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Sodium in PDB 4kca: Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library

Enzymatic activity of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library

All present enzymatic activity of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library:
3.2.1.99;

Protein crystallography data

The structure of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library, PDB code: 4kca was solved by C.R.Santos, C.C.Polo, M.C.M.F.Costa, A.F.Z.Nascimento, D.W.S.Wong, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.84 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.909, 114.318, 167.201, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.6

Other elements in 4kca:

The structure of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library also contains other interesting chemical elements:

Iodine (I) 63 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library (pdb code 4kca). 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 Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library, PDB code: 4kca:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4kca

Go back to Sodium Binding Sites List in 4kca
Sodium binding site 1 out of 2 in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library


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 Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na735

b:41.2
occ:1.00
O A:HOH918 2.3 24.8 1.0
O A:HOH813 2.4 29.7 1.0
O A:HOH992 2.4 33.3 1.0
O A:HOH1082 2.5 24.4 1.0
O A:HOH874 3.0 45.7 1.0
NE2 A:HIS475 3.3 26.3 1.0
CD2 A:HIS475 3.6 23.1 1.0
O A:HOH929 3.7 33.6 1.0
O A:PRO309 3.8 20.5 1.0
OG A:SER128 4.0 33.2 1.0
O A:SER378 4.1 19.9 1.0
CD2 A:TYR379 4.3 23.1 1.0
O A:ASN476 4.4 21.4 1.0
CE1 A:HIS475 4.5 22.3 1.0
CA A:ALA377 4.6 17.6 1.0
C A:ALA377 4.7 18.6 1.0
C A:PRO309 4.7 19.9 1.0
O A:ALA377 4.7 18.1 1.0
CB A:ALA377 4.8 18.9 1.0
O A:ASP308 4.9 19.4 1.0
CG A:HIS475 4.9 22.2 1.0
CE2 A:TYR379 4.9 26.1 1.0
C A:ASP308 4.9 19.2 1.0
O A:ALA218 5.0 24.1 1.0

Sodium binding site 2 out of 2 in 4kca

Go back to Sodium Binding Sites List in 4kca
Sodium binding site 2 out of 2 in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library


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 Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na732

b:40.1
occ:1.00
O B:HOH1068 2.2 30.1 1.0
O B:HOH873 2.4 26.2 1.0
O B:HOH845 2.5 30.4 1.0
O B:HOH864 2.5 24.7 1.0
O B:HOH1061 2.9 49.4 1.0
NE2 B:HIS475 3.3 27.1 1.0
CD2 B:HIS475 3.6 23.7 1.0
O B:PRO309 3.8 21.5 1.0
O B:HOH977 4.1 33.5 1.0
O B:SER378 4.1 20.3 1.0
OG B:SER128 4.1 30.2 1.0
CD2 B:TYR379 4.2 25.7 1.0
O B:ASN476 4.3 22.6 1.0
CE1 B:HIS475 4.5 23.8 1.0
CA B:ALA377 4.6 19.6 1.0
C B:ALA377 4.6 20.4 1.0
O B:ALA377 4.6 20.2 1.0
C B:PRO309 4.7 20.5 1.0
CB B:ALA377 4.8 20.2 1.0
CG B:HIS475 4.8 22.7 1.0
CE2 B:TYR379 4.9 27.0 1.0
O B:ASP308 4.9 20.7 1.0

Reference:

C.R.Santos, C.C.Polo, M.C.Costa, A.F.Nascimento, A.N.Meza, J.Cota, Z.B.Hoffmam, R.V.Honorato, P.S.Oliveira, G.H.Goldman, H.J.Gilbert, R.A.Prade, R.Ruller, F.M.Squina, D.W.Wong, M.T.Murakami. Mechanistic Strategies For Catalysis Adopted By Evolutionary Distinct Family 43 Arabinanases. J.Biol.Chem. V. 289 7362 2014.
ISSN: ISSN 0021-9258
PubMed: 24469445
DOI: 10.1074/JBC.M113.537167
Page generated: Tue Dec 15 06:49:39 2020

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