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Sodium in PDB 6eqe: High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis

Enzymatic activity of High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis

All present enzymatic activity of High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis:
3.1.1.101;

Protein crystallography data

The structure of High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis, PDB code: 6eqe was solved by H.P.Austin, M.D.Allen, C.W.Johnson, G.T.Beckham, J.E.Mcgeehan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.51 / 0.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.114, 51.388, 84.545, 90.00, 90.00, 90.00
R / Rfree (%) 10 / 11

Other elements in 6eqe:

The structure of High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis (pdb code 6eqe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis, PDB code: 6eqe:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6eqe

Go back to Sodium Binding Sites List in 6eqe
Sodium binding site 1 out of 2 in the High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:30.1
occ:1.00
 HA A:PHE191 2.6 9.2 1.0
H A:SER193 2.7 11.6 1.0
O A:HOH662 2.7 22.7 0.7
OG A:SER193 2.7 16.1 1.0
HG A:SER193 2.8 19.3 1.0
O A:ASN190 3.2 9.7 1.0
CA A:PHE191 3.5 7.7 1.0
N A:SER193 3.5 9.7 1.0
HB3 A:SER193 3.5 17.9 1.0
CB A:SER193 3.6 14.9 1.0
C A:PHE191 3.7 8.0 1.0
HD1 A:PHE191 3.7 8.8 1.0
HB1 A:ALA171 3.8 9.3 1.0
H A:SER192 3.9 10.3 1.0
N A:SER192 3.9 8.6 1.0
HB2 A:ALA171 4.0 9.3 1.0
CA A:SER193 4.1 11.4 1.0
C A:ASN190 4.1 8.7 1.0
HG23 A:VAL194 4.2 9.5 1.0
CD1 A:PHE191 4.2 7.4 1.0
N A:PHE191 4.2 8.2 1.0
O A:PHE191 4.3 7.8 1.0
O A:HOH585 4.3 20.3 0.4
CB A:ALA171 4.4 7.7 1.0
O A:HOH737 4.4 41.5 0.9
HB2 A:SER193 4.4 17.9 1.0
CB A:PHE191 4.4 7.1 1.0
H A:VAL194 4.5 10.2 1.0
HB3 A:PHE191 4.5 8.5 1.0
C A:SER192 4.6 9.7 1.0
CG A:PHE191 4.6 7.2 1.0
C A:SER193 4.8 10.2 1.0
CA A:SER192 4.8 9.3 1.0
N A:VAL194 4.8 8.5 1.0
HB3 A:ALA171 4.8 9.3 1.0
HA A:SER193 4.9 13.7 1.0
CE1 A:PHE191 4.9 8.2 1.0
HG A:SER192 5.0 14.1 1.0

Sodium binding site 2 out of 2 in 6eqe

Go back to Sodium Binding Sites List in 6eqe
Sodium binding site 2 out of 2 in the High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Crystal Structure of A Polyethylene Terephthalate Degrading Hydrolase From Ideonella Sakaiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:27.9
occ:1.00
 O A:HOH401 2.0 6.3 0.4
OD1 A:ASN233 2.4 15.1 1.0
OE1 A:GLU204 2.4 10.2 1.0
O A:HOH417 2.5 17.2 1.0
O A:HOH643 3.1 29.6 0.8
CD A:GLU204 3.2 9.9 1.0
O A:HOH745 3.2 11.5 0.3
OE2 A:GLU204 3.3 13.5 1.0
CG A:ASN233 3.5 11.6 1.0
H A:GLY234 3.5 9.7 1.0
HD21 A:ASN233 3.8 17.8 1.0
N A:GLY234 4.0 8.1 1.0
O A:HOH681 4.0 18.0 0.5
HB3 A:SER282 4.0 8.3 1.0
ND2 A:ASN233 4.0 14.8 1.0
O A:HOH603 4.1 21.9 0.6
O A:HOH449 4.1 21.5 0.9
HA A:ASN233 4.1 8.9 1.0
HA2 A:GLY234 4.2 10.9 1.0
CA A:GLY234 4.6 9.1 1.0
CG A:GLU204 4.6 8.2 1.0
CB A:ASN233 4.6 8.8 1.0
CA A:ASN233 4.7 7.4 1.0
C A:ASN233 4.7 7.8 1.0
HB2 A:SER282 4.7 8.3 1.0
HA3 A:GLY234 4.7 10.9 1.0
CB A:SER282 4.8 6.9 1.0
HG2 A:GLU204 4.8 9.9 1.0
HD21 A:ASN205 4.8 16.8 1.0
HD22 A:ASN233 4.9 17.8 1.0
HB3 A:GLU204 4.9 8.6 1.0

Reference:

H.P.Austin, M.D.Allen, B.S.Donohoe, N.A.Rorrer, F.L.Kearns, R.L.Silveira, B.C.Pollard, G.Dominick, R.Duman, K.El Omari, V.Mykhaylyk, A.Wagner, W.E.Michener, A.Amore, M.S.Skaf, M.F.Crowley, A.W.Thorne, C.W.Johnson, H.L.Woodcock, J.E.Mcgeehan, G.T.Beckham. Characterization and Engineering of A Plastic-Degrading Aromatic Polyesterase. Proc. Natl. Acad. Sci. V. 115 E4350 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29666242
DOI: 10.1073/PNAS.1718804115
Page generated: Tue Oct 8 08:28:13 2024

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