Sodium in PDB 7fjb: Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure

All present enzymatic activity of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure:
2.7.2.15;

The structure of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure, PDB code: 7fjb was solved by W.Wenyue, Q.Zhang, M.Bartlam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.40 / 2.44
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	101.22, 152.374, 131.011, 90, 90, 90
R / Rfree (%)	19.9 / 26.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure (pdb code 7fjb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure, PDB code: 7fjb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:39.7 occ:1.00 O A:ASP243 2.8 47.0 1.0 CD A:ARG307 3.0 27.3 1.0 NH1 A:ARG307 3.0 30.3 1.0 N A:ASP243 3.2 25.4 1.0 O A:SER241 3.3 29.4 1.0 O A:GLY234 3.5 22.3 1.0 CG B:PRO162 3.6 21.5 1.0 C A:ASP243 3.6 37.0 1.0 C A:GLY242 3.7 22.9 1.0 NE A:ARG307 3.7 32.1 1.0 CZ A:ARG307 3.8 35.4 1.0 CA A:GLY242 3.9 19.8 1.0 CA A:ASP243 3.9 27.4 1.0 CD B:PRO162 3.9 24.0 1.0 N A:MET236 4.0 27.6 1.0 CG A:ARG307 4.1 16.1 1.0 C A:SER241 4.3 30.3 1.0 C A:VAL235 4.3 18.9 1.0 CB A:ASP243 4.4 30.2 1.0 CA A:MET236 4.5 19.2 1.0 O A:GLY242 4.5 24.8 1.0 CB A:MET236 4.6 17.3 1.0 N A:GLY242 4.6 21.2 1.0 O A:VAL235 4.7 23.0 1.0 CA A:VAL235 4.7 17.3 1.0 C A:GLY234 4.7 22.0 1.0 CB A:ARG307 4.7 15.2 1.0 CB B:PRO162 4.8 21.2 1.0 N A:ILE244 4.8 42.5 1.0 NH2 A:ARG307 5.0 45.6 1.0

Sodium binding site 2 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:40.0 occ:1.00 OG A:SER226 2.8 16.6 1.0 O A:CYS212 2.8 27.0 1.0 O A:SER233 2.9 22.6 1.0 N A:VAL235 3.0 18.2 1.0 CA A:GLY234 3.2 19.4 1.0 CB A:SER226 3.3 14.1 1.0 C A:GLY234 3.5 22.0 1.0 CA A:SER213 3.6 16.9 1.0 CG2 A:VAL235 3.6 14.5 1.0 N A:MET227 3.6 29.5 1.0 CG A:MET227 3.6 17.8 1.0 C A:SER226 3.8 25.2 1.0 C A:SER233 3.8 26.1 1.0 C A:CYS212 3.8 20.0 1.0 CE A:MET237 3.9 20.0 1.0 CB A:SER213 4.0 21.8 1.0 N A:GLY234 4.0 24.4 1.0 CA A:VAL235 4.1 17.3 1.0 CA A:SER226 4.2 14.5 1.0 CA A:MET227 4.2 25.9 1.0 N A:SER213 4.2 16.2 1.0 CB A:VAL235 4.3 14.5 1.0 O A:SER226 4.3 34.6 1.0 O A:VAL235 4.3 23.0 1.0 CB A:MET227 4.4 16.3 1.0 CG1 A:VAL235 4.5 13.9 1.0 CE A:MET227 4.5 23.1 1.0 C A:SER213 4.7 16.0 1.0 C A:VAL235 4.7 18.9 1.0 N A:VAL214 4.7 13.4 1.0 SD A:MET227 4.7 25.7 1.0 O A:GLY234 4.7 22.3 1.0 N A:SER226 5.0 14.3 1.0

