Iodine in PDB 2i1w: Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes

All present enzymatic activity of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes:
2.7.1.23;

The structure of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes, PDB code: 2i1w was solved by G.Poncet-Montange, L.Assairi, S.Arold, S.Pochet, G.Labesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.37 / 2.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.612, 119.017, 67.937, 90.00, 102.08, 90.00
R / Rfree (%)	19.4 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes (pdb code 2i1w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 22 binding sites of Iodine where determined in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes, PDB code: 2i1w:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:36.4 occ:0.65 O A:HOH555 3.6 33.7 1.0 NE A:ARG247 3.7 41.2 1.0 N A:ASP77 3.8 37.3 1.0 N A:GLY66 3.8 37.1 1.0 CB A:ASP77 3.9 38.9 1.0 CD1 A:PHE245 3.9 35.0 1.0 C A:ALA76 4.1 37.7 1.0 CA A:ALA76 4.1 37.8 1.0 NH2 A:ARG247 4.3 41.6 1.0 CA A:ILE65 4.3 36.2 1.0 O A:TYR75 4.4 37.1 1.0 CZ A:ARG247 4.4 41.6 1.0 CG2 A:ILE65 4.4 37.5 1.0 O A:GLY66 4.4 37.1 1.0 N A:ALA76 4.5 37.3 1.0 CA A:ASP77 4.5 37.9 1.0 CD A:ARG247 4.5 40.8 1.0 CE1 A:PHE245 4.5 34.9 1.0 C A:TYR75 4.6 37.0 1.0 C A:ILE65 4.6 36.6 1.0 CA A:GLY66 4.7 37.6 1.0 O A:PHE64 4.7 34.5 1.0 O A:ALA246 4.7 38.0 1.0 CG A:PHE245 4.8 33.2 1.0 O A:ALA76 4.9 38.8 1.0 CB A:PHE245 4.9 33.5 1.0

Iodine binding site 2 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:43.6 occ:0.50 I A:IOD502 0.0 43.6 0.5 I A:IOD502 2.6 35.5 0.3 N A:TRP254 3.8 34.6 1.0 CB A:TRP254 3.9 34.7 1.0 O B:HOH576 3.9 37.8 1.0 C A:PRO252 4.1 34.5 1.0 CA A:PRO252 4.1 33.5 1.0 ND2 B:ASN140 4.1 35.2 1.0 N A:ARG255 4.2 34.6 1.0 N A:PHE253 4.2 34.7 1.0 CA A:TRP254 4.2 34.8 1.0 CD1 A:TRP254 4.3 35.5 1.0 CB B:ASN140 4.3 37.9 1.0 O A:PRO252 4.5 36.0 1.0 CG A:TRP254 4.5 35.7 1.0 CD1 B:ILE142 4.5 44.3 1.0 CB A:PRO252 4.6 33.6 1.0 C A:TRP254 4.6 34.6 1.0 C A:PHE253 4.8 35.3 1.0 CG B:ASN140 4.8 37.2 1.0 O B:ILE139 4.9 37.1 1.0 CA A:PHE253 5.0 35.5 1.0

Iodine binding site 3 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:35.5 occ:0.30 I A:IOD502 0.0 35.5 0.3 I A:IOD502 2.6 43.6 0.5 CE1 B:HIS205 3.5 36.9 1.0 N A:PHE253 3.6 34.7 1.0 O A:PHE251 3.8 32.0 1.0 ND2 B:ASN140 3.8 35.2 1.0 CD1 A:TRP254 3.8 35.5 1.0 N A:TRP254 4.0 34.6 1.0 NE2 B:HIS205 4.1 40.1 1.0 CB A:PHE253 4.2 35.0 1.0 C A:PRO252 4.2 34.5 1.0 NE2 A:HIS173 4.2 34.3 1.0 CA A:PRO252 4.3 33.5 1.0 CA A:PHE253 4.3 35.5 1.0 ND1 B:HIS205 4.4 35.7 1.0 CD2 A:HIS173 4.5 35.1 1.0 CG A:TRP254 4.6 35.7 1.0 NE1 A:TRP254 4.6 37.3 1.0 C A:PHE253 4.7 35.3 1.0 CB A:TRP254 4.7 34.7 1.0 C A:PHE251 4.8 32.4 1.0 CG B:ASN140 5.0 37.2 1.0

