Sodium in PDB 7zkt: Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine

The structure of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine, PDB code: 7zkt was solved by S.Morera, D.Kopecny, A.Vigouroux, P.Briozzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.55 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.01, 138.43, 129.78, 90, 94.03, 90
R / Rfree (%)	17.6 / 20.2

The binding sites of Sodium atom in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine (pdb code 7zkt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine, PDB code: 7zkt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:27.3 occ:1.00 OE2 A:GLU33 2.9 49.4 1.0 ND2 A:ASN181 3.2 27.5 1.0 N A:LEU178 3.2 30.9 1.0 C2P A:COA301 3.6 52.6 0.5 S1P A:COA301 3.7 28.4 0.5 C2P A:COA301 3.8 28.9 0.5 CB A:LEU178 3.8 31.6 1.0 CD A:GLU33 3.8 53.5 1.0 CG A:LEU178 3.8 34.6 1.0 CG2 A:VAL177 3.9 34.0 1.0 CA A:VAL177 3.9 29.8 1.0 CD1 A:LEU178 3.9 35.4 1.0 CG A:GLU33 4.0 35.8 1.0 C A:VAL177 4.0 32.9 1.0 CZ3 B:TRP199 4.0 36.4 1.0 CA A:LEU178 4.1 31.2 1.0 CG A:ASN181 4.1 37.8 1.0 CB A:ASN181 4.1 31.0 1.0 C3P A:COA301 4.3 28.5 0.5 CB A:VAL177 4.5 33.3 1.0 C3P A:COA301 4.6 52.2 0.5 CH2 B:TRP199 4.7 37.0 1.0 O5P A:COA301 4.8 19.7 0.5 CE A:LYS302 4.8 52.4 1.0 O5P A:COA301 4.9 49.2 0.5 O A:LEU178 4.9 36.6 1.0 O A:CYS176 4.9 31.4 1.0 CE3 B:TRP199 4.9 35.3 1.0 OE1 A:GLU33 5.0 52.1 1.0 N4P A:COA301 5.0 26.1 0.5 S1P A:COA301 5.0 53.0 0.5

Sodium binding site 2 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:30.2 occ:1.00 OE2 B:GLU33 2.7 67.3 1.0 ND2 B:ASN181 3.1 31.3 1.0 N B:LEU178 3.2 34.9 1.0 S1P B:COA301 3.4 48.9 0.5 C2P B:COA301 3.5 36.1 0.5 CG2 B:VAL177 3.8 34.5 1.0 CB B:LEU178 3.8 34.2 1.0 CA B:VAL177 3.8 31.3 1.0 CD B:GLU33 3.9 72.3 1.0 CG B:LEU178 3.9 38.2 1.0 C2P B:COA301 4.0 49.2 0.5 CB B:ASN181 4.0 37.2 1.0 C B:VAL177 4.0 36.0 1.0 CD1 B:LEU178 4.0 39.8 1.0 CG B:ASN181 4.1 49.4 1.0 CA B:LEU178 4.1 34.1 1.0 C3P B:COA301 4.2 49.4 0.5 CZ3 A:TRP199 4.2 39.5 1.0 CB B:VAL177 4.4 34.5 1.0 C3P B:COA301 4.6 35.2 0.5 CG B:GLU33 4.7 48.9 1.0 O5P B:COA301 4.7 38.6 0.5 O B:CYS176 4.7 34.4 0.5 O B:CYS176 4.8 34.3 0.5 OE1 B:GLU33 4.8 66.9 1.0 CE A:LYS304 4.8 64.1 1.0 O5P B:COA301 4.8 52.0 0.5 N4P B:COA301 4.8 49.7 0.5 S1P B:COA301 4.8 37.0 0.5 O B:LEU178 4.9 36.3 1.0 CH2 A:TRP199 4.9 40.5 1.0 N B:VAL177 5.0 30.4 1.0

