Magnesium in PDB 2jc5: Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis

All present enzymatic activity of Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis:
3.1.11.2;

The structure of Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis, PDB code: 2jc5 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.S.Baldwin, P.Freemont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.156, 79.511, 41.045, 90.00, 107.22, 90.00
R / Rfree (%)	12 / 15.9

The binding sites of Magnesium atom in the Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis (pdb code 2jc5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis, PDB code: 2jc5:

Magnesium binding site 1 out of 1 in the Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1260 b:11.5 occ:0.50 O A:HOH2045 1.8 14.9 1.0 O A:HOH2043 1.8 17.9 1.0 O A:HOH2292 1.9 11.6 1.0 O A:HOH2291 2.0 14.3 1.0 OE1 A:GLU36 2.1 5.9 0.5 OD1 A:ASN10 2.3 12.5 1.0 H1 A:HOH2045 2.5 14.9 1.0 H2 A:HOH2043 2.5 17.9 1.0 H2 A:HOH2292 2.5 11.6 1.0 OE1 A:GLU36 2.6 10.1 0.5 H1 A:HOH2291 2.6 14.3 1.0 H2 A:HOH2010 2.9 22.2 1.0 H1 A:HOH2293 2.9 17.6 1.0 CD A:GLU36 3.0 5.2 0.5 CD A:GLU36 3.1 9.8 0.5 OE2 A:GLU36 3.1 11.3 0.5 HA A:ASN10 3.2 7.1 1.0 OE2 A:GLU36 3.3 7.4 0.5 CG A:ASN10 3.3 11.2 1.0 H2 A:HOH2131 3.6 30.6 1.0 O A:HOH2293 3.7 17.6 1.0 HB2 A:ASN10 3.7 9.0 1.0 O A:HOH2010 3.8 22.2 1.0 CB A:ASN10 3.9 9.1 1.0 HE3 A:LYS38 3.9 11.7 1.0 H1 A:HOH2131 3.9 30.6 1.0 CA A:ASN10 3.9 6.8 1.0 OD1 A:ASP246 3.9 8.8 1.0 HD22 A:ASN8 4.0 7.2 0.0 OD2 A:ASP246 4.0 10.5 1.0 H1 A:HOH2132 4.1 28.3 1.0 HH A:TYR109 4.1 14.1 0.0 H2 A:HOH2293 4.2 17.6 1.0 OD1 A:ASN8 4.2 7.4 1.0 H2 A:HOH2132 4.2 28.3 1.0 O A:HOH2131 4.3 30.6 1.0 ND2 A:ASN10 4.3 11.8 1.0 H1 A:HOH2143 4.3 15.7 1.0 CG A:ASP246 4.4 8.8 1.0 H1 A:HOH2010 4.4 22.2 1.0 CG A:GLU36 4.4 5.0 0.5 HB3 A:GLU36 4.4 8.6 0.5 CG A:GLU36 4.4 9.1 0.5 HE2 A:LYS38 4.4 11.7 1.0 HD22 A:ASN10 4.5 11.9 0.0 HZ3 A:LYS38 4.5 13.0 0.0 HB3 A:GLU36 4.5 5.3 0.5 O A:HOH2132 4.6 28.3 1.0 CE A:LYS38 4.6 11.9 1.0 H A:ASN10 4.6 6.1 1.0 HE2 A:HIS247 4.6 9.4 0.0 HD2 A:HIS247 4.6 6.4 1.0 ND2 A:ASN8 4.7 7.0 1.0 HB2 A:GLU36 4.7 8.5 0.5 CB A:GLU36 4.8 8.7 0.5 HG3 A:GLU36 4.8 9.2 0.5 N A:ASN10 4.8 6.3 1.0 HB3 A:ASN10 4.8 9.2 1.0 HB2 A:GLU36 4.8 5.4 0.5 CB A:GLU36 4.8 5.5 0.5 H1 A:HOH2180 4.8 14.0 1.0 HG2 A:GLU36 4.9 5.2 0.5 CG A:ASN8 4.9 6.1 1.0 OH A:TYR109 4.9 14.1 1.0 HG3 A:GLU36 4.9 5.1 0.5 C A:ASN10 5.0 7.1 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