Nickel in PDB 1s3m: Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase

The structure of Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase, PDB code: 1s3m was solved by S.Chen, D.Busso, A.F.Yakunin, E.Kuznetsova, M.Proudfoot, J.Jancrick, R.Kim, S.-H.Kim, Berkeley Structural Genomicscenter (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.05 / 2.50
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	70.106, 70.106, 196.173, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.6

The binding sites of Nickel atom in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase (pdb code 1s3m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structural and Functional Characterization of A Novel Archaeal Phosphodiesterase, PDB code: 1s3m:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel 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 Nickel with other atoms in the Ni 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:Ni503 b:65.9 occ:1.00 NE2 A:HIS97 2.5 36.7 1.0 OD1 A:ASN59 2.6 44.3 1.0 O A:HOH647 2.7 28.3 1.0 ND1 A:HIS120 2.8 41.7 1.0 NI A:NI504 2.9 46.8 1.0 OD1 A:ASP36 2.9 38.5 1.0 CE1 A:HIS97 3.2 33.7 1.0 OD2 A:ASP36 3.5 39.2 1.0 CG A:ASN59 3.5 44.5 1.0 CE1 A:HIS120 3.6 41.3 1.0 CD2 A:HIS97 3.6 34.4 1.0 CG A:ASP36 3.6 39.7 1.0 OD1 A:ASP8 3.7 30.0 1.0 ND2 A:ASN60 3.7 46.3 1.0 CA A:HIS120 3.8 41.3 1.0 ND2 A:ASN59 3.8 45.0 1.0 O A:HIS120 3.8 42.6 1.0 CG A:HIS120 3.8 40.8 1.0 CB A:HIS120 4.1 40.3 1.0 C A:HIS120 4.3 40.7 1.0 ND1 A:HIS97 4.4 35.5 1.0 CG A:HIS97 4.7 38.4 1.0 N A:HIS120 4.7 41.9 1.0 NE2 A:HIS120 4.8 43.5 1.0 N A:ASN59 4.8 42.9 1.0 CG A:ASP8 4.8 30.6 1.0 NE2 A:HIS10 4.8 27.6 1.0 NE2 A:HIS122 4.8 39.0 1.0 CB A:ASN59 4.9 43.7 1.0 CD2 A:HIS120 4.9 41.7 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni504 b:46.8 occ:1.00 OD1 A:ASP8 2.2 30.0 1.0 NE2 A:HIS10 2.2 27.6 1.0 NE2 A:HIS122 2.4 39.0 1.0 OD1 A:ASP36 2.6 38.5 1.0 NI A:NI503 2.9 65.9 1.0 O A:HOH647 2.9 28.3 1.0 CE1 A:HIS10 3.0 27.3 1.0 CD2 A:HIS122 3.2 39.5 1.0 CG A:ASP8 3.3 30.6 1.0 CD2 A:HIS10 3.4 25.8 1.0 CE1 A:HIS122 3.4 39.7 1.0 CG A:ASP36 3.9 39.7 1.0 CB A:ASP8 4.0 29.1 1.0 O A:HIS120 4.1 42.6 1.0 ND1 A:HIS10 4.2 27.3 1.0 OD2 A:ASP8 4.2 30.7 1.0 ND2 A:ASN60 4.3 46.3 1.0 CG A:HIS10 4.4 27.6 1.0 CG A:HIS122 4.4 39.8 1.0 CE1 A:HIS97 4.4 33.7 1.0 ND1 A:HIS122 4.5 42.0 1.0 NE2 A:HIS97 4.5 36.7 1.0 OD2 A:ASP36 4.6 39.2 1.0 CA A:ASP8 4.8 28.8 1.0 CA A:HIS120 4.9 41.3 1.0 CB A:ASP36 4.9 41.9 1.0 C A:HIS120 4.9 40.7 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni501 b:66.4 occ:1.00 NE2 B:HIS297 2.4 35.6 1.0 OD1 B:ASN259 2.6 42.2 1.0 ND1 B:HIS320 2.6 42.1 1.0 O B:HOH646 2.9 27.6 1.0 NI B:NI502 2.9 46.0 1.0 OD1 B:ASP236 3.1 37.3 1.0 CE1 B:HIS297 3.2 33.9 1.0 CE1 B:HIS320 3.4 42.0 1.0 CD2 B:HIS297 3.5 33.4 1.0 CG B:ASN259 3.5 42.9 1.0 OD2 B:ASP236 3.5 39.5 1.0 CA B:HIS320 3.6 41.3 1.0 CG B:HIS320 3.7 41.0 1.0 O B:HIS320 3.7 43.3 1.0 CG B:ASP236 3.7 39.6 1.0 ND2 B:ASN259 3.8 43.4 1.0 OD1 B:ASP208 3.8 33.0 1.0 ND2 B:ASN260 3.9 44.9 1.0 CB B:HIS320 4.0 40.1 1.0 C B:HIS320 4.2 41.3 1.0 ND1 B:HIS297 4.4 37.2 1.0 CG B:HIS297 4.6 37.6 1.0 NE2 B:HIS320 4.6 44.7 1.0 N B:HIS320 4.6 42.3 1.0 N B:ASN259 4.8 43.4 1.0 CD2 B:HIS320 4.8 41.9 1.0 CG B:ASP208 4.8 32.0 1.0 CB B:ASN259 4.9 43.0 1.0 NE2 B:HIS322 4.9 36.0 1.0 O B:HOH640 4.9 50.0 1.0 NE2 B:HIS210 4.9 29.0 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni502 b:46.0 occ:1.00 OD1 B:ASP208 2.2 33.0 1.0 NE2 B:HIS210 2.3 29.0 1.0 NE2 B:HIS322 2.4 36.0 1.0 OD1 B:ASP236 2.6 37.3 1.0 O B:HOH646 2.7 27.6 1.0 NI B:NI501 2.9 66.4 1.0 CE1 B:HIS210 3.0 26.6 1.0 CD2 B:HIS322 3.2 37.5 1.0 CG B:ASP208 3.3 32.0 1.0 CD2 B:HIS210 3.5 26.3 1.0 CE1 B:HIS322 3.5 37.0 1.0 CG B:ASP236 3.8 39.6 1.0 CB B:ASP208 4.1 29.1 1.0 O B:HIS320 4.1 43.3 1.0 OD2 B:ASP208 4.1 31.5 1.0 ND1 B:HIS210 4.2 29.1 1.0 ND2 B:ASN260 4.3 44.9 1.0 CE1 B:HIS297 4.4 33.9 1.0 NE2 B:HIS297 4.4 35.6 1.0 CG B:HIS322 4.5 38.3 1.0 CG B:HIS210 4.5 28.1 1.0 OD2 B:ASP236 4.5 39.5 1.0 ND1 B:HIS322 4.6 39.2 1.0 CA B:HIS320 4.8 41.3 1.0 C B:HIS320 4.8 41.3 1.0 CA B:ASP208 4.8 29.0 1.0 CB B:ASP236 4.8 42.0 1.0 O B:HOH671 4.9 44.4 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