Sodium in PDB 4us5: Crystal Structure of Apo-MSNO8

The structure of Crystal Structure of Apo-MSNO8, PDB code: 4us5 was solved by S.Maier, T.Pflueger, S.Loesgen, K.Asmus, E.Broetz, T.Paululat, A.Zeeck, S.Andrade, A.Bechthold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.05 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.005, 102.902, 160.697, 90.00, 90.00, 90.00
R / Rfree (%)	18.795 / 21.65

The structure of Crystal Structure of Apo-MSNO8 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Apo-MSNO8 (pdb code 4us5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 26 binding sites of Sodium where determined in the Crystal Structure of Apo-MSNO8, PDB code: 4us5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 26 in the Crystal Structure of Apo-MSNO8


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 Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1335 b:28.1 occ:1.00 O A:SER20 2.7 19.4 1.0 O A:HOH2012 2.8 20.1 1.0 OE2 A:GLU7 2.8 25.1 1.0 NH1 A:ARG318 3.2 25.1 1.0 OG A:SER24 3.2 23.9 1.0 C A:SER20 3.6 18.9 1.0 CA A:ALA9 3.6 20.9 1.0 N A:SER24 3.6 17.3 1.0 CD A:GLU7 3.7 22.5 1.0 CA A:SER20 3.8 20.2 1.0 CB A:HIS23 3.9 18.7 1.0 OE1 A:GLU7 3.9 22.2 1.0 CB A:ALA9 4.0 21.5 1.0 C A:HIS23 4.1 17.9 1.0 CB A:SER20 4.1 22.0 1.0 CA A:SER24 4.1 17.9 1.0 CD A:PRO10 4.1 21.9 1.0 C A:ALA9 4.2 20.9 1.0 CB A:SER24 4.2 20.6 1.0 CZ A:ARG318 4.3 24.0 1.0 O A:PRO10 4.4 21.3 1.0 O A:HOH2030 4.4 35.0 1.0 N A:PRO10 4.4 21.7 1.0 CA A:HIS23 4.5 18.1 1.0 N A:ALA9 4.6 21.6 1.0 NH2 A:ARG318 4.7 25.6 1.0 O A:HOH2254 4.7 20.4 1.0 O A:HOH2033 4.7 22.9 1.0 O A:HIS23 4.7 18.8 1.0 N A:LEU21 4.8 19.8 1.0 CG A:GLU7 4.9 21.7 1.0 OG A:SER20 4.9 20.9 1.0 O A:HOH2032 4.9 27.0 1.0 O A:ALA9 4.9 19.0 1.0 N A:HIS23 5.0 17.9 1.0

Sodium binding site 2 out of 26 in the Crystal Structure of Apo-MSNO8


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 Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1336 b:31.7 occ:1.00 O A:HOH2254 2.7 20.4 1.0 N A:ILE312 2.8 21.9 1.0 NE A:ARG318 3.0 24.2 1.0 O A:SER310 3.1 19.1 1.0 OG A:SER310 3.3 22.9 1.0 C A:SER310 3.3 21.6 1.0 CZ A:ARG318 3.4 24.0 1.0 O A:ILE312 3.4 23.1 1.0 N A:MSE311 3.5 21.8 0.5 N A:MSE311 3.5 20.2 0.5 NH2 A:ARG318 3.6 25.6 1.0 CD A:ARG318 3.6 21.6 1.0 CA A:MSE311 3.6 21.3 0.5 CA A:MSE311 3.6 24.2 0.5 CG A:PRO10 3.7 21.1 1.0 CA A:ILE312 3.7 20.6 1.0 C A:MSE311 3.7 21.3 0.5 C A:MSE311 3.7 22.9 0.5 CB A:SER310 3.7 22.9 1.0 CB A:ILE312 3.8 21.9 1.0 C A:ILE312 4.0 23.6 1.0 CG A:ARG318 4.0 20.0 1.0 CA A:SER310 4.1 21.7 1.0 NH1 A:ARG318 4.2 25.1 1.0 CD A:PRO10 4.4 21.9 1.0 CG1 A:ILE312 4.5 19.8 1.0 CB A:ARG318 4.8 19.7 1.0 CB A:PRO10 4.9 22.4 1.0 O A:MSE311 4.9 22.7 0.5 O A:MSE311 4.9 24.2 0.5 NA A:NA1340 5.0 32.9 1.0 N A:SER310 5.0 20.0 1.0 CG2 A:ILE312 5.0 23.1 1.0 O A:HOH2012 5.0 20.1 1.0