Sodium binding site 3 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:29.8 occ:1.00 NH2 A:ARG309 2.6 17.4 1.0 O A:ASN345 2.8 14.4 1.0 O B:MET317 2.9 13.5 1.0 CB A:ASN345 3.4 15.4 1.0 C A:ASN345 3.6 18.6 1.0 O A:ARG344 3.6 24.2 1.0 N B:GLY320 3.6 14.9 1.0 CA B:GLY320 3.7 14.3 1.0 O B:GLN318 3.8 14.7 1.0 CZ A:ARG309 3.9 15.4 1.0 CD2 A:LEU346 4.0 13.4 1.0 CA A:ASN345 4.1 20.8 1.0 C B:GLN318 4.1 14.3 1.0 C B:MET317 4.2 18.5 1.0 C B:MET319 4.4 20.7 1.0 NH1 A:ARG309 4.4 23.2 1.0 C A:ARG344 4.5 17.2 1.0 CA B:GLN318 4.6 18.1 1.0 N A:LEU346 4.6 20.3 1.0 CG A:ASN345 4.6 43.3 1.0 N B:MET319 4.7 16.4 1.0 N A:ASN345 4.8 32.7 1.0 NE A:ARG309 4.9 13.9 1.0 N B:GLN318 4.9 13.6 1.0 ND2 A:ASN345 4.9 32.1 1.0 CG A:LEU346 5.0 18.2 1.0

Sodium binding site 4 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:53.0 occ:1.00 O A:MET317 2.9 27.8 1.0 O B:ASN345 2.9 33.4 1.0 N A:GLY320 3.1 27.5 1.0 NH2 B:ARG309 3.2 26.1 1.0 CA A:GLY320 3.3 17.7 1.0 O A:GLN318 3.4 18.2 1.0 C A:GLN318 3.7 15.3 1.0 C A:MET319 3.8 26.5 1.0 CB B:ASN345 4.0 51.7 1.0 C B:ASN345 4.0 31.6 1.0 O B:ARG344 4.0 18.6 1.0 C A:MET317 4.1 19.4 1.0 N A:MET319 4.2 20.0 1.0 CD2 B:LEU346 4.3 16.3 1.0 CA A:MET319 4.4 22.4 1.0 O A:MET319 4.4 28.6 1.0 CZ B:ARG309 4.4 17.4 1.0 CA A:GLN318 4.4 16.6 1.0 CA B:ASN345 4.5 37.1 1.0 CG B:ASN345 4.6 73.4 1.0 OD1 B:ASN345 4.6 83.2 1.0 N A:GLN318 4.7 18.0 1.0 C A:GLY320 4.8 23.4 1.0 NH1 B:ARG309 4.8 17.7 1.0 C B:ARG344 4.9 26.1 1.0

Sodium binding site 5 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:43.1 occ:1.00 NE2 A:GLN152 2.7 38.3 1.0 O A:TYR176 2.7 18.6 1.0 O A:THR148 3.1 37.6 1.0 C A:TYR176 3.5 25.2 1.0 CB A:THR148 3.5 19.5 1.0 CA A:TYR176 3.7 19.3 1.0 CB A:HIS151 3.7 17.0 1.0 CD A:GLN152 3.7 45.3 1.0 C A:THR148 3.8 18.7 1.0 C A:HIS151 3.8 19.9 1.0 N A:GLN152 3.9 19.0 1.0 CG A:GLN152 3.9 32.7 1.0 O A:HIS151 4.0 21.7 1.0 CD1 A:TYR176 4.0 27.5 1.0 CA A:THR148 4.0 18.6 1.0 CB A:TYR176 4.0 20.0 1.0 OG1 A:THR148 4.2 28.8 1.0 CA A:HIS151 4.2 18.7 1.0 CA A:GLN152 4.3 20.0 1.0 CG A:TYR176 4.5 25.7 1.0 CG2 A:THR148 4.5 19.6 1.0 O A:GLY177 4.6 29.7 1.0 N A:HIS151 4.6 19.4 1.0 NH2 A:ARG174 4.6 20.9 1.0 O A:GLY95 4.7 46.7 1.0 N A:GLY177 4.7 25.0 1.0 CB A:GLN152 4.7 33.3 1.0 CG A:HIS151 4.8 20.8 1.0 N A:ALA149 4.8 19.2 1.0 OE1 A:GLN152 4.9 49.9 1.0

