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Sodium in PDB 6ok1: LTP2-CHSH2(DUF35) Aldolase

Protein crystallography data

The structure of LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1 was solved by M.S.Kimber, E.Mallette, R.Aggett, S.Y.K.Seah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.83 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.680, 110.560, 120.140, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 16.8

Other elements in 6ok1:

The structure of LTP2-CHSH2(DUF35) Aldolase also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the LTP2-CHSH2(DUF35) Aldolase (pdb code 6ok1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6ok1

Go back to Sodium Binding Sites List in 6ok1
Sodium binding site 1 out of 2 in the LTP2-CHSH2(DUF35) Aldolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:27.8
occ:1.00
O A:ILE70 2.2 26.5 1.0
O A:HOH738 2.3 44.7 1.0
O A:VAL48 2.4 26.2 1.0
O A:GLU72 2.4 24.7 1.0
O A:HOH862 2.5 36.2 1.0
HG23 A:ILE70 3.4 29.5 1.0
HA A:ASP49 3.4 28.5 1.0
C A:ILE70 3.4 27.0 1.0
H A:GLU72 3.4 31.1 0.4
H A:GLU72 3.4 31.1 0.6
C A:GLU72 3.4 24.6 1.0
N A:GLU72 3.5 25.9 1.0
HG2 A:GLU72 3.5 35.5 0.4
HG22 A:ILE70 3.5 29.5 1.0
C A:VAL48 3.6 25.7 1.0
HG3 A:GLU72 3.7 35.5 0.4
C A:GLY71 3.9 28.8 1.0
HB2 A:GLU72 3.9 22.3 0.6
CG2 A:ILE70 3.9 24.6 1.0
O A:SER46 4.0 34.7 1.0
CA A:GLU72 4.0 25.9 0.6
CA A:GLU72 4.0 21.8 0.4
CG A:GLU72 4.0 29.5 0.4
HA3 A:GLY71 4.0 40.2 1.0
HD23 A:LEU73 4.1 28.6 1.0
HA A:SER46 4.1 34.2 1.0
HA A:ILE70 4.2 39.5 1.0
CA A:ASP49 4.2 23.7 1.0
N A:GLY71 4.3 28.7 1.0
CA A:GLY71 4.3 33.5 1.0
HB3 A:ASP49 4.3 27.0 1.0
CA A:ILE70 4.3 32.9 1.0
N A:ASP49 4.4 24.0 1.0
O A:GLY71 4.4 25.9 1.0
HA A:LEU73 4.4 26.3 1.0
O A:HOH728 4.4 38.1 1.0
CB A:GLU72 4.5 18.7 0.6
HB A:VAL48 4.5 31.2 1.0
O A:HOH607 4.5 45.8 1.0
C A:SER46 4.6 34.7 1.0
CB A:GLU72 4.6 57.9 0.4
H A:VAL48 4.6 31.8 1.0
N A:LEU73 4.6 24.7 1.0
CA A:VAL48 4.6 21.4 1.0
O A:HOH813 4.6 53.2 1.0
N A:VAL48 4.6 26.5 1.0
HG21 A:ILE70 4.6 29.5 1.0
O A:PRO45 4.7 29.2 1.0
CB A:ILE70 4.8 23.7 1.0
CB A:ASP49 4.8 22.4 1.0
CA A:SER46 4.9 28.5 1.0
HA A:GLU72 4.9 26.2 0.4
HA A:GLU72 4.9 31.1 0.6
HB3 A:GLU72 5.0 22.3 0.6
CD2 A:LEU73 5.0 23.8 1.0
HG12 A:VAL48 5.0 29.2 1.0

Sodium binding site 2 out of 2 in 6ok1

Go back to Sodium Binding Sites List in 6ok1
Sodium binding site 2 out of 2 in the LTP2-CHSH2(DUF35) Aldolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:24.8
occ:1.00
O C:ILE70 2.3 21.6 1.0
O C:VAL48 2.3 22.3 1.0
O C:GLU72 2.3 22.1 1.0
O C:HOH859 2.4 35.1 1.0
O C:HOH808 2.5 47.7 1.0
HA C:ASP49 3.3 19.8 1.0
HG23 C:ILE70 3.4 30.3 1.0
C C:GLU72 3.4 22.1 1.0
C C:ILE70 3.4 22.6 1.0
H C:GLU72 3.5 27.0 0.6
H C:GLU72 3.5 27.0 0.4
C C:VAL48 3.5 19.9 1.0
HG22 C:ILE70 3.5 30.3 1.0
HG2 C:GLU72 3.5 46.1 0.6
N C:GLU72 3.6 22.5 1.0
HG3 C:GLU72 3.7 46.1 0.6
HB2 C:GLU72 3.8 18.3 0.4
C C:GLY71 3.9 24.1 1.0
CG2 C:ILE70 3.9 25.3 1.0
O C:SER46 3.9 29.3 1.0
CA C:GLU72 4.0 37.7 0.4
CA C:GLU72 4.0 16.1 0.6
CG C:GLU72 4.0 38.4 0.6
HA3 C:GLY71 4.1 29.5 1.0
HA C:SER46 4.1 28.8 1.0
HD23 C:LEU73 4.1 25.7 1.0
CA C:ASP49 4.2 16.4 1.0
HB3 C:ASP49 4.2 24.7 1.0
HA C:ILE70 4.2 27.8 1.0
N C:ASP49 4.3 20.4 1.0
CA C:GLY71 4.3 24.6 1.0
N C:GLY71 4.3 23.4 1.0
HA C:LEU73 4.4 25.1 1.0
CA C:ILE70 4.4 23.1 1.0
O C:HOH843 4.4 47.8 1.0
O C:GLY71 4.4 24.1 1.0
CB C:GLU72 4.4 15.2 0.4
HB C:VAL48 4.5 24.5 1.0
H C:VAL48 4.6 25.8 1.0
C C:SER46 4.6 26.8 1.0
CA C:VAL48 4.6 18.5 1.0
N C:VAL48 4.6 21.5 1.0
N C:LEU73 4.6 19.8 1.0
O C:HOH780 4.6 30.5 1.0
O C:HOH606 4.6 47.2 1.0
CB C:GLU72 4.6 34.8 0.6
HG21 C:ILE70 4.6 30.3 1.0
CB C:ASP49 4.7 20.5 1.0
O C:PRO45 4.7 23.7 1.0
CB C:ILE70 4.8 21.5 1.0
CA C:SER46 4.8 23.9 1.0
HA C:GLU72 4.9 45.3 0.4
HA C:GLU72 4.9 19.4 0.6
HB3 C:GLU72 4.9 18.3 0.4
HG12 C:VAL48 4.9 27.0 1.0
CA C:LEU73 5.0 20.9 1.0

Reference:

R.Aggett, E.Mallette, S.E.Gilbert, M.A.Vachon, K.L.Schroeter, M.S.Kimber, S.Y.K.Seah. The Steroid Side-Chain-Cleaving Aldolase LTP2-CHSH2DUF35IS A Thiolase Superfamily Member with A Radically Repurposed Active Site. J.Biol.Chem. V. 294 11934 2019.
ISSN: ESSN 1083-351X
PubMed: 31209106
DOI: 10.1074/JBC.RA119.008889
Page generated: Tue Dec 15 12:41:22 2020

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