Sodium in PDB 9cip: Microed Structure of the C11 Cysteine Protease Clostripain

The binding sites of Sodium atom in the Microed Structure of the C11 Cysteine Protease Clostripain (pdb code 9cip). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Microed Structure of the C11 Cysteine Protease Clostripain, PDB code: 9cip:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Microed Structure of the C11 Cysteine Protease Clostripain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Microed Structure of the C11 Cysteine Protease Clostripain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:17.5 occ:1.00 OD2 A:ASP96 2.3 26.5 1.0 O A:ALA145 2.3 29.8 1.0 OG A:SER197 2.3 33.2 1.0 OD2 A:ASP195 2.6 32.7 1.0 OE2 A:GLU144 2.6 27.4 1.0 OD1 A:ASP195 2.6 29.7 1.0 OD2 A:ASP65 2.7 32.4 1.0 CG A:ASP195 2.9 29.9 1.0 CG A:ASP96 3.2 26.4 1.0 CB A:SER197 3.2 33.0 1.0 OD1 A:ASP96 3.4 28.8 1.0 C A:ALA145 3.5 26.4 1.0 CG A:ASP65 3.6 28.1 1.0 CD A:GLU144 3.6 30.8 1.0 CB A:ASP65 4.0 26.5 1.0 CG A:GLU144 4.1 26.8 1.0 N A:ALA145 4.4 29.1 1.0 CA A:ASN146 4.4 25.2 1.0 N A:ASN146 4.4 24.9 1.0 CA A:SER197 4.4 34.6 1.0 N A:SER197 4.4 32.5 1.0 CB A:ASP195 4.5 26.7 1.0 OD1 A:ASP65 4.5 32.7 1.0 CA A:ALA145 4.6 26.9 1.0 N A:MET147 4.6 22.9 1.0 CB A:ASP96 4.6 27.9 1.0 OD1 A:ASN198 4.6 39.4 1.0 OE1 A:GLU144 4.7 31.8 1.0 OG1 A:THR115 4.8 26.6 1.0 CG A:MET147 4.8 20.8 1.0

Sodium binding site 2 out of 7 in the Microed Structure of the C11 Cysteine Protease Clostripain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Microed Structure of the C11 Cysteine Protease Clostripain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:23.0 occ:1.00 OE2 A:GLU312 2.3 28.9 1.0 O A:ASP285 2.4 29.7 1.0 OD2 A:ASP316 2.4 22.1 1.0 OD1 A:ASP316 2.7 20.7 1.0 OE2 A:GLU293 2.9 26.5 1.0 CG A:ASP316 2.9 19.8 1.0 CD A:GLU312 3.5 27.3 1.0 C A:ASP285 3.6 28.6 1.0 CD A:GLU293 4.0 25.3 1.0 CG A:GLU312 4.2 24.8 1.0 CB A:ASP316 4.4 17.4 1.0 OE1 A:GLU312 4.4 26.7 1.0 N A:ASP285 4.4 35.3 1.0 CG A:GLU293 4.5 28.6 1.0 N A:ASP286 4.5 25.9 1.0 CA A:ASP286 4.6 29.1 1.0 CA A:ASP285 4.6 33.1 1.0 N A:LEU287 4.7 26.8 1.0 CB A:GLU284 4.7 37.0 1.0 CG A:LEU287 4.8 29.5 1.0 OE1 A:GLU284 4.8 39.0 1.0 OE1 A:GLU293 4.9 27.9 1.0 C A:GLU284 4.9 32.9 1.0

