Magnesium in PDB 1oxh: The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form
Enzymatic activity of The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form
All present enzymatic activity of The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form:
2.3.1.41;
Protein crystallography data
The structure of The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form, PDB code: 1oxh
was solved by
A.C.Price,
C.O.Rock,
S.W.White,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.19 /
2.09
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.520,
71.646,
96.100,
89.83,
83.09,
69.15
|
R / Rfree (%)
|
20.8 /
23.5
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form
(pdb code 1oxh). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form, PDB code: 1oxh:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1oxh
Go back to
Magnesium Binding Sites List in 1oxh
Magnesium binding site 1 out
of 4 in the The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg901
b:22.4
occ:1.00
|
OE1
|
A:GLU346
|
2.4
|
35.0
|
1.0
|
OD1
|
A:ASN301
|
2.7
|
32.4
|
1.0
|
O
|
A:ASN392
|
2.7
|
39.4
|
1.0
|
O
|
A:ASN301
|
2.7
|
32.9
|
1.0
|
OG
|
A:SER391
|
2.8
|
36.5
|
1.0
|
O
|
A:ALA302
|
3.1
|
35.1
|
1.0
|
CD
|
A:GLU346
|
3.4
|
36.2
|
1.0
|
C
|
A:ALA302
|
3.5
|
35.1
|
1.0
|
N
|
A:ASN392
|
3.5
|
37.5
|
1.0
|
C
|
A:ASN301
|
3.5
|
32.5
|
1.0
|
C
|
A:ASN392
|
3.6
|
38.9
|
1.0
|
CG
|
A:ASN301
|
3.7
|
30.0
|
1.0
|
CB
|
A:GLU346
|
3.7
|
35.4
|
1.0
|
N
|
A:HIS303
|
3.8
|
35.7
|
1.0
|
CG
|
A:GLU346
|
3.9
|
35.1
|
1.0
|
CB
|
A:SER391
|
4.0
|
35.9
|
1.0
|
C
|
A:SER391
|
4.0
|
36.4
|
1.0
|
O
|
A:HOH925
|
4.0
|
36.3
|
1.0
|
CB
|
A:ASN301
|
4.1
|
29.9
|
1.0
|
CA
|
A:ASN392
|
4.1
|
38.2
|
1.0
|
CA
|
A:SER391
|
4.1
|
36.3
|
1.0
|
N
|
A:ALA302
|
4.2
|
33.5
|
1.0
|
CA
|
A:HIS303
|
4.3
|
36.7
|
1.0
|
CA
|
A:ALA302
|
4.3
|
34.9
|
1.0
|
OE2
|
A:GLU346
|
4.4
|
33.7
|
1.0
|
CA
|
A:ASN301
|
4.4
|
30.8
|
1.0
|
CG2
|
A:THR393
|
4.5
|
40.3
|
1.0
|
O
|
A:HOH905
|
4.8
|
29.1
|
1.0
|
N
|
A:THR393
|
4.8
|
40.0
|
1.0
|
ND2
|
A:ASN301
|
4.8
|
29.1
|
1.0
|
NZ
|
A:LYS332
|
4.8
|
30.0
|
1.0
|
CB
|
A:ASN392
|
4.8
|
37.7
|
1.0
|
O
|
A:SER391
|
4.9
|
35.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1oxh
Go back to
Magnesium Binding Sites List in 1oxh
Magnesium binding site 2 out
of 4 in the The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg902
b:29.9
occ:1.00
|
OE1
|
B:GLU346
|
2.5
|
36.2
|
1.0
|
OG
|
B:SER391
|
2.5
|
37.0
|
1.0
|
O
|
B:ASN392
|
2.7
|
39.4
|
1.0
|
OD1
|
B:ASN301
|
2.7
|
39.8
|
1.0
|
O
|
B:ASN301
|
2.8
|
38.1
|
1.0
|
O
|
B:ALA302
|
2.9
|
40.3
|
1.0
|
N
|
B:ASN392
|
3.4
|
37.7
|
1.0
|
C
|
B:ALA302
|
3.5
|
40.7
|
1.0
|
CD
|
B:GLU346
|
3.5
|
36.5
|
1.0
|
C
|
B:ASN301
|
3.5
|
38.7
|
1.0
|
C
|
B:ASN392
|
3.6
|
38.9
|
1.0
|
CB
|
B:GLU346
|
3.7
|
36.2
|
1.0
|
CG
|
B:ASN301
|
3.7
|
37.6
|
1.0
|
CB
|
B:SER391
|
3.8
|
