Iodine in PDB 4kca: 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;

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

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

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 63;

Binding sites:

The binding sites of Iodine 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 Iodine atom.
In total 63 binding sites of Iodine where determined in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library, PDB code: 4kca:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 63 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 Iodine with other atoms in the I 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:I701 b:35.4 occ:1.00 N A:VAL212 3.6 22.8 1.0 CB A:ASN174 3.9 32.8 1.0 CB A:VAL212 4.1 22.4 1.0 O A:HOH1207 4.1 44.2 1.0 CG1 A:VAL212 4.1 22.4 1.0 CB A:THR200 4.2 26.6 1.0 CA A:ASN174 4.3 30.1 1.0 CA A:SER211 4.3 25.8 1.0 CG2 A:THR200 4.3 24.7 1.0 O A:HOH1098 4.4 46.6 1.0 CD2 A:TYR210 4.4 25.7 1.0 C A:SER211 4.4 23.6 1.0 CA A:VAL212 4.5 21.5 1.0 O A:TYR210 4.5 23.0 1.0 CE2 A:TYR210 4.5 22.9 1.0 OG1 A:THR200 4.5 29.9 1.0

Iodine binding site 2 out of 63 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 Iodine with other atoms in the I 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 A:I702 b:44.4 occ:1.00 O A:HOH901 3.0 30.5 1.0 O A:HOH1159 3.4 36.3 1.0 O A:HOH875 4.1 33.5 1.0 CD A:LYS365 4.1 27.9 1.0 CD1 A:TYR348 4.2 27.3 1.0 CG1 A:VAL359 4.3 24.6 1.0 CB A:LYS365 4.3 21.2 1.0 CG A:LYS365 4.3 24.0 1.0 CG2 A:VAL359 4.3 23.8 1.0 CE1 A:TYR348 4.5 30.4 1.0 O A:HOH1196 4.5 33.3 1.0 CE A:LYS365 4.7 33.2 1.0 O A:HOH1104 4.9 48.8 1.0

Iodine binding site 3 out of 63 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 Iodine with other atoms in the I binding site number 3 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:I703 b:80.1 occ:1.00 O A:HOH953 3.1 30.7 1.0 NH1 A:ARG428 3.5 27.8 1.0 CD A:ARG428 3.8 31.7 1.0 NE A:ARG627 4.1 40.9 1.0 CG A:ARG627 4.1 28.4 1.0 CB A:ASN628 4.2 23.6 1.0 CD A:ARG627 4.4 33.4 1.0 CA A:ASN628 4.5 22.7 1.0 CZ A:ARG428 4.6 30.0 1.0 N A:ASN628 4.6 21.4 1.0 NE A:ARG428 4.7 29.5 1.0 O A:HOH1193 4.8 38.7 1.0 CB A:ARG428 4.9 29.1 1.0 CG A:ARG428 5.0 30.2 1.0

Iodine binding site 4 out of 63 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 Iodine with other atoms in the I binding site number 4 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:I704 b:99.9 occ:1.00 O A:HOH1190 3.1 32.3 1.0 O A:HOH1027 3.5 48.9 1.0 O A:HOH892 3.8 28.2 1.0 CB A:SER530 4.0 22.0 1.0 N A:ALA531 4.1 27.4 1.0 CA A:ALA531 4.1 28.9 1.0 C A:SER530 4.2 25.3 1.0 CB A:ALA531 4.4 30.1 1.0 O A:SER530 4.4 25.9 1.0 O A:HOH841 4.5 28.6 1.0 O A:HOH810 4.5 29.8 1.0 OE1 A:GLN510 4.8 27.4 1.0 CA A:SER530 4.8 24.4 1.0 O A:HOH867 4.8 24.2 1.0 CA A:GLY384 4.9 26.4 1.0

Iodine binding site 5 out of 63 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 Iodine with other atoms in the I binding site number 5 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:I705 b:77.1 occ:1.00 N B:TYR405 3.8 28.4 1.0 N A:TYR405 3.9 30.2 1.0 CB B:TYR405 4.1 25.7 1.0 CB A:TYR405 4.1 27.0 1.0 OD1 B:ASP404 4.3 43.5 1.0 OD1 A:ASP404 4.4 45.4 1.0 CA B:TYR405 4.5 24.4 1.0 CA A:TYR405 4.6 26.1 1.0 O B:SER403 4.6 43.2 1.0 CA B:ASP404 4.6 33.9 1.0 N A:ASN406 4.7 25.9 1.0 C B:ASP404 4.7 30.9 1.0 N B:ASN406 4.7 24.1 1.0 CA A:ASP404 4.8 33.6 1.0 C A:ASP404 4.8 32.2 1.0 O A:HOH1048 4.8 49.0 1.0 O B:HOH995 4.9 45.7 1.0 O A:HOH1165 4.9 41.6 1.0 ND2 A:ASN406 4.9 38.2 1.0 O A:SER403 5.0 46.5 1.0

