Sodium in PDB 4hx0: Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution

The structure of Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution, PDB code: 4hx0 was solved by K.M.Boyko, M.A.Gorbacheva, D.A.Korzhenevskiy, A.V.Lipkin, V.O.Popov, M.V.Kovalchuk, I.A.Shumilin, W.Minor, I.G.Shabalin, A.M.Golubev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	63.196, 52.722, 53.508, 90.00, 105.05, 90.00
R / Rfree (%)	17.2 / 24.5

The binding sites of Sodium atom in the Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution (pdb code 4hx0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution, PDB code: 4hx0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution


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 A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:35.3 occ:1.00 N A:ILE2 3.2 30.0 1.0 O A:HOH317 3.3 35.7 1.0 CE1 A:HIS121 3.5 24.7 1.0 O A:HOH375 3.5 44.5 1.0 CA A:MET1 3.8 35.3 1.0 CG1 A:ILE2 3.9 27.0 1.0 CB A:ILE2 3.9 27.8 1.0 CD1 A:ILE2 3.9 26.8 1.0 C A:MET1 4.0 31.6 1.0 NE2 A:HIS-4 4.1 54.0 1.0 CD2 A:HIS-4 4.1 52.9 1.0 CA A:ILE2 4.1 28.5 1.0 NE2 A:HIS121 4.3 26.5 1.0 CB A:MET1 4.3 37.6 1.0 CD1 A:LEU7 4.3 23.3 1.0 CG A:MET1 4.4 42.3 1.0 O A:HIS0 4.4 36.4 1.0 ND1 A:HIS121 4.5 24.8 1.0 O A:ILE2 4.5 26.4 1.0 O A:HOH326 4.5 31.0 1.0 CD2 A:LEU7 4.6 24.4 1.0 C A:ILE2 4.8 27.5 1.0 CG A:LEU7 5.0 22.9 1.0 N A:MET1 5.0 35.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution


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 A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:38.3 occ:1.00 O A:ALA33 2.9 23.4 1.0 CD2 A:HIS-4 3.2 52.9 1.0 O A:VAL37 3.2 29.4 1.0 CA A:ALA33 3.6 21.1 1.0 C A:ALA33 3.6 23.3 1.0 C A:VAL37 3.7 29.4 1.0 NE2 A:HIS-4 3.7 54.0 1.0 C A:GLY36 3.8 27.3 1.0 CG A:HIS-4 3.8 52.7 1.0 O A:HIS0 3.8 36.4 1.0 N A:VAL37 3.9 26.9 1.0 CA A:GLY36 3.9 26.3 1.0 CB A:HIS0 3.9 44.1 1.0 CB A:ALA33 4.0 21.1 1.0 CA A:PRO38 4.0 31.9 1.0 N A:PRO38 4.1 29.8 1.0 ND1 A:HIS0 4.1 49.2 1.0 O A:GLY36 4.2 27.6 1.0 N A:GLY36 4.3 25.9 1.0 C A:HIS0 4.3 36.9 1.0 CB A:HIS-4 4.3 51.4 1.0 CG A:HIS0 4.4 45.1 1.0 CA A:VAL37 4.5 28.5 1.0 CE1 A:HIS-4 4.5 52.2 1.0 ND1 A:HIS-4 4.5 52.6 1.0 CA A:HIS0 4.7 39.3 1.0 CA A:HIS-4 4.7 47.7 1.0 N A:VAL39 4.8 31.9 1.0 O A:HIS-3 4.8 39.9 1.0 N A:ALA33 4.8 19.8 1.0 O A:PHE32 4.9 19.0 1.0 N A:LEU34 4.9 21.5 1.0 CB A:PRO38 4.9 30.8 1.0 O A:HOH395 4.9 33.2 1.0 C A:PRO38 5.0 33.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Putative Nucleotidyltransferase (TM1012) From Thermotoga Maritima at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:37.8 occ:1.00 O A:HOH381 2.9 44.2 1.0 ND2 A:ASN112 3.3 25.4 1.0 NZ A:LYS115 3.4 19.0 1.0 O A:HOH316 3.4 36.1 1.0 CB A:ASN23 3.6 21.0 1.0 OD1 A:ASN23 3.7 20.7 1.0 OD1 A:ASN112 3.7 22.1 1.0 CG A:ASN23 3.8 21.8 1.0 CA A:ASN23 3.8 20.4 1.0 CG A:ASN112 3.9 22.7 1.0 N A:ASN23 4.5 21.2 1.0 O A:VAL22 4.7 23.1 1.0 O A:HOH364 4.7 21.2 1.0 ND2 A:ASN23 4.8 22.2 1.0 CE A:LYS115 4.8 18.9 1.0 C A:VAL22 4.9 23.0 1.0

K.M.Boyko, M.A.Gorbacheva, D.A.Korzhenevskiy, A.V.Lipkin, V.O.Popov, M.V.Kovalchuk, I.A.Shumilin, W.Minor, I.G.Shabalin, A.M.Golubev. Crystal Structure of Putative Nucleotidyltransferase with Two Mpd Molecules in the Active Site. To Be Published.