Sodium binding site 3 out of 7 in the Microed Structure of the C11 Cysteine Protease Clostripain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Microed Structure of the C11 Cysteine Protease Clostripain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:20.1 occ:1.00 OD2 A:ASP512 2.3 24.1 1.0 O A:GLY519 2.4 25.8 1.0 OD1 A:ASN522 2.5 24.5 1.0 O A:TYR524 2.5 25.6 1.0 OD2 A:ASP508 2.9 22.6 1.0 OD1 A:ASP508 3.1 21.8 1.0 CG A:ASP512 3.2 26.0 1.0 C A:GLY519 3.2 26.8 1.0 CG A:ASP508 3.4 20.1 1.0 CG A:ASN522 3.6 21.9 1.0 C A:TYR524 3.7 24.8 1.0 CA A:GLY520 3.7 27.9 1.0 CB A:ASP512 3.8 26.4 1.0 N A:GLY520 3.8 26.7 1.0 N A:TYR524 4.1 23.0 1.0 OD1 A:ASP512 4.1 29.7 1.0 CA A:GLY519 4.1 26.2 1.0 N A:VAL521 4.2 27.3 1.0 ND2 A:ASN522 4.2 19.0 1.0 C A:GLY520 4.3 26.6 1.0 O A:THR514 4.3 28.2 1.0 N A:ASN522 4.4 23.2 1.0 CA A:TYR524 4.4 25.3 1.0 OD1 A:ASN515 4.4 28.4 1.0 CD1 A:TRP526 4.7 25.9 1.0 N A:HIS523 4.7 24.3 1.0 N A:GLN525 4.7 21.0 1.0 CB A:TYR524 4.8 23.4 1.0 CB A:ASN522 4.8 26.1 1.0 CB A:ASP508 4.9 21.1 1.0 CA A:GLN525 4.9 26.0 1.0 CA A:ASN522 5.0 26.6 1.0

Sodium binding site 4 out of 7 in the Microed Structure of the C11 Cysteine Protease Clostripain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Microed Structure of the C11 Cysteine Protease Clostripain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:25.6 occ:1.00 O B:ARG97 2.3 31.5 1.0 OD1 B:ASP96 2.4 25.9 1.0 O B:SER113 2.4 34.3 1.0 OD2 B:ASP65 2.5 30.1 1.0 OE2 B:GLU144 2.5 29.4 1.0 OE1 B:GLU144 3.2 33.4 1.0 CD B:GLU144 3.2 29.8 1.0 CG B:ASP96 3.4 24.4 1.0 C B:ARG97 3.4 34.4 1.0 CG B:ASP65 3.5 28.1 1.0 C B:SER113 3.6 31.5 1.0 OD2 B:ASP96 3.8 26.6 1.0 NA B:NA604 3.8 19.4 1.0 N B:ARG97 3.9 30.9 1.0 OD1 B:ASP65 4.2 34.3 1.0 CA B:ASP114 4.3 29.6 1.0 CA B:ARG97 4.3 35.0 1.0 CB B:ASP65 4.3 28.8 1.0 C B:ASP114 4.4 29.0 1.0 O B:ASP114 4.4 28.8 1.0 N B:ASP114 4.4 26.8 1.0 C B:ASP96 4.4 29.2 1.0 N B:SER98 4.4 34.4 1.0 CA B:SER113 4.6 31.6 1.0 CA B:SER98 4.6 40.2 1.0 CG B:GLU144 4.7 28.4 1.0 CB B:ASP96 4.7 26.0 1.0 OG1 B:THR115 4.8 25.4 1.0 CA B:ASP96 4.8 27.4 1.0 OG B:SER197 4.8 33.2 1.0 CB B:SER197 4.8 36.9 1.0 CB B:SER113 4.9 31.4 1.0 O B:ASP96 5.0 31.3 1.0 N B:THR115 5.0 28.1 1.0

Sodium binding site 5 out of 7 in the Microed Structure of the C11 Cysteine Protease Clostripain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Microed Structure of the C11 Cysteine Protease Clostripain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:21.6 occ:1.00 OE2 B:GLU312 2.3 27.8 1.0 O B:ASP285 2.4 29.4 1.0 OD2 B:ASP316 2.4 24.2 1.0 OE2 B:GLU293 2.7 27.8 1.0 OD1 B:ASP316 3.0 21.4 1.0 CG B:ASP316 3.0 23.9 1.0 CD B:GLU312 3.5 23.4 1.0 C B:ASP285 3.6 26.6 1.0 CD B:GLU293 3.7 27.4 1.0 CG B:GLU293 4.2 25.5 1.0 CG B:GLU312 4.2 24.9 1.0 N B:ASP285 4.3 36.7 1.0 CB B:GLU284 4.3 40.5 1.0 OE1 B:GLU284 4.4 45.0 1.0 N B:ASP286 4.5 25.6 1.0 CB B:ASP316 4.5 22.5 1.0 OE1 B:GLU312 4.5 24.8 1.0 CA B:ASP286 4.5 27.0 1.0 CA B:ASP285 4.5 33.2 1.0 OE1 B:GLU293 4.7 31.7 1.0 C B:GLU284 4.7 38.0 1.0 CD2 B:LEU287 4.7 33.2 1.0 N B:LEU287 4.8 25.8 1.0

