Sodium in PDB 4qm6: Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna

The structure of Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna, PDB code: 4qm6 was solved by U.Das, L.K.Wang, P.Smith, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.38 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.310, 74.420, 119.620, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.5

The structure of Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna (pdb code 4qm6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna, PDB code: 4qm6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:33.7 occ:1.00 O A:HOH1333 2.3 42.8 1.0 O A:HOH1287 2.5 46.7 1.0 NH2 A:ARG87 2.9 12.4 1.0 O A:HOH1166 3.3 25.8 1.0 O A:HOH1120 3.4 18.0 1.0 OG A:SER140 3.5 14.7 1.0 CA A:SER140 3.8 14.2 1.0 O A:HOH1196 3.8 34.5 1.0 CB A:GLU84 3.8 13.8 1.0 OE2 A:GLU147 3.9 17.1 1.0 O A:HOH1200 3.9 45.4 1.0 CB A:SER140 4.0 13.5 1.0 O A:HOH1192 4.1 27.1 1.0 CZ A:ARG87 4.2 11.7 1.0 O A:LYS139 4.4 20.1 1.0 O A:HOH1139 4.4 21.1 1.0 N A:GLU84 4.4 14.0 1.0 N A:SER140 4.5 13.8 1.0 CG A:GLU84 4.5 17.2 1.0 CA A:GLU84 4.6 13.6 1.0 NH1 A:ARG87 4.6 12.1 1.0 C A:LYS139 4.7 16.2 1.0 O A:SER140 4.7 14.4 1.0 C A:SER140 4.8 14.7 1.0 NZ A:LYS139 5.0 61.7 1.0

Sodium binding site 2 out of 5 in the Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:29.9 occ:1.00 CD B:ARG131 2.7 20.6 0.5 O B:ARG131 2.8 14.5 1.0 OE1 B:GLU110 2.8 21.0 1.0 O B:HOH1185 2.9 25.8 1.0 NE B:ARG131 3.1 17.3 0.5 O B:HOH1274 3.1 38.9 1.0 CG B:GLN135 3.2 22.7 1.0 C B:ARG131 3.6 12.3 1.0 CA B:ARG131 3.7 14.1 0.5 CA B:ARG131 3.7 12.8 0.5 CD B:GLU110 3.7 17.7 1.0 CB B:THR134 3.7 13.5 1.0 CG B:ARG131 3.7 20.6 0.5 N B:GLN135 3.7 13.5 1.0 CG B:ARG131 3.8 8.0 0.5 CD B:GLN135 4.0 42.8 1.0 CG2 B:THR134 4.0 14.5 1.0 CZ B:ARG131 4.2 13.3 0.5 NE2 B:GLN135 4.2 45.9 1.0 CB B:ARG131 4.2 12.8 0.5 CB B:GLN135 4.2 15.2 1.0 CB B:ARG131 4.3 16.5 0.5 O B:HOH1342 4.3 42.5 1.0 CA B:GLN135 4.3 14.8 1.0 CG B:GLU110 4.4 17.1 1.0 C B:THR134 4.4 12.9 1.0 CB B:GLU110 4.4 16.7 1.0 CA B:THR134 4.5 12.0 1.0 OE2 B:GLU110 4.6 20.6 1.0 O B:HOH1197 4.7 33.1 1.0 OG1 B:THR134 4.7 14.7 1.0 O B:ILE130 4.7 13.5 1.0 NH1 B:ARG131 4.8 14.6 0.5 OE1 B:GLN135 4.8 39.7 1.0 N B:LYS132 4.9 13.4 1.0 N B:THR134 4.9 11.4 1.0 O B:HOH1216 4.9 26.4 1.0 N B:ARG131 4.9 12.8 1.0 NH2 B:ARG131 4.9 21.3 0.5

Sodium binding site 3 out of 5 in the Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1004 b:37.0 occ:1.00 ND2 B:ASN49 2.3 30.8 1.0 O B:HOH1321 2.4 42.7 1.0 O D:HOH108 2.8 18.9 1.0 O B:GLN124 2.8 19.9 1.0 O B:HOH1327 3.1 49.6 1.0 CG B:ASN49 3.3 45.5 1.0 CG1 B:VAL125 3.4 14.5 1.0 OD1 B:ASN49 3.6 55.8 1.0 O B:HOH1266 3.6 39.3 1.0 C B:GLN124 3.8 17.6 1.0 CG B:ARG123 4.0 23.4 1.0 CA B:VAL125 4.1 13.0 1.0 O B:HOH1329 4.2 50.8 1.0 N B:VAL125 4.3 14.4 1.0 CB B:VAL125 4.3 14.1 1.0 C5 D:C1 4.4 13.4 1.0 CD B:ARG123 4.4 22.9 1.0 O B:HOH1137 4.4 16.9 1.0 C6 D:C1 4.4 13.0 1.0 O B:HOH1224 4.5 31.7 1.0 CB B:ASN49 4.7 18.5 1.0 O B:ASN49 4.7 19.6 1.0 NE2 B:GLN51 4.8 15.2 1.0 N B:GLN124 4.8 18.2 1.0 O5' D:C1 4.9 24.1 0.4 CA B:GLN124 4.9 16.4 1.0 NH1 B:ARG123 5.0 17.6 1.0 O B:HOH1117 5.0 15.5 1.0 CA B:ASN49 5.0 17.8 1.0

Sodium binding site 4 out of 5 in the Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1005 b:39.3 occ:1.00 O A:HOH1241 2.6 33.1 1.0 O B:HOH1191 2.6 29.6 1.0 OE2 B:GLU160 2.7 19.7 1.0 O A:HOH1298 3.3 48.2 1.0 CD B:GLU160 3.5 19.1 1.0 CG B:GLU160 3.6 15.1 1.0 CD A:ARG146 3.6 30.9 1.0 CG A:ARG146 4.0 20.9 1.0 OG B:SER157 4.3 18.8 1.0 O B:HOH1118 4.3 18.0 1.0 O A:HOH1233 4.3 27.5 1.0 OE1 B:GLU160 4.7 16.5 1.0 CB A:ARG146 4.9 15.8 1.0 NH1 A:ARG146 4.9 28.2 1.0 NE A:ARG146 5.0 29.5 1.0

Sodium binding site 5 out of 5 in the Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Bacterial Polynucleotide Kinase Bound to Gtp and Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1006 b:42.8 occ:1.00 OD2 B:ASP59 2.8 19.3 1.0 C B:GLY55 3.5 13.2 1.0 O B:GLY55 3.5 14.1 1.0 O B:HOH1285 3.5 44.6 1.0 CG B:ASP59 3.7 16.7 1.0 CA B:GLY55 3.8 15.0 1.0 N B:ALA56 3.9 14.1 1.0 OD1 B:ASP59 4.0 19.9 1.0 O D:HOH129 4.2 50.1 1.0 O B:HOH1204 4.3 31.3 1.0 CA B:ALA56 4.5 13.1 1.0 O B:HOH1138 4.8 21.8 1.0 CB B:ASP59 4.9 13.2 1.0

U.Das, L.K.Wang, P.Smith, A.Munir, S.Shuman. Structures of Bacterial Polynucleotide Kinase in A Michaelis Complex with NTPMG2+ and 5'-Oh Rna and A Mixed Substrate-Product Complex with NTPMG2+ and A 5'-Phosphorylated Oligonucleotide. J.Bacteriol. 2014.
ISSN: ESSN 1098-5530
PubMed: 25266383
DOI: 10.1128/JB.02197-14