Sodium in PDB 8jc1: Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum

The structure of Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum, PDB code: 8jc1 was solved by N.Jantarit, G.Kurisu, H.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.49 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.279, 138.553, 68.947, 90, 94.18, 90
R / Rfree (%)	19.5 / 23.9

The structure of Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum (pdb code 8jc1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum, PDB code: 8jc1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:56.9 occ:1.00 OG1 C:THR258 2.5 36.2 1.0 OD2 A:ASP56 2.8 54.0 1.0 OD1 A:ASN80 2.9 47.7 1.0 O3 C:GOL301 3.0 56.9 1.0 CB C:THR258 3.4 34.5 1.0 C3 C:GOL301 3.5 57.5 1.0 N C:THR258 3.5 35.1 1.0 CB A:ASP56 3.6 51.2 1.0 CG A:ASP56 3.6 57.5 1.0 C C:GLY257 3.8 39.4 1.0 CG A:ASN80 3.9 47.4 1.0 O A:HOH448 4.0 36.8 1.0 CA C:THR258 4.0 41.1 1.0 CA C:GLY257 4.1 36.2 1.0 ND2 A:ASN80 4.1 46.5 1.0 C1 C:GOL301 4.2 55.2 1.0 O C:GLY257 4.5 32.4 1.0 C2 C:GOL301 4.6 55.0 1.0 CG2 C:THR258 4.7 37.0 1.0 O1 C:GOL301 4.7 52.1 1.0 CA A:ASP56 4.8 49.5 1.0 OD1 A:ASP56 4.8 55.5 1.0 N C:GLY257 4.9 36.4 1.0 O A:HOH420 4.9 42.0 1.0 CD C:ARG218 5.0 39.5 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:56.3 occ:1.00 O A:HOH421 2.4 48.5 1.0 O A:HOH507 2.6 50.6 1.0 O A:LYS245 4.0 42.9 1.0 OE2 A:GLU104 4.0 39.0 1.0 CD1 A:PHE246 4.3 35.7 1.0 CG A:GLU104 4.5 39.2 1.0 CA A:PHE246 4.5 33.6 1.0 CD2 A:PHE107 4.6 31.3 1.0 CE2 A:PHE107 4.6 32.2 1.0 O A:PHE246 4.6 37.3 1.0 CD A:GLU104 4.7 39.6 1.0 CE1 A:PHE246 4.9 32.5 1.0 CE3 D:TRP238 4.9 32.4 1.0 CZ3 D:TRP238 4.9 30.2 1.0 C A:LYS245 5.0 36.4 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:52.8 occ:1.00 O A:HOH508 2.4 55.9 1.0 N A:SER174 3.1 39.4 1.0 OG A:SER175 3.2 53.7 1.0 CA A:ILE173 3.6 40.9 1.0 O A:SER174 3.6 45.4 1.0 O A:ASP172 3.8 39.4 1.0 C A:SER174 3.8 45.9 1.0 C A:ILE173 3.9 40.2 1.0 CG2 A:ILE173 4.0 41.0 1.0 CA A:SER174 4.1 42.6 1.0 CB A:SER175 4.2 42.6 1.0 CD1 A:ILE173 4.2 37.4 1.0 CB A:ILE173 4.3 41.0 1.0 N A:SER175 4.4 39.5 1.0 N A:ILE173 4.6 35.7 1.0 C A:ASP172 4.6 41.8 1.0 CA A:SER175 4.7 41.0 1.0 O A:HOH516 4.8 51.1 1.0 CG1 A:ILE173 4.9 37.7 1.0 CB A:SER174 4.9 43.7 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:45.4 occ:1.00 O A:HOH529 2.2 47.2 1.0 OD1 A:ASP127 2.9 32.8 1.0 NH2 A:ARG130 3.0 34.3 1.0 O A:HOH408 3.3 38.1 1.0 CG A:ASP127 3.7 33.1 1.0 O A:HOH438 3.7 37.1 1.0 OD1 D:ASP114 3.7 40.4 