Sodium binding site 6 out of 7 in the Microed Structure of the C11 Cysteine Protease Clostripain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Microed Structure of the C11 Cysteine Protease Clostripain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:15.5 occ:1.00 OD2 B:ASP512 2.3 23.2 1.0 O B:TYR524 2.4 22.8 1.0 OD1 B:ASN522 2.5 20.8 1.0 O B:GLY519 2.5 23.7 1.0 OD2 B:ASP508 2.6 21.4 1.0 OD1 B:ASP508 2.9 20.0 1.0 CG B:ASP508 3.1 20.4 1.0 CG B:ASP512 3.3 22.9 1.0 C B:GLY519 3.4 25.4 1.0 CG B:ASN522 3.6 18.9 1.0 C B:TYR524 3.6 23.1 1.0 CB B:ASP512 3.8 21.8 1.0 CA B:GLY520 4.0 21.3 1.0 ND2 B:ASN522 4.1 16.6 1.0 N B:GLY520 4.1 23.2 1.0 N B:TYR524 4.1 20.8 1.0 CA B:GLY519 4.2 22.7 1.0 OD1 B:ASP512 4.3 26.1 1.0 CA B:TYR524 4.3 21.7 1.0 N B:VAL521 4.5 23.2 1.0 OD1 B:ASN515 4.5 25.1 1.0 N B:ASN522 4.5 20.6 1.0 O B:THR514 4.5 25.6 1.0 C B:GLY520 4.5 23.7 1.0 CB B:ASP508 4.6 20.1 1.0 CD1 B:TRP526 4.6 23.1 1.0 N B:GLN525 4.6 22.6 1.0 CB B:TYR524 4.7 18.1 1.0 CA B:GLN525 4.8 24.3 1.0 N B:HIS523 4.8 23.4 1.0 CB B:ASN522 4.8 21.9 1.0

Sodium binding site 7 out of 7 in the Microed Structure of the C11 Cysteine Protease Clostripain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Microed Structure of the C11 Cysteine Protease Clostripain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na604 b:19.4 occ:1.00 O B:ALA145 2.3 31.4 1.0 OD2 B:ASP96 2.3 26.6 1.0 OD2 B:ASP195 2.4 33.3 1.0 OG B:SER197 2.4 33.2 1.0 OD1 B:ASP195 2.6 34.2 1.0 OD2 B:ASP65 2.7 30.1 1.0 CG B:ASP195 2.8 34.4 1.0 OE2 B:GLU144 2.9 29.4 1.0 CG B:ASP96 3.3 24.4 1.0 CB B:SER197 3.5 36.9 1.0 C B:ALA145 3.5 28.8 1.0 OD1 B:ASP96 3.5 25.9 1.0 CG B:ASP65 3.5 28.1 1.0 NA B:NA601 3.8 25.6 1.0 CD B:GLU144 4.0 29.8 1.0 CB B:ASP65 4.1 28.8 1.0 OD1 B:ASN198 4.2 40.6 1.0 CB B:ASP195 4.3 35.6 1.0 N B:ALA145 4.4 27.6 1.0 N B:ASN146 4.4 26.2 1.0 CA B:ASN146 4.4 28.1 1.0 N B:MET147 4.4 25.6 1.0 OD1 B:ASP65 4.4 34.3 1.0 CG B:GLU144 4.5 28.4 1.0 CA B:ALA145 4.5 26.1 1.0 N B:SER197 4.6 35.3 1.0 CA B:SER197 4.6 39.1 1.0 CB B:ASP96 4.6 26.0 1.0 OG1 B:THR115 4.9 25.4 1.0 OE1 B:GLU144 5.0 33.4 1.0 C B:ASN146 5.0 25.7 1.0

Y.N.Ruma, G.Bu, J.Hattne, T.Gonen. Microed Structure of the C11 Cysteine Protease Clostripain. J Struct Biol X V. 10 00107 2024.
ISSN: ESSN 2590-1524
PubMed: 39100863
DOI: 10.1016/J.YJSBX.2024.100107