Sodium in PDB 5mrt: Crystal Structure of L5 Protease Lysobacter Sp. XL1

The structure of Crystal Structure of L5 Protease Lysobacter Sp. XL1, PDB code: 5mrt was solved by A.Gabdulkhakov, S.Tishchenko, A.Lisov, A.Leontievsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.33 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.549, 66.668, 96.642, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 22.7

The structure of Crystal Structure of L5 Protease Lysobacter Sp. XL1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of L5 Protease Lysobacter Sp. XL1 (pdb code 5mrt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of L5 Protease Lysobacter Sp. XL1, PDB code: 5mrt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of L5 Protease Lysobacter Sp. XL1


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 L5 Protease Lysobacter Sp. XL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:33.8 occ:1.00 O A:HOH450 2.2 19.1 1.0 OD1 A:ASN65 2.3 17.7 1.0 OG1 A:THR133 2.4 13.4 1.0 O A:HOH501 2.4 22.8 1.0 O A:HOH566 2.7 30.3 1.0 O A:THR133 2.7 13.9 1.0 C A:THR133 3.3 13.1 1.0 CG A:ASN65 3.4 16.0 1.0 CB A:THR133 3.6 12.9 1.0 N A:THR133 3.6 12.9 1.0 CA A:THR133 3.7 12.1 1.0 CA A:ASN65 3.8 10.2 1.0 O A:HOH418 3.9 33.4 1.0 CB A:ASN65 4.1 12.2 1.0 N A:ASN65 4.1 10.7 1.0 O A:HOH586 4.2 35.2 1.0 N A:VAL134 4.3 13.9 1.0 ND2 A:ASN65 4.5 18.8 1.0 CG2 A:THR133 4.6 12.8 1.0 OG A:SER135 4.7 20.7 1.0 CA A:VAL134 4.7 14.0 1.0 C A:GLY132 4.8 16.7 1.0 O A:HOH552 5.0 35.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of L5 Protease Lysobacter Sp. XL1


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 L5 Protease Lysobacter Sp. XL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:38.7 occ:1.00 O A:HOH419 2.2 30.5 1.0 O A:HOH613 2.3 37.0 1.0 O A:HOH505 2.3 31.4 1.0 O A:THR204 2.4 10.6 1.0 O A:HOH551 2.5 11.9 1.0 C A:THR204 3.5 8.7 1.0 N A:THR204 3.9 7.9 1.0 CG1 A:VAL203 4.0 9.1 1.0 OG1 A:THR204 4.1 11.3 1.0 CA A:THR204 4.2 7.9 1.0 O A:HOH603 4.3 15.5 1.0 O1 A:FMT302 4.5 20.4 1.0 O A:HOH553 4.5 27.4 1.0 N A:SER205 4.5 8.1 1.0 CA A:SER205 4.7 8.9 1.0 O A:HOH578 4.8 24.6 1.0 C A:VAL203 4.8 9.2 1.0 CB A:THR204 4.9 8.8 1.0 O A:HOH441 4.9 32.0 1.0

A.Gabdulkhakov, S.Tishchenko, A.Lisov, A.Leontievsky. Crystal Structure of L5 Protease Lysobacter Sp. XL1 To Be Published.