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Sodium in PDB 3stc: Crystal Structure of Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3stc 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) 36.56 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.780, 85.760, 163.220, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.5

Other elements in 3stc:

The structure of Crystal Structure of Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis (pdb code 3stc). 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 Loop 7 Truncated Mutant of 3-Deoxy-D-Manno- Octulosonate 8-Phosphate Synthase (KDO8PS) From Neisseria Meningitidis, PDB code: 3stc:

Sodium binding site 1 out of 1 in 3stc

Go back to Sodium Binding Sites List in 3stc
Sodium binding site 1 out of 1 in the Crystal Structure of Loop 7 Truncated 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 Loop 7 Truncated 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:Na272

b:32.4
occ:1.00
 O C:HOH631 2.1 26.7 1.0
O C:HOH630 2.3 25.8 1.0
O C:ALA103 2.3 18.1 1.0
OD1 C:ASN130 2.4 20.5 0.5
OD1 C:ASN130 2.5 21.2 0.5
O C:CYS106 2.5 19.7 1.0
C C:CYS106 3.3 18.9 1.0
CG C:ASN130 3.4 19.6 0.5
C C:ALA103 3.5 18.9 1.0
CG C:ASN130 3.5 19.9 0.5
CA C:ASP107 3.8 19.6 1.0
N C:ASP107 3.9 19.1 1.0
ND2 C:ASN130 3.9 19.9 0.5
ND2 C:ASN130 3.9 20.1 0.5
N C:CYS106 4.1 18.3 1.0
CA C:ALA103 4.2 17.9 1.0
O C:HOH340 4.2 40.4 1.0
CA C:CYS106 4.3 18.8 1.0
O C:HOH293 4.4 19.3 1.0
C C:ASP107 4.4 20.0 1.0
C C:GLU104 4.4 20.5 1.0
O C:ASP107 4.4 21.1 1.0
C C:VAL105 4.5 19.2 1.0
N C:GLU104 4.5 19.2 1.0
N C:VAL105 4.6 19.3 1.0
O C:GLU104 4.6 19.0 1.0
CA C:GLU104 4.7 21.1 1.0
CB C:ASN130 4.7 19.3 0.5
O C:VAL105 4.8 19.4 1.0
CB C:ALA103 4.8 17.8 1.0
CB C:ASN130 4.9 19.6 0.5

Reference:

T.M.Allison, R.D.Hutton, W.Jiao, B.J.Gloyne, E.B.Nimmo, G.B.Jameson, E.J.Parker. An Extended (Beta)7(Alpha)7 Substrate-Binding Loop Is Essential For Efficient Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase Biochemistry V. 50 9318 2011.
ISSN: ISSN 0006-2960
PubMed: 21942786
DOI: 10.1021/BI201231E
Page generated: Mon Oct 7 13:00:14 2024

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