Sodium in PDB 2jc4: 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis

All present enzymatic activity of 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis:
3.1.11.2;

The structure of 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis, PDB code: 2jc4 was solved by E.P.Carpenter, A.Corbett, H.Thomson, J.Adacha, K.Jensen, J.Bergeron, I.Kasampalidis, R.Exley, M.Winterbotham, C.Tang, G.Baldwin, P.Freemont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.193, 58.618, 88.635, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 20.2

The structure of 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis (pdb code 2jc4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis, PDB code: 2jc4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1257 b:18.3 occ:1.00 O A:HOH2134 3.8 28.5 1.0 O A:HOH2131 3.9 24.2 1.0 O A:HOH2032 3.9 25.3 1.0 O A:HOH2030 4.1 23.4 1.0 O A:HOH2079 4.9 28.2 1.0 O A:HOH2081 4.9 16.6 1.0 O A:HOH2284 5.0 29.6 1.0 O A:HOH2037 5.0 21.3 1.0

Sodium binding site 2 out of 2 in the 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1258 b:16.7 occ:1.00 O A:VAL234 2.3 11.3 1.0 O A:HOH2110 2.4 18.2 1.0 O A:HOH2255 2.5 20.2 1.0 O A:HOH2254 2.5 13.9 1.0 C A:VAL234 3.4 11.2 1.0 N A:VAL234 3.8 11.5 1.0 O A:HOH2087 3.9 13.8 1.0 O A:HOH2108 4.1 23.2 1.0 CA A:VAL234 4.2 11.7 1.0 N A:LEU236 4.4 12.3 1.0 O A:HOH2001 4.4 13.9 1.0 CB A:ARG233 4.5 14.5 1.0 N A:ASP235 4.5 10.3 1.0 CG A:LEU236 4.6 11.3 1.0 O A:HOH2257 4.6 21.7 1.0 CB A:VAL234 4.6 11.0 1.0 O A:HOH2111 4.7 14.8 1.0 CA A:ASP235 4.7 11.9 1.0 C A:ARG233 4.7 12.8 1.0 CB A:LEU236 4.9 11.0 1.0 CA A:ARG233 4.9 13.2 1.0 CD1 A:LEU236 5.0 12.1 1.0

E.P.Carpenter, A.Corbett, H.Thomson, J.Adacha, K.Jensen, J.Bergeron, I.Kasampalidis, R.Exley, M.Winterbotham, C.Tang, G.S.Baldwin, P.Freemont. Ap Endonuclease Paralogues with Distinct Activities in Dna Repair and Bacterial Pathogenesis. Embo J. V. 26 1363 2007.
ISSN: ISSN 0261-4189
PubMed: 17318183
DOI: 10.1038/SJ.EMBOJ.7601593