Sodium binding site 6 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:46.2 occ:1.00 OG1 A:THR225 2.8 27.6 1.0 N A:PHE178 3.0 16.5 1.0 O A:PHE178 3.1 15.5 1.0 CB A:MET227 3.1 16.3 1.0 CB A:SER213 3.4 21.8 1.0 N A:MET227 3.4 29.5 1.0 SD A:MET227 3.7 25.7 1.0 C A:PHE178 3.7 16.1 1.0 CG A:MET227 3.7 17.8 1.0 CA A:GLY177 3.8 16.8 1.0 CA A:MET227 3.8 25.9 1.0 OG A:SER213 3.8 24.9 1.0 CA A:PHE178 3.9 16.6 1.0 C A:GLY177 3.9 16.9 1.0 CB A:THR225 3.9 24.5 1.0 CG2 A:THR225 4.0 15.4 1.0 NE2 A:HIS151 4.1 16.8 1.0 N A:SER226 4.1 14.3 1.0 O A:MET227 4.1 35.0 1.0 C A:MET227 4.4 24.1 1.0 C A:THR225 4.5 14.9 1.0 CB A:PHE178 4.5 17.1 1.0 C A:SER226 4.6 25.2 1.0 OG A:SER226 4.6 16.6 1.0 CE1 A:HIS151 4.6 15.3 1.0 CD2 A:HIS151 4.7 17.5 1.0 CA A:THR225 4.8 19.9 1.0 N A:HIS179 4.8 16.2 1.0 CA A:SER213 4.8 16.9 1.0 O A:VAL214 4.9 15.9 1.0 CA A:SER226 4.9 14.5 1.0 CB A:HIS179 4.9 19.8 1.0 NE2 A:HIS183 4.9 14.0 1.0

Sodium binding site 7 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:71.1 occ:1.00 O B:GLY320 3.1 31.9 1.0 N A:HIS347 3.1 30.9 1.0 N A:PHE348 3.3 24.0 1.0 CB A:HIS347 3.3 42.2 1.0 O A:ASN345 3.4 14.4 1.0 CA A:HIS347 3.6 34.5 1.0 C A:HIS347 3.8 25.4 1.0 C A:ASN345 3.8 18.6 1.0 ND1 A:HIS347 3.9 68.4 1.0 C B:GLY320 3.9 21.5 1.0 CA B:GLY320 4.0 14.3 1.0 CG A:HIS347 4.1 62.8 1.0 C A:LEU346 4.1 18.9 1.0 CB A:PHE348 4.3 14.7 1.0 CA A:PHE348 4.3 20.8 1.0 N A:LEU346 4.3 20.3 1.0 CA A:LEU346 4.4 14.3 1.0 CA A:ASN345 4.5 20.8 1.0 CD1 A:PHE348 4.5 15.8 1.0 CB A:ASN345 4.7 15.4 1.0 O A:HIS347 4.9 17.1 1.0 CG A:PHE348 4.9 14.1 1.0