Iodine binding site 4 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I513 b:49.9 occ:0.40 CG2 A:THR6 3.3 42.2 1.0 CG A:GLN54 3.9 45.0 1.0 CB A:GLN54 3.9 42.7 1.0 CA A:ALA51 4.0 39.0 1.0 CE2 A:TYR55 4.3 41.1 1.0 OG1 A:THR6 4.3 40.3 1.0 CB A:THR6 4.4 41.1 1.0 O A:SER50 4.5 39.9 1.0 N A:ALA51 4.5 39.4 1.0 CB A:ALA51 4.5 38.8 1.0 CE A:MET4 4.6 40.6 1.0 CD A:GLN54 4.6 47.3 1.0 C A:SER50 4.7 39.5 1.0 OH A:TYR55 4.9 41.4 1.0

Iodine binding site 5 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I533 b:48.9 occ:0.30 O A:HOH610 2.0 53.2 1.0 CG1 A:VAL98 3.6 41.0 1.0 NH1 A:ARG247 3.7 42.8 1.0 I A:IOD534 3.7 39.2 0.2 CE1 A:TYR100 3.8 40.9 1.0 CE1 A:HIS173 4.0 32.7 1.0 CB A:PHE251 4.5 31.9 1.0 OH A:TYR100 4.5 43.9 1.0 NE2 A:HIS173 4.6 34.3 1.0 CZ A:TYR100 4.6 41.9 1.0 CD1 A:TYR100 4.7 40.7 1.0 CG A:PRO174 4.9 39.1 1.0 CB A:VAL98 4.9 40.7 1.0 CZ A:ARG247 4.9 41.6 1.0

Iodine binding site 6 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I534 b:39.2 occ:0.20 N A:PHE251 3.2 32.8 1.0 CB A:PHE251 3.7 31.9 1.0 I A:IOD533 3.7 48.9 0.3 CA A:SER250 4.0 33.9 1.0 CA A:PHE251 4.0 32.4 1.0 C A:SER250 4.1 32.8 1.0 CG2 A:VAL98 4.1 41.2 1.0 O A:ARG249 4.2 35.0 1.0 NH1 A:ARG247 4.2 42.8 1.0 CG1 A:VAL98 4.4 41.0 1.0 CG A:ARG247 4.5 39.5 1.0 OG A:SER250 4.5 35.7 1.0 CD A:ARG247 4.6 40.8 1.0 CB A:ARG247 4.8 37.6 1.0 O A:PHE251 4.8 32.0 1.0 CB A:VAL98 4.8 40.7 1.0 CB A:SER250 4.9 33.7 1.0 C A:PHE251 4.9 32.4 1.0 N A:SER250 5.0 34.8 1.0 C A:ARG249 5.0 35.6 1.0 O A:HOH610 5.0 53.2 1.0

Iodine binding site 7 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I530 b:45.3 occ:0.30 O A:HOH596 2.3 42.5 1.0 N C:ALA185 3.9 40.1 1.0 CD2 C:LEU167 3.9 37.4 1.0 CD2 A:LEU167 4.1 37.9 1.0 N A:ALA185 4.3 37.8 1.0 CB C:ALA185 4.4 40.5 1.0 CA C:ALA185 4.5 40.1 1.0 CA C:MET184 4.5 41.0 1.0 C C:MET184 4.6 40.3 1.0 CA A:MET184 4.7 38.5 1.0 O C:HOH547 4.7 19.6 1.0 O C:GLU183 4.9 39.1 1.0 C A:MET184 4.9 38.1 1.0 CB A:MET184 5.0 38.9 1.0 CB A:ALA185 5.0 36.9 1.0 CA A:ALA185 5.0 37.5 1.0