Iodine binding site 6 out of 63 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 Iodine with other atoms in the I binding site number 6 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:I706 b:72.7 occ:1.00 NH1 A:ARG560 3.5 28.1 1.0 CD A:ARG560 3.9 26.6 1.0 O A:ALA402 4.0 48.3 1.0 N A:TYR405 4.0 30.2 1.0 C A:SER403 4.1 44.6 1.0 O A:SER403 4.1 46.5 1.0 CB A:TYR405 4.1 27.0 1.0 N A:ASP404 4.4 38.0 1.0 CA A:SER403 4.4 41.2 1.0 CD2 A:TYR405 4.4 24.1 1.0 CA A:TYR405 4.4 26.1 1.0 CZ A:ARG560 4.5 28.4 1.0 C A:ASP404 4.6 32.2 1.0 NE A:ARG560 4.7 24.7 1.0 CA A:ASP404 4.8 33.6 1.0 CG A:TYR405 4.8 24.3 1.0 C A:ALA402 4.9 40.9 1.0 O A:HOH1165 5.0 41.6 1.0

Iodine binding site 7 out of 63 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 Iodine with other atoms in the I binding site number 7 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:I707 b:64.9 occ:1.00 O A:HOH969 3.3 46.4 1.0 N A:SER123 3.5 22.2 1.0 CA A:VAL122 4.0 22.1 1.0 CB A:VAL122 4.2 23.4 1.0 C A:VAL122 4.3 21.2 1.0 CB A:ALA158 4.3 24.6 1.0 O A:SER123 4.3 24.7 1.0 CG1 A:VAL122 4.3 25.5 1.0 CB A:SER123 4.4 22.0 1.0 CA A:SER123 4.4 21.6 1.0 O A:HOH1012 4.4 41.2 1.0 OG A:SER123 4.7 23.0 1.0 C A:SER123 4.8 23.2 1.0

Iodine binding site 8 out of 63 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 Iodine with other atoms in the I binding site number 8 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:I708 b:86.2 occ:1.00 OD2 A:ASP513 3.5 45.8 1.0 ND2 A:ASN511 3.8 23.5 1.0 O A:LEU625 4.0 20.6 1.0 O A:HOH949 4.1 39.0 1.0 CD1 A:TRP515 4.3 25.3 1.0 CD2 A:LEU625 4.3 27.6 1.0 CG A:LEU625 4.4 26.8 1.0 N A:ARG627 4.4 23.1 1.0 CG A:ASP513 4.5 39.0 1.0 CB A:ASP513 4.5 29.3 1.0 C A:ASN626 4.6 22.5 1.0 C A:LEU625 4.6 21.4 1.0 CB A:LYS604 4.7 26.0 1.0 CG A:ASN511 4.8 22.9 1.0 O A:HOH1184 4.8 50.9 1.0 CB A:LEU625 4.8 22.7 1.0 CA A:ARG627 4.9 22.9 1.0 CG A:TRP515 4.9 22.9 1.0 OD1 A:ASN511 4.9 22.3 1.0 CA A:ASN626 4.9 22.7 1.0 CG A:LYS604 5.0 33.2 1.0 NE1 A:TRP515 5.0 23.2 1.0

Iodine binding site 9 out of 63 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 Iodine with other atoms in the I binding site number 9 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:I709 b:57.3 occ:1.00 O A:HOH932 3.0 28.9 1.0 O A:HOH1208 3.2 43.4 1.0 CB A:ASN542 3.7 34.2 1.0 CA A:ASN542 3.8 31.5 1.0 N A:ASN542 4.2 28.8 1.0 OG1 A:THR541 4.2 39.8 1.0 C A:THR541 4.5 28.3 1.0 O A:THR541 4.6 26.4 1.0 O A:HOH868 4.6 28.9 1.0 O A:HOH879 4.8 35.0 1.0 O A:HOH1073 4.8 49.1 1.0

Iodine binding site 10 out of 63 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 Iodine with other atoms in the I binding site number 10 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:I710 b:58.4 occ:1.00 O A:HOH1017 3.5 40.8 1.0 N A:ASP575 3.9 30.2 1.0 N A:ALA574 3.9 29.8 1.0 CG A:ASP575 3.9 37.5 1.0 OD2 A:ASP575 4.1 37.9 1.0 CB A:ASP575 4.2 34.0 1.0 CB A:ASN573 4.2 29.1 1.0 OD1 A:ASP575 4.2 34.1 1.0 O A:HOH1016 4.2 49.0 1.0 CB A:ALA574 4.3 34.6 1.0 CA A:ALA574 4.5 30.7 1.0 C A:ALA574 4.6 32.7 1.0 C A:ASN573 4.6 26.6 1.0 CA A:ASP575 4.7 33.2 1.0 CA A:ASN573 4.9 27.0 1.0 CG A:ASN573 5.0 30.4 1.0 O A:HOH1131 5.0 44.6 1.0

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