Sodium binding site 3 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:24.1 occ:1.00 OE2 C:GLU33 2.7 54.8 1.0 ND2 C:ASN181 3.1 30.4 1.0 N C:LEU178 3.2 29.0 1.0 C2P C:COA301 3.2 30.8 0.5 S1P C:COA301 3.5 31.5 0.5 C2P C:COA301 3.6 49.7 0.5 CD C:GLU33 3.7 53.0 1.0 CA C:VAL177 3.8 29.0 1.0 CG2 C:VAL177 3.9 32.1 1.0 CB C:LEU178 3.9 28.5 1.0 CG C:LEU178 3.9 32.5 1.0 CG C:GLU33 3.9 41.8 1.0 C C:VAL177 4.0 32.4 1.0 CD1 C:LEU178 4.0 32.8 1.0 CG C:ASN181 4.1 37.5 1.0 CB C:ASN181 4.1 27.7 1.0 CA C:LEU178 4.1 28.8 1.0 CZ3 D:TRP199 4.2 32.8 1.0 C3P C:COA301 4.2 28.5 0.5 CB C:VAL177 4.5 32.4 1.0 S1P C:COA301 4.7 52.5 0.5 O5P C:COA301 4.7 29.7 0.5 O C:CYS176 4.8 32.3 0.5 C3P C:COA301 4.8 45.1 0.5 OE1 C:GLU33 4.8 43.4 1.0 CH2 D:TRP199 4.8 34.1 1.0 O5P C:COA301 4.9 42.0 0.5 O C:CYS176 4.9 31.1 0.5 CE D:LYS301 4.9 51.6 1.0 O C:LEU178 4.9 34.8 1.0 N4P C:COA301 4.9 26.9 0.5 N C:VAL177 5.0 29.8 1.0

Sodium binding site 4 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:39.9 occ:1.00 ND2 D:ASN181 3.1 36.0 1.0 OE2 D:GLU33 3.1 84.5 1.0 N D:LEU178 3.3 38.2 1.0 S1P D:COA302 3.3 53.1 0.5 C2P D:COA302 3.5 38.4 0.5 CG2 D:VAL177 3.8 37.4 1.0 CA D:VAL177 3.8 35.1 1.0 CB D:LEU178 3.9 41.9 1.0 CG D:LEU178 4.0 46.7 1.0 C D:VAL177 4.0 39.3 1.0 CG D:ASN181 4.0 49.7 1.0 CD D:GLU33 4.1 83.0 1.0 CB D:ASN181 4.1 36.8 1.0 C2P D:COA302 4.1 51.5 0.5 CD1 D:LEU178 4.2 48.1 1.0 CA D:LEU178 4.2 40.0 1.0 CZ3 C:TRP199 4.2 41.6 1.0 C3P D:COA302 4.3 50.0 0.5 CG D:GLU33 4.4 60.5 1.0 C3P D:COA302 4.4 37.0 0.5 CB D:VAL177 4.4 36.8 1.0 CE C:LYS303 4.6 55.8 1.0 O D:CYS176 4.7 37.4 0.5 O5P D:COA302 4.7 42.3 0.5 O5P D:COA302 4.8 54.9 0.5 O D:CYS176 4.8 37.7 0.5 CH2 C:TRP199 4.9 43.2 1.0 N4P D:COA302 4.9 50.2 0.5 O D:LEU178 4.9 43.9 1.0 S1P D:COA302 4.9 40.7 0.5 NZ C:LYS303 4.9 57.6 1.0 N D:VAL177 5.0 35.3 1.0 N4P D:COA302 5.0 37.4 0.5