Iodine binding site 8 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I531 b:46.0 occ:0.30 O A:HOH535 2.4 29.2 1.0 CG2 A:THR117 3.0 41.7 1.0 CG A:LEU119 3.9 40.0 1.0 NZ A:LYS241 4.0 48.0 1.0 C A:TYR118 4.2 39.1 1.0 CG A:LYS104 4.2 37.3 1.0 N A:LEU119 4.3 37.9 1.0 O A:TYR118 4.3 40.0 1.0 N A:TYR118 4.4 39.9 1.0 CD2 A:LEU119 4.4 40.5 1.0 CB A:THR117 4.5 41.0 1.0 CE A:LYS104 4.6 38.1 1.0 C A:THR117 4.6 40.3 1.0 CB A:LEU119 4.6 38.4 1.0 CA A:TYR118 4.7 39.7 1.0 CA A:LEU119 4.7 37.7 1.0 CD1 A:LEU119 4.8 40.4 1.0 CD A:LYS104 4.8 37.7 1.0 CB A:LYS104 4.8 37.3 1.0 O A:THR117 4.9 39.6 1.0

Iodine binding site 9 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:I532 b:41.3 occ:0.30 OE1 A:GLU123 3.1 48.5 1.0 C A:ASP222 3.6 50.0 1.0 CA A:ASP222 3.6 48.5 1.0 N A:HIS223 3.7 51.7 1.0 OD1 A:ASN122 3.8 44.0 1.0 CB A:ASP222 4.0 48.0 1.0 O A:ASP222 4.1 49.5 1.0 CD A:GLU123 4.1 43.0 1.0 CB A:ASN122 4.2 38.2 1.0 CD2 A:LEU49 4.3 39.3 1.0 OD1 A:ASP222 4.4 45.5 1.0 OE2 A:GLU123 4.4 43.1 1.0 CG A:ASN122 4.4 39.2 1.0 CG A:ASP222 4.6 46.9 1.0 O A:HOH570 4.7 27.5 1.0 N A:ASP222 4.9 48.1 1.0 CA A:HIS223 5.0 53.3 1.0

Iodine binding site 10 out of 22 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes


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 Nad Kinase 1 From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:I508 b:37.3 occ:0.70 I B:IOD508 0.0 37.3 0.7 I B:IOD508 3.1 41.3 0.3 O A:HOH543 3.4 24.2 1.0 CB B:TRP254 3.9 37.3 1.0 N B:TRP254 4.0 36.4 1.0 CA B:PRO252 4.0 35.1 1.0 ND2 A:ASN140 4.1 32.9 1.0 N B:ARG255 4.1 37.5 1.0 CD1 B:TRP254 4.1 34.6 1.0 C B:PRO252 4.1 35.5 1.0 N B:PHE253 4.3 35.7 1.0 CA B:TRP254 4.3 37.0 1.0 CB B:PRO252 4.3 35.2 1.0 CB A:ASN140 4.4 37.0 1.0 CG B:TRP254 4.4 37.0 1.0 O B:PRO252 4.6 35.3 1.0 O A:ILE139 4.6 37.5 1.0 C B:TRP254 4.7 37.7 1.0 CD1 A:ILE142 4.7 37.5 1.0 CG A:ASN140 4.8 36.6 1.0 CB B:ARG255 4.9 37.3 1.0 C B:PHE253 4.9 36.4 1.0

G.Poncet-Montange, L.Assairi, S.Arold, S.Pochet, G.Labesse. Nad Kinases Use Substrate-Assisted Catalysis For Specific Recognition of Nad. J.Biol.Chem. V. 282 33925 2007.
ISSN: ISSN 0021-9258
PubMed: 17686780
DOI: 10.1074/JBC.M701394200