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Sodium in PDB 2wd4: Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide

Enzymatic activity of Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide

All present enzymatic activity of Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide:
1.11.1.11;

Protein crystallography data

The structure of Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide, PDB code: 2wd4 was solved by S.K.Badyal, C.L.Metcalfe, A.Gumiero, E.L.Raven, P.C.E.Moody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.03 / 1.40
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.067, 82.067, 75.137, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.6

Other elements in 2wd4:

The structure of Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide (pdb code 2wd4). 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 Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide, PDB code: 2wd4:

Sodium binding site 1 out of 1 in 2wd4

Go back to Sodium Binding Sites List in 2wd4
Sodium binding site 1 out of 1 in the Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ascorbate Peroxidase As A Heme Oxygenase: W41A Variant Product with T- Butyl Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1251

b:19.4
occ:1.00
 O A:THR164 2.3 12.7 1.0
O A:ILE185 2.4 11.4 1.0
O A:ASN182 2.5 12.7 1.0
OD1 A:ASN182 2.7 16.3 0.5
OG1 A:THR180 2.7 14.0 1.0
OG1 A:THR164 3.1 17.4 1.0
CG A:ASN182 3.4 15.1 0.5
C A:THR164 3.4 12.1 1.0
C A:ASN182 3.4 13.3 1.0
CB A:THR180 3.5 13.3 1.0
C A:ILE185 3.6 10.5 1.0
OD1 A:ASP187 3.6 16.5 1.0
OG A:SER189 3.8 15.0 0.5
CG2 A:THR180 3.9 13.2 1.0
CB A:THR164 4.0 13.3 1.0
ND2 A:ASN182 4.1 16.9 0.5
CA A:THR164 4.1 12.7 1.0
CB A:ASN182 4.2 14.2 0.5
CA A:ASN182 4.2 13.8 0.5
CA A:ASN182 4.2 13.9 0.5
CB A:ASN182 4.2 14.5 0.5
N A:ILE185 4.2 10.0 1.0
CA A:ILE185 4.3 10.2 1.0
N A:PRO183 4.3 12.9 1.0
CB A:ILE185 4.4 10.8 1.0
CA A:PRO183 4.4 12.6 1.0
CG A:ASP187 4.4 15.6 1.0
N A:ASN182 4.5 14.0 1.0
N A:ILE165 4.5 11.2 1.0
CG2 A:THR164 4.6 12.3 1.0
N A:PHE186 4.7 9.9 1.0
N A:ASP187 4.7 11.4 1.0
OD2 A:ASP187 4.7 21.6 1.0
CA A:ILE165 4.8 10.6 1.0
CB A:SER189 4.8 14.4 0.5
C A:PRO183 4.8 12.0 1.0
CG2 A:ILE165 4.8 10.7 1.0
O A:HOH2122 4.9 12.1 1.0
CA A:PHE186 4.9 9.6 1.0
CA A:THR180 5.0 13.0 1.0
CG2 A:ILE185 5.0 11.4 1.0

Reference:

E.L.Raven, S.K.Badyal, G.Eaton, S.Mistry, Z.Pipirou, J.Basran, C.L.Metcalfe, A.Gumiero, S.Handa, P.C.E.Moody. Evidence For Heme Oxygenase Activity in A Heme Peroxidase. Biochemistry V. 48 4738 2009.
ISSN: ISSN 0006-2960
PubMed: 19309109
DOI: 10.1021/BI900118J
Page generated: Mon Oct 7 04:37:31 2024

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