Sodium binding site 5 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na305 b:72.2 occ:1.00 OE2 D:GLU44 3.6 88.0 1.0 N D:GLU43 3.9 65.2 1.0 NH2 D:ARG27 4.0 74.3 1.0 CA D:THR42 4.2 59.9 1.0 CG D:GLU43 4.3 82.3 1.0 CB D:THR42 4.3 61.8 1.0 OE2 D:GLU43 4.3 109.4 1.0 CD D:GLU43 4.5 113.2 1.0 CD D:GLU44 4.5 110.1 1.0 OE1 D:GLU44 4.6 106.5 1.0 CB D:GLU43 4.6 69.9 1.0 C D:THR42 4.6 65.3 1.0 CG2 D:THR42 4.7 56.4 1.0 NH1 D:ARG27 4.8 70.2 1.0 CZ D:ARG27 4.9 88.4 1.0 CA D:GLU43 4.9 65.5 1.0

Sodium binding site 6 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ E:Na302 b:37.5 occ:1.00 OE2 E:GLU33 2.9 73.0 1.0 ND2 E:ASN181 3.1 49.3 1.0 N E:LEU178 3.2 46.5 1.0 S1P E:COA301 3.5 53.4 0.5 C2P E:COA301 3.5 51.4 0.5 CG2 E:VAL177 3.8 52.0 1.0 CD E:GLU33 3.8 69.5 1.0 CA E:VAL177 3.9 47.0 1.0 CB E:LEU178 3.9 44.8 1.0 C2P E:COA301 3.9 52.7 0.5 CG E:LEU178 3.9 46.0 1.0 C E:VAL177 4.0 49.3 1.0 CD1 E:LEU178 4.0 44.4 1.0 CG E:ASN181 4.0 69.7 1.0 CG E:GLU33 4.1 50.9 1.0 CB E:ASN181 4.1 51.0 1.0 CZ3 F:TRP199 4.1 48.1 1.0 CA E:LEU178 4.1 46.0 1.0 C3P E:COA301 4.2 53.2 0.5 CB E:VAL177 4.4 51.5 1.0 C3P E:COA301 4.6 51.6 0.5 CH2 F:TRP199 4.7 48.0 1.0 CE F:LYS301 4.8 56.9 1.0 O5P E:COA301 4.8 50.7 0.5 O5P E:COA301 4.9 53.0 0.5 S1P E:COA301 4.9 50.0 0.5 O E:CYS176 4.9 53.1 1.0 O E:LEU178 4.9 51.9 1.0 N4P E:COA301 4.9 51.5 0.5 OE1 E:GLU33 5.0 66.1 1.0

Sodium binding site 7 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ F:Na303 b:48.0 occ:1.00 S1P F:COA302 2.8 69.0 0.5 OE2 F:GLU33 3.1 107.7 1.0 ND2 F:ASN181 3.1 61.9 1.0 C2P F:COA302 3.4 48.3 0.5 N F:LEU178 3.4 48.9 1.0 C2P F:COA302 3.5 70.0 0.5 CG2 F:VAL177 3.8 49.4 1.0 CA F:VAL177 3.9 46.4 1.0 C3P F:COA302 4.1 70.2 0.5 C F:VAL177 4.1 50.1 1.0 CD F:GLU33 4.1 106.8 1.0 CG F:ASN181 4.1 69.5 1.0 CB F:LEU178 4.1 53.5 1.0 CG F:LEU178 4.1 59.2 1.0 CZ3 E:TRP199 4.2 60.4 1.0 CB F:ASN181 4.2 55.5 1.0 CD1 F:LEU178 4.3 61.7 1.0 CA F:LEU178 4.4 51.5 1.0 CE E:LYS303 4.4 80.0 1.0 CB F:VAL177 4.4 49.1 1.0 C3P F:COA302 4.4 46.2 0.5 CG F:GLU33 4.4 79.4 1.0 O5P F:COA302 4.5 51.5 0.5 O5P F:COA302 4.6 76.9 0.5 O F:CYS176 4.6 49.5 1.0 S1P F:COA302 4.7 49.5 0.5 N4P F:COA302 4.8 72.2 0.5 CH2 E:TRP199 4.8 63.0 1.0 NZ E:LYS303 5.0 87.8 1.0 N F:VAL177 5.0 46.4 1.0 C5P F:COA302 5.0 75.0 0.5

