 A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na281

b:27.5
occ:1.00
 O B:THR127 2.3 22.1 1.0
O B:HOH664 2.3 27.5 1.0
O B:HOH665 2.4 32.4 1.0
O B:HOH662 2.4 30.3 1.0
O B:HOH357 2.5 33.6 1.0
C B:THR127 3.5 21.9 1.0
OD1 B:ASN129 4.0 22.8 1.0
O B:HOH661 4.1 34.5 1.0
O B:HOH722 4.2 46.6 1.0
O B:HOH715 4.3 39.6 1.0
CA B:GLY128 4.4 22.1 1.0
N B:GLY128 4.4 20.0 1.0
CA B:THR127 4.5 22.0 1.0
C B:GLY128 4.6 21.3 1.0
O B:HOH310 4.7 29.9 1.0
N B:ASN129 4.9 18.4 1.0

Sodium binding site 2 out of 2 in 3qq0

Go back to Sodium Binding Sites List in 3qq0
Sodium binding site 2 out of 2 in the Crystal Structure of A Deletion Mutant (N59) 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 A Deletion Mutant (N59) of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na282

b:33.5
occ:1.00
 O B:HOH721 2.1 47.0 1.0
O B:HOH722 2.2 46.6 1.0
O B:HOH593 2.3 45.9 1.0
O B:HOH661 2.3 34.5 1.0
O B:HOH313 2.5 30.4 1.0
O B:HOH714 3.4 40.7 1.0
O B:HOH436 3.8 54.0 1.0
O B:HOH665 3.9 32.4 1.0
O B:HOH384 4.3 39.0 1.0
O B:ALA102 4.3 19.0 1.0
O B:GLU103 4.3 23.3 1.0
OE2 B:GLU103 4.6 38.5 1.0
O B:HOH664 4.7 27.5 1.0
O B:HOH662 4.7 30.3 1.0
O B:HOH392 4.9 29.2 1.0
C B:GLU103 5.0 23.2 1.0

Reference:

T.M.Allison, R.D.Hutton, F.C.Cochrane, J.A.Yeoman, G.B.Jameson, E.J.Parker. Targeting the Role of A Key Conserved Motif For Substrate Selection and Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase Biochemistry V. 50 3686 2011.
ISSN: ISSN 0006-2960
PubMed: 21438567
DOI: 10.1021/BI200251F
Page generated: Mon Oct 7 12:41:26 2024

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