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

Protein crystallography data

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

Nickel Binding Sites:

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 1s3m

Go back to Nickel Binding Sites List in 1s3m
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 1s3m

Go back to Nickel Binding Sites List in 1s3m
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 1s3m

Go back to Nickel Binding Sites List in 1s3m
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 1s3m

Go back to Nickel Binding Sites List in 1s3m
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

Reference:

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
Page generated: Fri Sep 25 08:01:07 2020
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