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Sodium in PDB 4kav: Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis:
3.1.3.27;

Protein crystallography data

The structure of Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis, PDB code: 4kav was solved by A.Vrielink, C.Wanty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.26 / 1.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.696, 44.923, 50.179, 70.26, 69.36, 61.13
R / Rfree (%) 11.6 / 15.7

Other elements in 4kav:

The structure of Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom
Copper (Cu) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis (pdb code 4kav). 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 Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis, PDB code: 4kav:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4kav

Go back to Sodium Binding Sites List in 4kav
Sodium binding site 1 out of 2 in the Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A 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 Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:21.7
occ:1.00
 O A:HOH854 2.4 23.6 1.0
O A:GLU393 2.7 10.9 1.0
HG3 A:GLU393 2.8 19.6 1.0
HB3 A:ARG396 3.0 6.2 1.0
HZ2 A:LYS397 3.1 20.2 0.3
HG2 A:GLU393 3.2 19.6 1.0
O A:HOH1105 3.2 30.9 1.0
CG A:GLU393 3.4 16.3 1.0
O A:ARG396 3.5 9.5 1.0
HZ1 A:LYS397 3.6 20.2 0.3
C A:GLU393 3.6 9.3 1.0
HA A:GLU393 3.7 10.8 1.0
NZ A:LYS397 3.7 16.9 0.3
CB A:ARG396 4.0 5.2 1.0
H A:ARG396 4.0 7.5 1.0
HZ3 A:LYS397 4.0 20.2 0.3
CA A:GLU393 4.1 9.0 1.0
C A:ARG396 4.3 6.1 1.0
CB A:GLU393 4.3 12.0 1.0
HH11 A:ARG396 4.4 9.6 1.0
HB2 A:ARG396 4.4 6.2 1.0
HD3 A:ARG396 4.5 7.5 1.0
CD A:GLU393 4.5 22.2 1.0
CA A:ARG396 4.5 5.4 1.0
HA A:ALA394 4.5 11.7 1.0
OE2 A:GLU393 4.5 24.1 1.0
N A:ARG396 4.6 6.3 1.0
HG2 A:ARG396 4.6 6.8 1.0
HB2 A:GLU393 4.7 14.4 1.0
HD2 A:LYS397 4.7 14.5 0.3
N A:ALA394 4.7 9.1 1.0
CG A:ARG396 4.8 5.6 1.0

Sodium binding site 2 out of 2 in 4kav

Go back to Sodium Binding Sites List in 4kav
Sodium binding site 2 out of 2 in the Crystal Structure of the Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A 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 Soluble Domain of Lipooligosaccharide Phosphoethanolamine Transferase A From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:30.3
occ:1.00
 O A:HOH940 2.5 30.1 1.0
OE2 A:GLU352 2.6 27.0 1.0
HD1 A:HIS383 2.9 15.2 1.0
HB3 A:HIS383 3.1 7.7 1.0
ND1 A:HIS383 3.2 12.7 1.0
HH22 A:ARG390 3.2 6.9 1.0
HD11 A:ILE380 3.3 9.9 1.0
O A:GLY384 3.5 9.1 1.0
CG A:HIS383 3.6 11.0 1.0
CD A:GLU352 3.7 21.4 1.0
NH2 A:ARG390 3.7 5.7 1.0
HH21 A:ARG390 3.8 6.9 1.0
HG1 A:THR386 3.8 14.3 1.0
CB A:HIS383 3.8 6.4 1.0
OG1 A:THR386 3.8 11.9 1.0
CE1 A:HIS383 3.9 15.2 1.0
C A:GLY384 4.1 8.2 1.0
OE1 A:GLU352 4.1 20.6 1.0
HE1 A:HIS383 4.2 18.2 1.0
H A:THR386 4.2 8.6 1.0
CD1 A:ILE380 4.2 8.2 1.0
C A:HIS383 4.3 3.8 1.0
O A:HIS383 4.3 5.7 1.0
CD2 A:HIS383 4.4 14.8 1.0
HD2 A:PRO385 4.4 10.2 1.0
N A:GLY384 4.5 3.6 1.0
HB2 A:HIS383 4.5 7.7 1.0
HH12 A:ARG390 4.5 9.5 1.0
HA2 A:GLY384 4.6 6.3 1.0
CZ A:ARG390 4.6 5.8 1.0
NE2 A:HIS383 4.6 15.3 1.0
O A:HOH1039 4.6 30.0 1.0
CA A:GLY384 4.7 5.3 1.0
HD12 A:ILE380 4.7 9.9 1.0
HD13 A:ILE380 4.7 9.9 1.0
O A:HOH1003 4.7 29.4 1.0
HG13 A:ILE380 4.7 7.7 1.0
HG12 A:ILE380 4.7 7.7 1.0
CA A:HIS383 4.7 4.7 1.0
HG2 A:GLU352 4.8 18.6 1.0
H A:GLY384 4.8 4.3 1.0
N A:PRO385 4.8 7.2 1.0
CG1 A:ILE380 4.9 6.5 1.0
CG A:GLU352 4.9 15.5 1.0
NH1 A:ARG390 4.9 7.9 1.0

Reference:

C.Wanty, A.Anandan, S.Piek, J.Walshe, J.Ganguly, R.W.Carlson, K.A.Stubbs, C.M.Kahler, A.Vrielink. The Structure of the Neisserial Lipooligosaccharide Phosphoethanolamine Transferase A (Lpta) Required For Resistance to Polymyxin. J.Mol.Biol. V. 425 3389 2013.
ISSN: ISSN 0022-2836
PubMed: 23810904
DOI: 10.1016/J.JMB.2013.06.029
Page generated: Mon Oct 7 16:27:51 2024

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