Atomistry » Manganese » PDB 1r2m-1sfy » 1s3n
Atomistry »
  Manganese »
    PDB 1r2m-1sfy »
      1s3n »

Manganese in PDB 1s3n: 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: 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

Manganese Binding Sites:

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 1s3n

Go back to Manganese Binding Sites List in 1s3n
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 1s3n

Go back to Manganese Binding Sites List in 1s3n
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 1s3n

Go back to Manganese Binding Sites List in 1s3n
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 1s3n

Go back to Manganese Binding Sites List in 1s3n
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

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: Tue Dec 15 03:55:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy