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Sodium in PDB 5a25: Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst

Enzymatic activity of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst

All present enzymatic activity of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst:
4.2.1.1;

Protein crystallography data

The structure of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst, PDB code: 5a25 was solved by A.Warden, J.Newman, T.S.Peat, S.Seabrook, M.Williams, G.Dojchinov, V.Haritos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.84 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.331, 79.440, 61.521, 90.00, 106.98, 90.00
R / Rfree (%) 15.308 / 19.689

Other elements in 5a25:

The structure of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst (pdb code 5a25). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst, PDB code: 5a25:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5a25

Go back to Sodium Binding Sites List in 5a25
Sodium binding site 1 out of 4 in the Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1262

b:28.8
occ:1.00
 O A:HOH2152 2.4 31.4 1.0
OG A:SER172 2.5 12.8 1.0
O3 A:GOL1261 2.5 31.0 1.0
O A:HOH2151 2.7 20.1 1.0
O A:SER172 2.7 11.4 1.0
C A:SER172 3.3 12.4 1.0
CB A:SER172 3.6 11.9 1.0
C3 A:GOL1261 3.7 34.5 1.0
CA A:SER172 3.8 11.5 1.0
N A:SER172 3.8 11.5 1.0
O A:HOH2153 4.0 24.2 1.0
O2 A:GOL1261 4.1 35.4 1.0
O A:HOH2150 4.1 17.9 1.0
O A:HOH2145 4.1 27.2 1.0
N A:THR173 4.2 11.3 1.0
O A:HOH2065 4.2 20.2 1.0
CA A:THR173 4.5 12.0 1.0
C2 A:GOL1261 4.6 38.6 1.0
O A:HOH2155 4.7 33.1 1.0

Sodium binding site 2 out of 4 in 5a25

Go back to Sodium Binding Sites List in 5a25
Sodium binding site 2 out of 4 in the Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1263

b:38.7
occ:1.00
 O A:HOH2202 2.3 30.8 1.0
OE2 A:GLU69 2.6 19.4 1.0
OD2 B:ASP72 2.9 18.2 1.0
O A:HOH2066 3.1 19.8 1.0
OD1 B:ASP72 3.1 18.8 1.0
O A:HOH2201 3.2 23.4 1.0
CG B:ASP72 3.3 17.9 1.0
CD A:GLU69 3.6 19.4 1.0
O A:HOH2077 3.9 30.6 1.0
O A:HOH2083 3.9 17.9 1.0
C4 B:BOG1263 3.9 17.8 1.0
O A:HOH2079 3.9 17.0 1.0
NH1 A:ARG58 3.9 18.1 1.0
OE1 A:GLU69 4.0 20.4 1.0
O A:HOH2078 4.2 34.5 1.0
C6 B:BOG1263 4.2 17.0 1.0
O4 B:BOG1263 4.3 16.7 1.0
O A:HOH2081 4.5 26.0 1.0
C5 B:BOG1263 4.5 17.8 1.0
CB B:ASP72 4.8 16.6 1.0
O B:HOH2061 4.8 21.2 1.0
CG2 B:VAL91 4.8 15.7 1.0
O5 B:BOG1263 4.9 17.9 1.0
CG A:GLU69 4.9 17.3 1.0
O3 B:BOG1263 4.9 19.0 1.0
C3 B:BOG1263 4.9 19.1 1.0

Sodium binding site 3 out of 4 in 5a25

Go back to Sodium Binding Sites List in 5a25
Sodium binding site 3 out of 4 in the Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1261

b:29.5
occ:1.00
 O B:HOH2123 2.4 30.9 1.0
O B:SER172 2.5 16.1 1.0
O B:SER165 2.5 18.0 1.0
O B:HOH2126 2.5 22.4 1.0
C B:SER172 3.6 15.5 1.0
C B:SER165 3.7 18.4 1.0
O B:HOH2122 3.8 24.3 1.0
CB B:THR173 3.9 17.4 1.0
NA B:NA1262 4.0 36.6 1.0
CB B:SER165 4.1 19.2 1.0
CA B:THR173 4.1 16.9 1.0
CA B:SER165 4.3 17.7 1.0
OG1 B:THR173 4.3 18.9 1.0
N B:THR173 4.3 15.2 1.0
N B:SER172 4.4 14.4 1.0
O B:HOH2118 4.5 36.1 1.0
CA B:SER172 4.7 14.8 1.0
CG2 B:ILE166 4.8 16.6 1.0
N B:ILE166 4.8 16.4 1.0
O B:HOH2124 4.9 27.7 1.0

Sodium binding site 4 out of 4 in 5a25

Go back to Sodium Binding Sites List in 5a25
Sodium binding site 4 out of 4 in the Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1262

b:36.6
occ:1.00
 O B:SER172 2.7 16.1 1.0
O B:HOH2122 2.7 24.3 1.0
O B:HOH2123 2.7 30.9 1.0
OG B:SER172 2.7 15.5 1.0
O B:HOH2180 2.8 20.7 1.0
C B:SER172 3.4 15.5 1.0
CB B:SER172 3.9 16.0 1.0
N B:SER172 3.9 14.4 1.0
CA B:SER172 3.9 14.8 1.0
NA B:NA1261 4.0 29.5 1.0
N B:THR173 4.2 15.2 1.0
O A:HOH2085 4.4 21.0 1.0
CA B:THR173 4.5 16.9 1.0
O A:HOH2121 4.6 28.2 1.0
O B:HOH2126 4.9 22.4 1.0
O B:HOH2124 4.9 27.7 1.0

Reference:

A.Warden, J.Newman, T.S.Peat, S.Seabrook, M.Williams, G.Dojchinov, V.Haritos. Rational Engineering of A Mesophilic Carbonic Anhydrase to An Extreme Halotolerant Biocatalyst To Be Published.
Page generated: Mon Oct 7 19:48:26 2024

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