Manganese in PDB 1s3n: Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase

The structure of Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase, PDB code: 1s3n was solved by S.Chen, D.Busso, A.F.Yakunin, E.Kuznetsova, M.Proudfoot, J.Jancrick, R.Kim, S.-H.Kim, Berkeley Structural Genomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.20 / 2.50
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	70.398, 70.398, 196.705, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.3

The binding sites of Manganese atom in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase (pdb code 1s3n). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase, PDB code: 1s3n:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:52.7 occ:1.00 NE2 A:HIS97 2.4 38.5 1.0 OD1 A:ASN59 2.4 43.9 1.0 OD1 A:ASP36 2.6 35.7 1.0 ND1 A:HIS120 2.6 41.4 1.0 MN A:MN504 2.9 58.6 1.0 O A:HOH641 2.9 25.5 1.0 CE1 A:HIS120 3.3 39.4 1.0 CD2 A:HIS97 3.4 38.5 1.0 CE1 A:HIS97 3.4 36.7 1.0 CG A:ASN59 3.5 42.8 1.0 CG A:ASP36 3.6 38.4 1.0 ND2 A:ASN60 3.6 47.1 1.0 CG A:HIS120 3.7 39.3 1.0 OD2 A:ASP36 3.9 42.2 1.0 ND2 A:ASN59 3.9 39.8 1.0 O A:HIS120 3.9 39.2 1.0 CA A:HIS120 3.9 40.1 1.0 OD1 A:ASP8 3.9 38.5 1.0 CB A:HIS120 4.2 37.6 1.0 C A:HIS120 4.4 39.7 1.0 ND1 A:HIS97 4.5 37.4 1.0 NE2 A:HIS120 4.5 42.6 1.0 CG A:HIS97 4.5 40.0 1.0 N A:ASN59 4.6 51.3 1.0 CD2 A:HIS120 4.8 41.8 1.0 CB A:ASN59 4.8 44.2 1.0 CB A:ASP36 4.9 40.4 1.0 CG A:ASN60 5.0 49.3 1.0

Manganese binding site 2 out of 4 in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn504 b:58.6 occ:1.00 OD1 A:ASP8 2.3 38.5 1.0 NE2 A:HIS10 2.4 35.6 1.0 OD1 A:ASP36 2.6 35.7 1.0 CE1 A:HIS10 2.8 34.8 1.0 NE2 A:HIS122 2.8 41.7 1.0 MN A:MN503 2.9 52.7 1.0 O A:HOH641 3.1 25.5 1.0 CG A:ASP8 3.5 37.2 1.0 CD2 A:HIS122 3.6 42.4 1.0 CD2 A:HIS10 3.7 33.7 1.0 CG A:ASP36 3.8 38.4 1.0 CE1 A:HIS122 3.9 44.3 1.0 O A:HIS120 3.9 39.2 1.0 ND1 A:HIS10 4.1 35.9 1.0 ND2 A:ASN60 4.1 47.1 1.0 CB A:ASP8 4.2 36.1 1.0 CB A:ASP36 4.2 40.4 1.0 NE2 A:HIS97 4.3 38.5 1.0 CE1 A:HIS97 4.4 36.7 1.0 OD2 A:ASP8 4.4 36.1 1.0 CG A:HIS10 4.5 33.7 1.0 CA A:HIS120 4.7 40.1 1.0 C A:HIS120 4.8 39.7 1.0 OD2 A:ASP36 4.8 42.2 1.0 ND1 A:HIS120 4.8 41.4 1.0 CG A:HIS122 4.9 43.7 1.0 CA A:ASP8 4.9 36.5 1.0 ND1 A:HIS122 5.0 46.1 1.0

Manganese binding site 3 out of 4 in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:54.7 occ:1.00 OD1 B:ASN259 2.4 45.5 1.0 NE2 B:HIS297 2.4 37.9 1.0 OD1 B:ASP236 2.5 38.1 1.0 ND1 B:HIS320 2.6 39.7 1.0 MN B:MN502 2.9 59.8 1.0 O B:HOH640 2.9 23.7 1.0 CE1 B:HIS320 3.3 39.0 1.0 CE1 B:HIS297 3.4 35.8 1.0 CD2 B:HIS297 3.4 36.8 1.0 CG B:ASN259 3.5 44.7 1.0 CG B:ASP236 3.6 40.0 1.0 ND2 B:ASN260 3.6 46.5 1.0 CG B:HIS320 3.8 39.3 1.0 ND2 B:ASN259 3.9 41.4 1.0 OD2 B:ASP236 3.9 42.2 1.0 O B:HIS320 3.9 38.5 1.0 OD1 B:ASP208 4.0 38.8 1.0 CA B:HIS320 4.0 39.8 1.0 CB B:HIS320 4.2 37.3 1.0 C B:HIS320 4.4 39.2 1.0 ND1 B:HIS297 4.5 36.3 1.0 NE2 B:HIS320 4.6 42.7 1.0 N B:ASN259 4.6 51.2 1.0 CG B:HIS297 4.6 38.6 1.0 CD2 B:HIS320 4.8 40.7 1.0 CB B:ASN259 4.8 46.3 1.0 CB B:ASP236 4.8 40.6 1.0 CG B:ASN260 4.9 50.4 1.0

Manganese binding site 4 out of 4 in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:59.8 occ:1.00 OD1 B:ASP208 2.3 38.8 1.0 NE2 B:HIS210 2.4 35.2 1.0 OD1 B:ASP236 2.6 38.1 1.0 CE1 B:HIS210 2.8 34.8 1.0 NE2 B:HIS322 2.8 41.0 1.0 MN B:MN501 2.9 54.7 1.0 O B:HOH640 3.1 23.7 1.0 CG B:ASP208 3.5 37.4 1.0 CD2 B:HIS322 3.6 41.8 1.0 CD2 B:HIS210 3.7 33.0 1.0 CG B:ASP236 3.8 40.0 1.0 CE1 B:HIS322 3.9 42.9 1.0 O B:HIS320 4.0 38.5 1.0 ND1 B:HIS210 4.1 36.2 1.0 ND2 B:ASN260 4.2 46.5 1.0 CB B:ASP208 4.2 35.9 1.0 CB B:ASP236 4.2 40.6 1.0 NE2 B:HIS297 4.3 37.9 1.0 CE1 B:HIS297 4.4 35.8 1.0 OD2 B:ASP208 4.4 37.2 1.0 CG B:HIS210 4.5 33.5 1.0 CA B:HIS320 4.7 39.8 1.0 C B:HIS320 4.8 39.2 1.0 OD2 B:ASP236 4.8 42.2 1.0 ND1 B:HIS320 4.8 39.7 1.0 CG B:HIS322 4.8 43.0 1.0 CA B:ASP208 4.9 36.5 1.0 ND1 B:HIS322 5.0 45.2 1.0

S.Chen, A.F.Yakunin, E.Kuznetsova, D.Busso, R.Pufan, M.Proudfoot, R.Kim, S.-H.Kim. Structural and Functional Characterization of A Novel Phosphodiesterase From Methanococcus Jannaschii J.Biol.Chem. V. 279 31854 2004.
ISSN: ISSN 0021-9258
PubMed: 15128743
DOI: 10.1074/JBC.M401059200