Sodium in PDB 6qug: Ghk Tagged Mbp-NUP98(1-29)

The structure of Ghk Tagged Mbp-NUP98(1-29), PDB code: 6qug was solved by T.Huyton, D.Gorlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.14 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.910, 286.780, 110.780, 90.00, 92.01, 90.00
R / Rfree (%)	19.7 / 22.8

The structure of Ghk Tagged Mbp-NUP98(1-29) also contains other interesting chemical elements:

Copper

(Cu)

12 atoms

The binding sites of Sodium atom in the Ghk Tagged Mbp-NUP98(1-29) (pdb code 6qug). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Ghk Tagged Mbp-NUP98(1-29), PDB code: 6qug:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Ghk Tagged Mbp-NUP98(1-29)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ghk Tagged Mbp-NUP98(1-29) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:43.1 occ:0.92 O A:LEU160 2.5 48.6 1.0 O A:GLY187 2.8 49.5 1.0 N A:ASP164 2.9 46.8 1.0 O A:ILE161 3.1 40.6 1.0 CB A:ASP164 3.3 52.0 1.0 CD2 A:PHE250 3.4 47.9 1.0 CE2 A:PHE250 3.5 52.0 1.0 CA A:ASP164 3.6 48.9 1.0 C A:ILE161 3.6 43.3 1.0 CA A:GLY191 3.6 47.3 1.0 N A:ALA163 3.7 43.1 1.0 C A:LEU160 3.7 44.8 1.0 N A:GLY191 3.8 48.4 1.0 C A:GLY187 3.8 48.0 1.0 CB A:ALA163 3.8 44.6 1.0 C A:ALA163 3.9 47.4 1.0 CA A:ALA163 4.0 44.2 1.0 CA A:ILE161 4.0 46.2 1.0 C A:ASP164 4.2 55.4 1.0 C A:ALA162 4.3 45.3 1.0 N A:ILE161 4.3 43.6 1.0 N A:ALA162 4.4 46.5 1.0 N A:GLY165 4.5 58.3 1.0 CA A:GLY187 4.5 49.8 1.0 CG A:PHE250 4.6 50.8 1.0 CG A:ASP164 4.7 53.2 1.0 N A:ALA188 4.7 46.8 1.0 O A:ALA162 4.8 43.6 1.0 CZ A:PHE250 4.8 52.2 1.0 C A:ALA190 4.8 47.5 1.0 CA A:ALA162 4.8 44.7 1.0 CA A:ALA188 4.9 45.6 1.0 CA A:LEU160 4.9 46.5 1.0 C A:GLY191 5.0 47.0 1.0

Sodium binding site 2 out of 5 in the Ghk Tagged Mbp-NUP98(1-29)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ghk Tagged Mbp-NUP98(1-29) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:69.9 occ:1.00 O B:ALA77 2.4 61.5 1.0 O B:ILE104 2.7 53.9 1.0 N B:ILE266 2.8 64.5 1.0 CA B:GLY265 3.5 58.0 1.0 O B:ILE266 3.5 61.1 1.0 C B:ILE104 3.5 57.7 1.0 C B:ALA77 3.6 61.7 1.0 C B:GLY265 3.6 61.6 1.0 CG2 B:ILE79 3.6 60.8 1.0 CA B:ILE266 3.7 63.5 1.0 N B:ALA77 3.8 63.9 1.0 CB B:ILE266 3.9 65.7 1.0 CB B:LEU76 4.0 57.5 1.0 C B:ILE266 4.0 61.3 1.0 CA B:ALA77 4.1 63.2 1.0 CA B:ILE104 4.2 58.2 1.0 N B:ALA105 4.3 56.2 1.0 CD2 B:LEU76 4.3 56.9 1.0 C B:LEU76 4.4 61.1 1.0 CA B:LEU76 4.4 60.0 1.0 CG1 B:ILE266 4.4 62.7 1.0 CB B:ALA77 4.5 60.5 1.0 CA B:ALA105 4.5 56.5 1.0 CG B:LEU76 4.6 56.4 1.0 N B:GLU78 4.7 63.3 1.0 CD1 B:LEU76 4.8 57.5 1.0 O B:GLY265 4.8 58.6 1.0 CB B:ILE104 4.9 57.2 1.0 N B:GLY265 4.9 55.5 1.0 CD1 B:ILE266 4.9 62.7 1.0 N B:ILE79 5.0 65.6 1.0 CB B:ILE79 5.0 63.9 1.0