Sodium binding site 3 out of 26 in the Crystal Structure of Apo-MSNO8


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 Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1337 b:33.8 occ:1.00 O A:GLY106 2.8 23.4 1.0 N A:SER79 2.9 24.0 1.0 N A:ALA108 3.1 37.0 1.0 OG A:SER79 3.2 38.1 1.0 N A:LEU78 3.2 20.6 1.0 O A:HOH2087 3.2 29.3 1.0 C A:LEU77 3.3 18.5 1.0 CB A:SER79 3.4 30.1 1.0 CB A:ALA108 3.4 40.7 1.0 CA A:LEU77 3.5 20.7 1.0 C A:ARG107 3.6 35.4 1.0 CA A:ARG107 3.7 35.4 1.0 CA A:SER79 3.7 25.6 1.0 CA A:ALA108 3.8 40.7 1.0 C A:GLY106 3.9 27.0 1.0 O A:LEU77 3.9 21.4 1.0 CB A:LEU77 3.9 20.2 1.0 C A:LEU78 3.9 21.5 1.0 CA A:LEU78 4.0 19.3 1.0 CD1 A:LEU133 4.1 30.2 1.0 N A:ARG107 4.3 32.7 1.0 O A:ARG107 4.5 32.6 1.0 CD2 A:LEU133 4.6 31.2 1.0 CD2 A:LEU77 4.6 24.2 1.0 CB A:LEU78 4.6 21.1 1.0 C A:SER79 4.7 25.5 1.0 N A:LEU80 4.7 23.2 1.0 CG A:LEU77 4.8 22.2 1.0 O A:VAL76 4.8 20.7 1.0 N A:LEU77 4.9 20.7 1.0 CG A:LEU133 4.9 31.2 1.0 CB A:ARG107 5.0 39.2 1.0

Sodium binding site 4 out of 26 in the Crystal Structure of Apo-MSNO8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1338 b:26.5 occ:1.00 OE1 A:GLU56 2.8 19.8 1.0 OE1 A:GLU43 2.9 20.1 1.0 O A:HOH2276 3.0 24.7 1.0 NZ B:LYS85 3.0 20.8 1.0 OH A:TYR81 3.4 21.0 1.0 CD A:GLU56 3.6 18.3 1.0 CD A:GLU43 3.6 20.9 1.0 CE2 A:TYR81 3.6 21.3 1.0 OE2 A:GLU56 3.6 21.6 1.0 CZ A:TYR81 3.7 21.8 1.0 CD A:PRO55 3.7 18.8 1.0 OE2 A:GLU43 3.8 21.1 1.0 CG A:PRO55 4.1 19.9 1.0 CE B:LYS85 4.2 20.9 1.0 CG2 A:VAL76 4.3 21.9 1.0 O A:PRO53 4.3 21.2 1.0 CG1 A:VAL76 4.3 23.7 1.0 CA A:ALA54 4.4 18.0 1.0 N A:PRO55 4.5 17.0 1.0 CD2 A:TYR81 4.6 21.3 1.0 CE1 A:TYR81 4.6 21.2 1.0 CG A:GLU43 4.6 18.4 1.0 CB A:VAL76 4.7 22.2 1.0 O A:HOH2026 4.8 26.7 1.0 O A:HOH2070 4.8 22.4 1.0 C A:ALA54 4.9 17.6 1.0 CA A:VAL76 4.9 21.3 1.0 CG A:GLU56 5.0 16.6 1.0

Sodium binding site 5 out of 26 in the Crystal Structure of Apo-MSNO8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1339 b:39.7 occ:1.00 O A:ASN50 2.7 21.3 1.0 OG B:SER155 2.7 29.3 1.0 O A:GLU47 2.9 29.4 1.0 O A:HIS44 3.0 17.4 1.0 N A:GLU47 3.1 25.1 1.0 CB B:SER155 3.3 33.5 1.0 N A:ALA46 3.5 22.4 1.0 C A:HIS44 3.6 19.5 1.0 C A:GLU47 3.7 27.9 1.0 C A:HIS45 3.7 22.0 1.0 CA A:GLU47 3.7 27.6 1.0 CB A:GLU47 3.7 28.4 1.0 C A:ASN50 3.7 21.7 1.0 CA A:HIS45 3.9 20.6 1.0 N A:HIS45 4.0 20.0 1.0 C A:ALA46 4.1 24.6 1.0 CA A:ALA46 4.2 24.1 1.0 O A:HIS45 4.3 23.3 1.0 CB A:ASN50 4.3 21.5 1.0 CB A:HIS44 4.3 21.6 1.0 O A:HOH2065 4.4 33.9 1.0 CA A:ASN50 4.4 20.2 1.0 N A:ASN50 4.6 20.7 1.0 CA A:HIS44 4.6 19.4 1.0 CG A:GLU47 4.7 30.2 1.0 N A:ALA51 4.7 20.1 1.0 CA B:SER155 4.8 28.4 1.0 N A:VAL52 4.9 20.8 1.0 O A:HOH2062 4.9 26.5 1.0 N A:ILE48 5.0 25.6 1.0 OE1 A:GLU47 5.0 31.3 1.0 C A:ALA51 5.0 21.5 1.0