Sodium binding site 8 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:50.8 occ:1.00 O A:ARG90 2.7 30.4 1.0 N A:ALA10 2.9 28.1 1.0 ND2 A:ASN126 3.1 41.8 1.0 CA A:ASN9 3.4 25.9 1.0 C A:ASN9 3.6 27.4 1.0 O A:ILE8 3.7 35.3 1.0 CG A:ASN126 3.8 31.1 1.0 C A:ARG90 3.8 25.9 1.0 N A:ARG90 3.8 24.1 1.0 CB A:ALA10 3.9 31.9 1.0 CA A:ASN126 3.9 31.3 1.0 CA A:ALA10 3.9 40.9 1.0 CB A:ASN126 3.9 25.3 1.0 N A:ASN9 4.1 30.7 1.0 C A:ILE8 4.1 24.0 1.0 OD1 A:ASN9 4.2 37.5 1.0 O A:ASN126 4.2 36.9 1.0 CA A:ARG90 4.2 21.8 1.0 O A:ALA10 4.3 35.6 1.0 CB A:HIS89 4.3 25.1 1.0 C A:HIS89 4.5 26.7 1.0 CB A:ARG90 4.5 24.2 1.0 C A:ASN126 4.5 36.4 1.0 CG2 A:ILE8 4.5 26.3 1.0 C A:ALA10 4.5 38.0 1.0 CA A:HIS89 4.6 25.8 1.0 CB A:ASN9 4.6 22.6 1.0 OD1 A:ASN126 4.7 43.1 1.0 CD2 A:HIS89 4.7 28.8 1.0 CG A:ASN9 4.8 32.3 1.0 O A:ASN9 4.9 37.2 1.0 CG A:HIS89 4.9 28.6 1.0 N A:VAL91 5.0 28.8 1.0

Sodium binding site 9 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:48.0 occ:1.00 O A:GLN152 2.9 26.9 1.0 O A:LEU154 2.9 20.6 1.0 NH2 A:ARG174 3.2 20.9 1.0 C A:GLN152 3.2 20.2 1.0 CA A:GLN152 3.5 20.0 1.0 N A:LEU154 3.5 21.8 1.0 O A:HIS151 3.6 21.7 1.0 CD1 A:TRP159 3.7 21.3 1.0 C A:LEU154 3.8 19.7 1.0 NH1 A:ARG174 3.8 26.7 1.0 OE1 A:GLN152 3.8 49.9 1.0 CB A:LEU154 3.9 18.2 1.0 CA A:LEU154 4.0 18.7 1.0 CZ A:ARG174 4.0 27.7 1.0 CD A:GLN152 4.0 45.3 1.0 NE1 A:TRP159 4.0 22.6 1.0 NE2 A:GLN152 4.0 38.3 1.0 N A:THR153 4.1 19.4 1.0 C A:THR153 4.3 19.3 1.0 CB A:GLN152 4.5 33.3 1.0 C A:HIS151 4.5 19.9 1.0 N A:GLN152 4.5 19.0 1.0 CG A:TRP159 4.6 21.3 1.0 CA A:THR153 4.6 19.7 1.0 CG A:GLN152 4.8 32.7 1.0 CE2 A:TRP159 4.9 23.5 1.0

Sodium binding site 10 out of 14 in the Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:40.6 occ:1.00 OG1 A:THR153 2.5 23.6 1.0 O A:PHE150 2.7 20.5 1.0 CG2 A:THR153 3.1 20.0 1.0 N A:SER222 3.1 28.0 1.0 CB A:THR153 3.3 19.3 1.0 CA A:GLN221 3.5 17.8 1.0 CB A:GLN221 3.7 18.5 1.0 C A:GLN221 3.8 26.4 1.0 C A:PHE150 3.9 17.6 1.0 CB A:SER222 3.9 16.0 1.0 CE1 A:PHE150 3.9 17.1 1.0 CD1 A:PHE150 3.9 24.5 1.0 CG A:GLN221 3.9 23.9 1.0 CA A:SER222 4.0 20.2 1.0 N A:THR153 4.4 19.4 1.0 O A:SER222 4.4 17.3 1.0 CG A:PHE150 4.4 28.2 1.0 CZ A:PHE150 4.4 16.4 1.0 CA A:THR153 4.5 19.7 1.0 CA A:PHE150 4.5 17.8 1.0 O A:GLY220 4.6 30.3 1.0 C A:SER222 4.7 18.2 1.0 N A:GLN221 4.8 26.1 1.0 CD2 A:PHE150 4.8 20.1 1.0 CE2 A:PHE150 4.8 15.8 1.0 CD A:GLN221 4.9 33.8 1.0 N A:HIS151 4.9 19.4 1.0

W.Wu, Q.Zhang, M.Bartlam. Kpacka (Pduw) with Amppnp, Sodium Acetate Complex Structure To Be Published.