Sodium binding site 3 out of 5 in the Ghk Tagged Mbp-NUP98(1-29)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ghk Tagged Mbp-NUP98(1-29) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na404 b:43.2 occ:1.00 ND2 H:ASN150 3.6 53.8 1.0 CB H:TYR210 4.1 54.2 1.0 N H:TYR210 4.1 54.5 1.0 OD1 H:ASN150 4.1 51.5 1.0 CG H:ASN150 4.2 53.2 1.0 CB H:GLN152 4.3 57.9 1.0 CB H:ASP209 4.3 54.1 1.0 CG H:GLU153 4.5 58.3 1.0 CA H:TYR210 4.7 53.6 1.0 CG H:GLN152 4.9 57.9 1.0 CA H:ASP209 4.9 53.4 1.0

Sodium binding site 4 out of 5 in the Ghk Tagged Mbp-NUP98(1-29)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ghk Tagged Mbp-NUP98(1-29) within 5.0Å range: probe atom residue distance (Å) B Occ I:Na405 b:61.0 occ:0.95 O3 I:GLC401 2.5 44.0 1.0 OE1 I:GLU111 2.7 53.6 1.0 OH I:TYR155 2.8 44.5 1.0 CZ I:TYR155 3.4 43.7 1.0 CA I:GLY260 3.5 45.9 1.0 C2 I:GLC401 3.6 51.4 1.0 CE1 I:TYR155 3.6 44.7 1.0 C3 I:GLC401 3.6 50.6 1.0 CB I:GLU111 3.6 52.0 1.0 N I:GLY260 3.8 44.6 1.0 O2 I:GLC401 3.8 60.9 1.0 CD I:GLU111 3.8 52.5 1.0 CE I:MET330 4.0 49.0 1.0 CB I:ALA63 4.1 45.3 1.0 CG I:GLU111 4.2 51.0 1.0 C I:GLY260 4.2 45.1 1.0 O I:GLY260 4.4 47.6 1.0 O I:GLU111 4.4 52.0 1.0 CE2 I:TYR155 4.5 41.7 1.0 C4 I:GLC401 4.5 49.8 1.0 CD1 I:TYR155 4.8 43.7 1.0 C I:GLU111 4.8 49.2 1.0 C I:VAL259 4.8 46.3 1.0 CA I:GLU111 4.8 50.4 1.0 C1 I:GLC401 4.9 47.8 1.0 CH2 I:TRP230 5.0 46.0 1.0 OE2 I:GLU111 5.0 60.2 1.0

Sodium binding site 5 out of 5 in the Ghk Tagged Mbp-NUP98(1-29)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ghk Tagged Mbp-NUP98(1-29) within 5.0Å range: probe atom residue distance (Å) B Occ J:Na404 b:46.0 occ:1.00 O J:ILE104 2.4 50.0 1.0 O J:ALA77 2.5 53.0 1.0 N J:ILE266 2.9 44.0 1.0 C J:ILE104 3.3 51.0 1.0 O J:ILE266 3.5 42.1 1.0 CA J:GLY265 3.5 46.0 1.0 C J:GLY265 3.7 46.0 1.0 C J:ALA77 3.7 45.1 1.0 N J:ALA77 3.7 40.9 1.0 CB J:LEU76 3.8 36.9 1.0 CA J:ILE266 3.8 43.1 1.0 CG2 J:ILE79 3.9 45.3 1.0 CD2 J:LEU76 4.0 34.6 1.0 CA J:ILE104 4.0 49.2 1.0 C J:ILE266 4.1 41.4 1.0 CB J:ILE266 4.1 45.6 1.0 N J:ALA105 4.2 47.0 1.0 CA J:LEU76 4.2 37.7 1.0 C J:LEU76 4.3 38.7 1.0 CA J:ALA77 4.3 43.7 1.0 CG J:LEU76 4.3 34.9 1.0 CD1 J:LEU76 4.4 35.8 1.0 CA J:ALA105 4.5 44.6 1.0 CB J:ILE104 4.6 48.7 1.0 CB J:ALA77 4.7 42.4 1.0 CG1 J:ILE266 4.7 50.2 1.0 N J:GLU78 4.8 48.7 1.0 O J:GLY265 4.8 46.8 1.0 CB J:ALA105 4.9 43.2 1.0 N J:GLY265 4.9 44.1 1.0

T.Huyton, D.Goerlich. Using the Copper Binding Peptide Ghk For Phasing Structures To Be Published.