Sodium binding site 6 out of 26 in the Crystal Structure of Apo-MSNO8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1340 b:32.9 occ:1.00 OE1 A:GLN8 2.6 26.6 1.0 O A:VAL6 2.8 19.8 1.0 N A:SER310 2.8 20.0 1.0 NH2 A:ARG318 3.0 25.6 1.0 O A:SER310 3.2 19.1 1.0 OG A:SER310 3.5 22.9 1.0 CA A:VAL309 3.6 19.5 1.0 C A:VAL309 3.6 20.7 1.0 CD A:GLN8 3.6 26.1 1.0 CG1 A:VAL309 3.7 22.8 1.0 OE1 A:GLU7 3.7 22.2 1.0 CA A:SER310 3.7 21.7 1.0 CA A:GLU7 3.8 19.0 1.0 OH A:TYR322 3.8 19.2 1.0 C A:VAL6 3.9 17.7 1.0 C A:SER310 3.9 21.6 1.0 N A:GLN8 4.0 21.3 1.0 NE2 A:GLN8 4.0 25.7 1.0 CB A:VAL309 4.2 19.3 1.0 CB A:SER310 4.2 22.9 1.0 CZ A:ARG318 4.3 24.0 1.0 N A:GLU7 4.3 18.0 1.0 C A:GLU7 4.5 21.0 1.0 O A:VAL308 4.5 18.7 1.0 CD A:GLU7 4.7 22.5 1.0 NE A:ARG318 4.8 24.2 1.0 N A:VAL309 4.8 17.6 1.0 CB A:GLU7 4.8 20.0 1.0 O A:VAL309 4.8 20.6 1.0 CG2 A:VAL309 4.9 20.3 1.0 NA A:NA1336 5.0 31.7 1.0 CG A:GLN8 5.0 24.4 1.0

Sodium binding site 7 out of 26 in the Crystal Structure of Apo-MSNO8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1335 b:26.6 occ:1.00 O B:SER20 2.7 16.0 1.0 OE2 B:GLU7 2.8 23.3 1.0 O B:HOH2018 2.9 16.9 1.0 OG B:SER24 3.1 21.2 1.0 NH1 B:ARG318 3.3 24.5 1.0 C B:SER20 3.5 16.4 1.0 CA B:ALA9 3.6 18.3 1.0 CD B:GLU7 3.6 21.1 1.0 N B:SER24 3.7 17.5 1.0 CA B:SER20 3.8 16.5 1.0 CB B:HIS23 3.9 17.8 1.0 OE1 B:GLU7 3.9 21.7 1.0 CB B:ALA9 4.0 18.0 1.0 CB B:SER20 4.1 16.8 1.0 CA B:SER24 4.1 16.0 1.0 C B:HIS23 4.1 16.9 1.0 CB B:SER24 4.2 18.7 1.0 C B:ALA9 4.2 17.3 1.0 CD B:PRO10 4.2 18.4 1.0 CZ B:ARG318 4.4 27.0 1.0 N B:PRO10 4.4 17.7 1.0 O B:PRO10 4.4 16.4 1.0 CA B:HIS23 4.5 17.6 1.0 N B:ALA9 4.6 18.2 1.0 NH2 B:ARG318 4.7 32.5 1.0 N B:LEU21 4.7 17.6 1.0 O B:HOH2035 4.8 20.9 1.0 O B:HIS23 4.8 18.3 1.0 O B:HOH2242 4.8 19.3 1.0 CG B:GLU7 4.8 19.4 1.0 OG B:SER20 4.8 17.9 1.0 O B:HOH2245 4.9 34.9 1.0 O B:ALA9 4.9 17.9 1.0 N B:HIS23 5.0 17.6 1.0