Sodium binding site 8 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ G:Na302 b:36.8 occ:1.00 OE2 G:GLU33 3.0 94.8 1.0 ND2 G:ASN181 3.1 39.0 1.0 S1P G:COA301 3.2 51.4 0.5 N G:LEU178 3.2 43.9 1.0 C2P G:COA301 3.7 39.2 0.5 C2P G:COA301 3.8 51.5 0.5 CA G:VAL177 3.8 42.6 1.0 CG2 G:VAL177 3.9 47.6 1.0 CB G:LEU178 3.9 45.5 1.0 CG G:LEU178 4.0 49.9 1.0 C G:VAL177 4.0 46.1 1.0 CD G:GLU33 4.0 84.2 1.0 CZ3 H:TRP199 4.1 52.0 1.0 CG G:ASN181 4.1 48.4 1.0 CD1 G:LEU178 4.1 50.8 1.0 CA G:LEU178 4.2 45.1 1.0 CB G:ASN181 4.2 44.4 1.0 C3P G:COA301 4.2 52.6 0.5 CG G:GLU33 4.3 57.7 1.0 CB G:VAL177 4.5 47.3 1.0 CE H:LYS301 4.6 68.5 1.0 C3P G:COA301 4.6 39.6 0.5 O G:CYS176 4.6 45.0 1.0 O5P G:COA301 4.7 40.5 0.5 O5P G:COA301 4.7 55.9 0.5 CH2 H:TRP199 4.7 53.8 1.0 S1P G:COA301 4.8 37.9 0.5 N4P G:COA301 4.9 53.8 0.5 N G:VAL177 4.9 42.4 1.0 NZ H:LYS301 4.9 74.0 1.0 O G:LEU178 4.9 48.1 1.0

Sodium binding site 9 out of 9 in the Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Moss Spermine/Spermidine Acetyl Transferase (Ppssat) in Complex with Coa and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:40.5 occ:1.00 OE2 H:GLU33 2.9 72.5 1.0 ND2 H:ASN181 3.1 56.0 1.0 N H:LEU178 3.2 45.4 1.0 S1P H:COA302 3.4 47.9 0.5 C2P H:COA302 3.7 75.1 0.5 CD H:GLU33 3.8 77.4 1.0 CG2 H:VAL177 3.9 51.0 1.0 C2P H:COA302 3.9 47.6 0.5 CB H:LEU178 3.9 44.6 1.0 CA H:VAL177 3.9 44.0 1.0 CG H:LEU178 3.9 46.8 1.0 CD1 H:LEU178 4.0 48.2 1.0 C H:VAL177 4.0 47.6 1.0 CZ3 G:TRP199 4.1 49.7 1.0 CG H:GLU33 4.1 55.2 1.0 CG H:ASN181 4.1 63.6 1.0 CB H:ASN181 4.1 45.3 1.0 CA H:LEU178 4.2 44.0 1.0 C3P H:COA302 4.4 46.4 0.5 CB H:VAL177 4.5 49.6 1.0 CH2 G:TRP199 4.6 50.5 1.0 O5P H:COA302 4.6 36.9 0.5 CE G:LYS303 4.7 65.8 1.0 C3P H:COA302 4.7 78.3 0.5 O H:CYS176 4.8 47.7 1.0 O5P H:COA302 4.8 81.3 0.5 O H:LEU178 4.9 47.1 1.0 OE1 H:GLU33 5.0 72.6 1.0

J.Belicek, E.Luptakova, D.Kopecny, J.Frommel, A.Vigouroux, S.Cavar Zeljkovic, F.Jagic, P.Briozzo, D.J.Kopecny, P.Tarkowski, J.Nisler, N.De Diego, S.Morera, M.Kopecna. Biochemical and Structural Basis of Polyamine, Lysine and Ornithine Acetylation Catalyzed By Spermine/Spermidine N-Acetyl Transferase in Moss and Maize. Plant J. 2023.
ISSN: ESSN 1365-313X
PubMed: 36786691
DOI: 10.1111/TPJ.16148