Sodium in PDB 9mm2: Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T

The structure of Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T, PDB code: 9mm2 was solved by V.Carbone, K.Reilly, C.Sang, L.Schofield, R.Ronimus, G.T.Attwood, N.Palevich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.78 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.297, 61.95, 77.369, 90, 105.39, 90
R / Rfree (%)	12 / 14

The structure of Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T (pdb code 9mm2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T, PDB code: 9mm2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T


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 Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:18.4 occ:1.00 O A:HOH703 2.8 15.4 1.0 O A:HOH760 2.9 20.2 1.0 N A:ILE59 3.1 7.5 1.0 O A:HOH1140 3.2 22.9 1.0 NH2 A:ARG35 3.3 11.2 1.0 O A:ILE59 3.5 9.2 1.0 CA A:LEU58 3.7 7.1 1.0 C A:LEU58 3.9 7.1 1.0 CA A:ILE59 4.0 7.7 1.0 NH1 A:ARG35 4.1 11.8 1.0 C A:ILE59 4.1 8.1 1.0 CZ A:ARG35 4.1 10.6 1.0 CB A:LEU58 4.3 7.3 1.0 OG A:SER28 4.3 7.1 0.3 CD2 A:LEU58 4.3 10.1 1.0 CB A:ILE59 4.4 8.7 1.0 CG2 A:ILE31 4.4 11.5 1.0 O A:MET57 4.4 8.6 1.0 CD1 A:ILE31 4.6 11.7 1.0 O A:HOH893 4.7 25.1 1.0 O A:HOH1180 4.7 21.7 1.0 CB A:ILE31 4.7 9.6 1.0 O A:HOH1227 4.7 35.3 1.0 CB A:SER28 4.8 7.4 0.3 OG A:SER28 4.8 18.3 0.7 N A:LEU58 4.8 6.9 1.0 CA A:SER28 4.9 7.8 0.3 CG1 A:ILE59 4.9 9.8 1.0 CA A:SER28 4.9 10.2 0.7 CG A:LEU58 5.0 8.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T


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 Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:12.2 occ:1.00 O A:HOH1122 2.3 30.0 1.0 O A:HOH892 2.9 15.1 1.0 O A:HOH992 3.0 9.5 1.0 N A:GLU167 3.1 7.6 1.0 O A:HOH959 3.3 15.4 1.0 O A:HOH842 3.6 17.6 1.0 CA A:SER166 3.7 7.1 1.0 CB A:GLU167 3.7 9.4 1.0 CB A:SER166 3.8 7.3 1.0 C A:SER166 3.9 7.6 1.0 OE1 A:GLN55 3.9 7.5 1.0 CA A:GLU167 4.0 8.5 1.0 CE2 A:TYR164 4.1 6.8 1.0 CD A:GLN55 4.2 8.0 1.0 O A:HOH982 4.2 30.7 1.0 NE2 A:GLN55 4.3 9.8 1.0 ND2 A:ASN53 4.5 8.8 1.0 CE A:LYS193 4.6 19.3 0.7 O A:HOH1050 4.7 17.4 1.0 CD2 A:TYR164 4.9 6.9 1.0 OH A:TYR164 4.9 7.7 1.0 OE2 A:GLU167 4.9 14.1 1.0 O A:VAL165 5.0 7.6 1.0 CZ A:TYR164 5.0 6.9 1.0 N A:SER166 5.0 6.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T


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 Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:23.9 occ:1.00 O A:HOH607 2.6 29.6 1.0 O A:PRO131 2.8 14.0 1.0 OG A:SER133 2.9 14.2 1.0 O A:SER133 3.1 9.3 1.0 N A:SER133 3.5 9.5 1.0 O A:HOH646 3.6 29.5 1.0 CE1 A:HIS99 3.6 7.5 1.0 C A:SER133 3.9 9.2 1.0 C A:PRO131 3.9 9.1 1.0 ND1 A:HIS99 3.9 6.7 1.0 CA A:SER133 4.0 9.5 1.0 CB A:SER133 4.0 10.4 1.0 C A:GLY132 4.0 10.4 1.0 CA A:GLY132 4.4 10.2 1.0 N A:GLY132 4.6 9.6 1.0 O A:HOH1110 4.6 21.6 1.0 O A:GLY132 4.7 10.4 1.0 NE2 A:HIS99 4.8 7.0 1.0 CA A:PRO131 4.9 9.4 1.0

V.Carbone, K.Reilly, C.Sang, L.Schofield, R.Ronimus, G.T.Attwood, N.Palevich. Crystal Structure of Bacterial Pectin Methylesterase PMEC5 From B. Fibrisolvens D1T To Be Published.