Magnesium in PDB 4lnd: Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor

All present enzymatic activity of Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor:
4.2.99.18;

The structure of Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor, PDB code: 4lnd was solved by B.A.Manvilla, E.Pozharski, E.A.Toth, A.C.Drohat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 1.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	165.795, 90.940, 94.030, 90.00, 123.22, 90.00
R / Rfree (%)	21.7 / 24.1

The binding sites of Magnesium atom in the Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor (pdb code 4lnd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor, PDB code: 4lnd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:33.2 occ:1.00 O A:HOH502 1.9 35.4 1.0 OE1 A:GLU96 1.9 31.5 1.0 O A:HOH504 2.0 26.2 1.0 O A:HOH501 2.1 31.0 1.0 OD1 A:ASP70 2.1 27.0 1.0 O A:HOH503 2.2 31.2 1.0 CD A:GLU96 2.9 31.2 1.0 CG A:ASP70 3.1 27.2 1.0 OE2 A:GLU96 3.2 33.4 1.0 CB A:ASP70 3.8 26.5 1.0 OD2 A:ASP70 4.0 28.3 1.0 CA A:ASP70 4.0 26.3 1.0 OD2 A:ASP308 4.0 26.6 1.0 OD1 A:ASP308 4.1 26.6 1.0 O A:HOH514 4.2 29.4 1.0 NZ A:LYS98 4.3 35.2 1.0 CG A:GLU96 4.3 30.6 1.0 OD1 A:ASN68 4.4 23.6 1.0 CG A:ASP308 4.5 25.6 1.0 CE A:LYS98 4.7 34.8 1.0 ND2 A:ASN68 4.9 23.5 1.0 N A:ASP70 5.0 25.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:35.6 occ:1.00 OE1 B:GLU96 2.0 31.0 1.0 OD1 B:ASP70 2.0 29.1 1.0 O B:HOH504 2.1 32.8 1.0 O B:HOH502 2.1 34.1 1.0 O B:HOH503 2.1 36.6 1.0 O B:HOH501 2.2 31.4 1.0 CD B:GLU96 3.0 30.9 1.0 CG B:ASP70 3.1 28.7 1.0 OE2 B:GLU96 3.3 33.3 1.0 CB B:ASP70 3.8 27.8 1.0 OD2 B:ASP70 4.0 29.6 1.0 OD2 B:ASP308 4.0 28.5 1.0 NZ B:LYS98 4.0 37.6 1.0 CA B:ASP70 4.0 27.0 1.0 OD1 B:ASP308 4.2 26.2 1.0 CG B:GLU96 4.3 30.4 1.0 CE B:LYS98 4.4 36.0 1.0 OD1 B:ASN68 4.5 25.3 1.0 CG B:ASP308 4.5 27.4 1.0 C B:ASP70 5.0 27.3 1.0 ND2 B:ASN68 5.0 25.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with Essential MG2+ Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:36.0 occ:1.00 OE1 C:GLU96 1.9 33.3 1.0 OD1 C:ASP70 1.9 31.7 1.0 O C:HOH501 2.0 38.6 1.0 O C:HOH502 2.1 35.7 1.0 O C:HOH504 2.1 40.1 1.0 O C:HOH503 2.1 35.7 1.0 CD C:GLU96 2.9 34.8 1.0 CG C:ASP70 3.0 30.7 1.0 OE2 C:GLU96 3.2 35.5 1.0 CB C:ASP70 3.7 29.4 1.0 CA C:ASP70 3.9 28.6 1.0 OD2 C:ASP70 3.9 31.2 1.0 NZ C:LYS98 4.0 36.9 1.0 OD2 C:ASP308 4.1 29.9 1.0 OD1 C:ASP308 4.2 28.6 1.0 CG C:GLU96 4.2 33.9 1.0 CE C:LYS98 4.3 36.5 1.0 OD1 C:ASN68 4.4 29.6 1.0 CG C:ASP308 4.6 28.9 1.0 C C:ASP70 4.9 28.9 1.0 N C:ASP70 4.9 28.3 1.0

B.A.Manvilla, E.Pozharski, E.A.Toth, A.C.Drohat. Structure of Human Apurinic/Apyrimidinic Endonuclease 1 with the Essential Mg(2+) Cofactor. Acta Crystallogr.,Sect.D V. 69 2555 2013.
ISSN: ISSN 0907-4449
PubMed: 24311596
DOI: 10.1107/S0907444913027042