1.0 O D:HOH401 3.8 37.3 1.0 OD2 A:ASP127 3.8 33.3 1.0 CD1 A:LEU119 4.0 30.1 1.0 CG A:LEU119 4.1 33.0 1.0 CZ A:ARG130 4.2 36.0 1.0 O A:HOH440 4.5 39.9 1.0 CD2 A:LEU119 4.6 33.7 1.0 NE A:ARG130 4.7 32.9 1.0 OD2 A:ASP114 4.7 51.0 1.0 CG D:ASP114 4.8 36.1 1.0 NZ A:LYS140 4.9 37.9 1.0 CB A:ASP127 5.0 31.7 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:74.9 occ:1.00 OD1 B:ASP19 3.2 81.7 1.0 N B:ALA2 3.3 72.5 1.0 OD1 B:ASP20 3.3 84.1 1.0 O A:HOH489 3.5 42.1 1.0 O A:HOH519 3.9 47.7 1.0 CG B:ASP19 4.3 78.4 1.0 CB B:SER18 4.3 79.4 1.0 CG B:ASP20 4.4 83.9 1.0 CA B:ALA2 4.6 68.8 1.0 OD2 B:ASP19 4.7 76.0 1.0 N B:ASP19 4.9 76.9 1.0 C B:ALA2 4.9 74.4 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:60.8 occ:1.00 CB B:ASP244 2.7 44.4 1.0 CG B:ASP244 3.0 46.6 1.0 O B:THR240 3.7 35.0 1.0 CG2 B:THR240 3.9 47.5 1.0 CA B:ASP244 4.0 40.2 1.0 C B:THR240 4.4 34.7 1.0 N B:ASP244 4.5 38.9 1.0 CA B:GLY241 4.7 36.2 1.0 N B:GLY241 4.9 36.7 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ C:Na307 b:48.7 occ:1.00 O C:HOH470 2.9 46.2 1.0 OD1 C:ASN145 3.1 41.8 1.0 N C:ASP260 3.1 40.1 1.0 O C:THR258 3.6 38.9 1.0 CA C:LEU259 3.8 37.1 1.0 C C:LEU259 3.9 40.0 1.0 CB C:ASP260 3.9 44.5 1.0 CG C:ASP260 4.0 48.6 1.0 OD2 C:ASP260 4.1 53.5 1.0 O C:HOH427 4.1 45.4 1.0 CA C:ASP260 4.1 42.8 1.0 CG C:ASN145 4.1 44.1 1.0 CD1 C:LEU259 4.3 41.4 1.0 C C:THR258 4.4 37.3 1.0 OD1 C:ASP260 4.4 50.4 1.0 ND2 C:ASN145 4.5 40.7 1.0 N C:LEU259 4.6 35.7 1.0 O A:HOH496 4.8 40.4 1.0 CG C:LEU259 4.8 39.4 1.0 O C:ASP260 4.8 38.9 1.0 CB C:LEU259 4.8 34.5 1.0 C C:ASP260 5.0 42.3 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of Pectocin M1 From Pectobacterium Carotovorum


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 Pectocin M1 From Pectobacterium Carotovorum within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:63.7 occ:1.00 OD1 D:ASP152 2.4 54.3 1.0 CG D:ASP152 3.5 46.7 1.0 O D:HOH448 3.9 34.6 1.0 N D:SER154 4.1 36.7 1.0 CB D:SER154 4.2 44.0 1.0 O D:ARG264 4.3 39.5 1.0 OG D:SER154 4.6 47.8 1.0 N D:VAL153 4.7 37.8 1.0 CH2 D:TRP211 4.7 38.5 1.0 CB D:ASP152 4.7 37.6 1.0 CA D:SER154 4.8 37.7 1.0 CB D:VAL153 4.8 38.0 1.0 N D:ARG264 4.9 37.3 1.0 CZ2 D:TRP211 4.9 40.7 1.0

N.Jantarit, H.Tanaka, Y.Lin, Y.H.Lee, G.Kurisu. Crystal Structure of Pectocin M1 Reveals Diverse Conformations and Interactions During Its Initial Step Via the Ferredoxin Uptake System. Febs Open Bio 2024.
ISSN: ESSN 2211-5463
PubMed: 39123319
DOI: 10.1002/2211-5463.13874