Sodium binding site 8 out of 26 in the Crystal Structure of Apo-MSNO8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1336 b:24.9 occ:1.00 O B:HOH2242 2.7 19.3 1.0 N B:ILE312 2.9 18.1 1.0 O B:SER310 2.9 17.2 1.0 NE B:ARG318 3.0 24.6 1.0 OG B:SER310 3.1 19.0 1.0 C B:SER310 3.2 16.9 1.0 CZ B:ARG318 3.4 27.0 1.0 N B:MSE311 3.5 18.0 0.5 N B:MSE311 3.5 16.3 0.5 O B:ILE312 3.5 18.2 1.0 CA B:MSE311 3.6 19.6 0.5 CA B:MSE311 3.6 16.5 0.5 NH2 B:ARG318 3.6 32.5 1.0 CB B:SER310 3.7 17.5 1.0 CD B:ARG318 3.7 21.2 1.0 CG B:PRO10 3.7 19.2 1.0 C B:MSE311 3.7 17.3 0.5 C B:MSE311 3.7 19.1 0.5 CA B:ILE312 3.8 17.1 1.0 CB B:ILE312 3.9 17.2 1.0 CA B:SER310 4.0 17.2 1.0 C B:ILE312 4.1 18.1 1.0 CG B:ARG318 4.1 20.2 1.0 NH1 B:ARG318 4.2 24.5 1.0 CD B:PRO10 4.4 18.4 1.0 CG1 B:ILE312 4.6 16.5 1.0 N B:SER310 4.8 17.3 1.0 NA B:NA1341 4.9 31.8 1.0 O B:MSE311 4.9 19.6 0.5 O B:MSE311 4.9 21.4 0.5 CB B:PRO10 4.9 18.7 1.0 CB B:ARG318 4.9 17.9 1.0

Sodium binding site 9 out of 26 in the Crystal Structure of Apo-MSNO8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1337 b:35.3 occ:1.00 O B:GLY106 2.7 23.3 1.0 N B:SER79 3.0 22.5 1.0 N B:ALA108 3.1 37.5 1.0 OG B:SER79 3.1 34.6 1.0 N B:LEU78 3.2 20.8 1.0 O B:HOH2084 3.2 30.0 1.0 C B:LEU77 3.3 18.4 1.0 CB B:SER79 3.4 27.4 1.0 CA B:LEU77 3.5 19.3 1.0 CB B:ALA108 3.5 37.3 1.0 C B:ARG107 3.6 33.3 1.0 CA B:ARG107 3.6 32.8 1.0 C B:GLY106 3.7 25.7 1.0 CA B:SER79 3.8 25.9 1.0 CA B:ALA108 3.9 36.5 1.0 CB B:LEU77 3.9 20.4 1.0 O B:LEU77 3.9 18.4 1.0 C B:LEU78 4.0 21.6 1.0 CD1 B:LEU133 4.0 31.4 1.0 CA B:LEU78 4.1 20.6 1.0 N B:ARG107 4.2 29.0 1.0 CD2 B:LEU133 4.4 33.4 1.0 O B:ARG107 4.5 33.5 1.0 CD2 B:LEU77 4.6 19.7 1.0 CB B:LEU78 4.6 20.7 1.0 O B:VAL76 4.8 18.9 1.0 CG B:LEU133 4.8 33.1 1.0 C B:SER79 4.8 25.7 1.0 CG B:LEU77 4.8 19.6 1.0 N B:LEU77 4.9 19.4 1.0 N B:LEU80 4.9 22.6 1.0 CB B:ARG107 4.9 36.4 1.0

Sodium binding site 10 out of 26 in the Crystal Structure of Apo-MSNO8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Apo-MSNO8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1338 b:27.7 occ:1.00 O B:HOH2266 2.8 23.9 1.0 OE1 B:GLU56 2.9 16.5 1.0 OE1 B:GLU43 2.9 17.5 1.0 NZ A:LYS85 3.0 19.3 1.0 OH B:TYR81 3.4 20.3 1.0 CD B:GLU43 3.5 17.9 1.0 CE2 B:TYR81 3.6 20.9 1.0 CD B:GLU56 3.6 17.5 1.0 CZ B:TYR81 3.6 19.5 1.0 OE2 B:GLU56 3.7 20.2 1.0 OE2 B:GLU43 3.8 19.1 1.0 CD B:PRO55 3.8 17.6 1.0 CG B:PRO55 4.1 17.4 1.0 CE A:LYS85 4.2 18.8 1.0 CG2 B:VAL76 4.2 20.6 1.0 CG1 B:VAL76 4.2 20.1 1.0 O B:PRO53 4.3 18.7 1.0 CD2 B:TYR81 4.5 19.6 1.0 CA B:ALA54 4.5 18.3 1.0 CE1 B:TYR81 4.6 21.1 1.0 N B:PRO55 4.7 15.7 1.0 CG B:GLU43 4.7 16.6 1.0 CB B:VAL76 4.7 19.2 1.0 O A:HOH2094 4.8 24.5 1.0 O A:HOH2027 4.8 28.3 1.0 CA B:VAL76 4.9 18.3 1.0 C B:ALA54 5.0 17.4 1.0

S.Maier, T.Pflueger, S.Loesgen, K.Asmus, E.Broetz, T.Paululat, A.Zeeck, S.Andrade, A.Bechthold. Insights Into the Bioactivity of Mensacarcin and Epoxide Formation By MSNO8. Chembiochem V. 15 749 2014.
ISSN: ISSN 1439-4227
PubMed: 24554499
DOI: 10.1002/CBIC.201300704