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: Sat Oct 5 12:22:06 2024
|