Atomistry » Sodium » PDB 4jvl-4khs » 4kav
Atomistry »
  Sodium »
    PDB 4jvl-4khs »
      4kav »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy