Manganese in PDB 1zm8: Apo Crystal Structure of Nuclease A From Anabaena Sp.

The structure of Apo Crystal Structure of Nuclease A From Anabaena Sp., PDB code: 1zm8 was solved by M.Ghosh, G.Meiss, A.Pingoud, R.E.London, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.87 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.690, 66.682, 81.730, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.6

The structure of Apo Crystal Structure of Nuclease A From Anabaena Sp. also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Apo Crystal Structure of Nuclease A From Anabaena Sp. (pdb code 1zm8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Apo Crystal Structure of Nuclease A From Anabaena Sp., PDB code: 1zm8:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Apo Crystal Structure of Nuclease A From Anabaena Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Apo Crystal Structure of Nuclease A From Anabaena Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn275 b:37.6 occ:1.00 OD1 A:ASN155 2.0 38.1 1.0 O A:HOH282 2.1 31.3 1.0 O4 A:SO4278 2.1 59.5 1.0 O A:HOH281 2.2 30.4 1.0 O A:HOH284 2.3 29.6 1.0 O A:HOH283 2.4 35.6 1.0 CG A:ASN155 3.2 36.7 1.0 S A:SO4278 3.4 61.0 1.0 ND2 A:ASN155 3.7 35.6 1.0 O2 A:SO4278 3.8 60.0 1.0 O3 A:SO4278 3.8 59.9 1.0 N A:HIS124 4.0 34.8 1.0 O A:HOH300 4.1 32.0 1.0 OE1 A:GLU163 4.1 34.6 1.0 OE2 A:GLU163 4.1 32.2 1.0 ND1 A:HIS124 4.3 34.0 1.0 OE1 A:GLN150 4.3 42.7 1.0 O A:ASN155 4.4 37.1 1.0 CB A:ASN155 4.4 36.3 1.0 CD1 A:TRP159 4.5 34.6 1.0 CB A:HIS124 4.5 33.5 1.0 CA A:GLY123 4.5 36.8 1.0 CD A:GLU163 4.5 32.6 1.0 O A:HIS124 4.5 32.1 1.0 O1 A:SO4278 4.5 63.3 1.0 CA A:ASN155 4.7 37.3 1.0 C A:GLY123 4.7 36.9 1.0 CA A:HIS124 4.8 33.4 1.0 C A:ASN155 4.8 37.9 1.0 CG A:HIS124 4.8 33.5 1.0 NE1 A:TRP159 4.9 34.3 1.0

Manganese binding site 2 out of 3 in the Apo Crystal Structure of Nuclease A From Anabaena Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Apo Crystal Structure of Nuclease A From Anabaena Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn276 b:39.7 occ:1.00 OD1 A:ASP246 2.1 27.7 0.7 OE1 A:GLU249 2.1 35.4 1.0 OE1 A:GLU269 2.1 39.8 1.0 O A:HOH285 2.4 46.2 1.0 CD A:GLU249 3.1 36.1 1.0 CD A:GLU269 3.3 43.0 1.0 CG A:ASP246 3.3 29.8 0.7 OE2 A:GLU249 3.5 34.3 1.0 CB A:GLU269 3.6 43.2 1.0 MN A:MN277 3.7 42.9 1.0 CG A:GLU269 4.0 41.9 1.0 OD2 A:ASP246 4.0 30.4 0.7 O A:HOH325 4.1 39.3 1.0 OE2 A:GLU269 4.3 41.1 1.0 CA A:ASP246 4.3 32.3 1.0 CB A:ASP246 4.4 30.8 0.7 CG A:GLU249 4.4 35.0 1.0 N A:ASP246 4.7 32.7 1.0 CA A:GLU269 4.9 43.9 1.0 OE1 A:GLN265 5.0 36.8 1.0

Manganese binding site 3 out of 3 in the Apo Crystal Structure of Nuclease A From Anabaena Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Apo Crystal Structure of Nuclease A From Anabaena Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn277 b:42.9 occ:1.00 OD1 A:ASP255 2.4 36.4 1.0 OE2 A:GLU249 2.4 34.3 1.0 O A:PHE256 2.5 32.8 1.0 OE1 A:GLN265 2.5 36.8 1.0 OE1 A:GLU269 2.5 39.8 1.0 OE2 A:GLU269 2.7 41.1 1.0 CD A:GLU269 2.9 43.0 1.0 CD A:GLU249 3.5 36.1 1.0 C A:PHE256 3.6 33.1 1.0 N A:PHE256 3.6 30.9 1.0 CG A:ASP255 3.6 34.9 1.0 CD A:GLN265 3.6 39.0 1.0 MN A:MN276 3.7 39.7 1.0 OE1 A:GLU249 3.8 35.4 1.0 C A:ASP255 4.0 31.6 1.0 CA A:PHE256 4.1 30.9 1.0 CA A:ASP255 4.3 31.9 1.0 CG A:GLN265 4.4 41.2 1.0 OD2 A:ASP255 4.4 33.8 1.0 CG A:GLU269 4.4 41.9 1.0 CB A:ASP255 4.5 31.4 1.0 NE2 A:GLN265 4.6 36.3 1.0 O A:HOH310 4.7 35.1 1.0 N A:LEU257 4.7 32.2 1.0 C A:LEU257 4.7 35.5 1.0 O A:ASP255 4.8 30.1 1.0 CB A:PHE256 4.8 31.0 1.0 CG A:GLU249 4.8 35.0 1.0 CB A:GLN265 4.8 42.6 1.0 O A:LEU257 4.8 36.8 1.0 O A:HOH285 4.8 46.2 1.0 CB A:LEU257 4.9 35.0 1.0 N A:SER258 4.9 36.9 1.0

M.Ghosh, G.Meiss, A.Pingoud, R.E.London, L.C.Pedersen. Structural Insights Into the Mechanism of Nuclease A, A Beta Beta Alpha Metal Nuclease From Anabaena. J.Biol.Chem. V. 280 27990 2005.
ISSN: ISSN 0021-9258
PubMed: 15897201
DOI: 10.1074/JBC.M501798200