36.0
|
1.0
|
C
|
B:SER391
|
3.9
|
36.4
|
1.0
|
CG
|
B:GLU346
|
3.9
|
35.6
|
1.0
|
O
|
B:HOH936
|
4.0
|
37.0
|
1.0
|
CA
|
B:SER391
|
4.0
|
36.5
|
1.0
|
CA
|
B:ASN392
|
4.0
|
38.3
|
1.0
|
N
|
B:HIS303
|
4.1
|
40.4
|
1.0
|
N
|
B:ALA302
|
4.1
|
39.6
|
1.0
|
CB
|
B:ASN301
|
4.1
|
37.9
|
1.0
|
CA
|
B:ALA302
|
4.3
|
40.9
|
1.0
|
CA
|
B:HIS303
|
4.4
|
41.1
|
1.0
|
CA
|
B:ASN301
|
4.4
|
37.8
|
1.0
|
OE2
|
B:GLU346
|
4.6
|
34.2
|
1.0
|
CG2
|
B:THR393
|
4.6
|
41.0
|
1.0
|
O
|
B:HOH915
|
4.8
|
29.0
|
1.0
|
CB
|
B:ASN392
|
4.8
|
37.9
|
1.0
|
N
|
B:THR393
|
4.8
|
40.2
|
1.0
|
O
|
B:SER391
|
4.8
|
36.5
|
1.0
|
ND2
|
B:ASN301
|
4.9
|
41.5
|
1.0
|
NZ
|
B:LYS332
|
5.0
|
30.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1oxh
Go back to
Magnesium Binding Sites List in 1oxh
Magnesium binding site 3 out
of 4 in the The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg903
b:25.1
occ:1.00
|
OE1
|
C:GLU346
|
2.5
|
35.1
|
1.0
|
OD1
|
C:ASN301
|
2.6
|
38.5
|
1.0
|
O
|
C:ASN301
|
2.6
|
36.0
|
1.0
|
O
|
C:ASN392
|
2.6
|
39.6
|
1.0
|
OG
|
C:SER391
|
2.8
|
36.2
|
1.0
|
O
|
C:ALA302
|
3.0
|
39.6
|
1.0
|
N
|
C:ASN392
|
3.4
|
38.1
|
1.0
|
C
|
C:ALA302
|
3.5
|
39.1
|
1.0
|
CD
|
C:GLU346
|
3.5
|
36.1
|
1.0
|
C
|
C:ASN301
|
3.5
|
36.9
|
1.0
|
C
|
C:ASN392
|
3.6
|
39.0
|
1.0
|
CG
|
C:ASN301
|
3.7
|
37.0
|
1.0
|
CB
|
C:GLU346
|
3.8
|
35.2
|
1.0
|
N
|
C:HIS303
|
3.9
|
39.4
|
1.0
|
CB
|
C:SER391
|
4.0
|
36.3
|
1.0
|
C
|
C:SER391
|
4.0
|
36.5
|
1.0
|
CG
|
C:GLU346
|
4.0
|
35.1
|
1.0
|
O
|
C:HOH926
|
4.0
|
35.9
|
1.0
|
CA
|
C:ASN392
|
4.1
|
38.2
|
1.0
|
CA
|
C:SER391
|
4.1
|
36.2
|
1.0
|
CB
|
C:ASN301
|
4.1
|
36.0
|
1.0
|
CA
|
C:HIS303
|
4.2
|
40.0
|
1.0
|
N
|
C:ALA302
|
4.3
|
37.9
|
1.0
|
CA
|
C:ALA302
|
4.3
|
39.1
|
1.0
|
CA
|
C:ASN301
|
4.4
|
35.3
|
1.0
|
CG2
|
C:THR393
|
4.5
|
40.6
|
1.0
|
OE2
|
C:GLU346
|
4.5
|
33.6
|
1.0
|
O
|
C:HOH907
|
4.6
|
29.9
|
1.0
|
N
|
C:THR393
|
4.7
|
40.0
|
1.0
|
CB
|
C:ASN392
|
4.8
|
37.8
|
1.0
|
NZ
|
C:LYS332
|
4.8
|
30.0
|
1.0
|
ND2
|
C:ASN301
|
4.8
|
37.6
|
1.0
|
O
|
C:SER391
|
4.9
|
35.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1oxh
Go back to
Magnesium Binding Sites List in 1oxh
Magnesium binding site 4 out
of 4 in the The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of The Crystal Structure of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase II From Streptococcus Pneumoniae, Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg904
b:21.4
occ:1.00
|
OE1
|
D:GLU346
|
2.5
|
35.8
|
1.0
|
OD1
|
D:ASN301
|
2.6
|
37.5
|
1.0
|
O
|
D:ASN392
|
2.6
|
38.7
|
1.0
|
OG
|
D:SER391
|
2.6
|
36.7
|
1.0
|
O
|
D:ALA302
|
2.7
|
38.5
|
1.0
|
O
|
D:ASN301
|
2.8
|
33.8
|
1.0
|
N
|
D:ASN392
|
3.3
|
37.3
|
1.0
|
CD
|
D:GLU346
|
3.4
|
36.3
|
1.0
|
C
|
D:ALA302
|
3.5
|
37.8
|
1.0
|
C
|
D:ASN301
|
3.5
|
34.5
|
1.0
|
C
|
D:ASN392
|
3.5
|
38.9
|
1.0
|
CG
|
D:ASN301
|
3.6
|
34.4
|
1.0
|
CB
|
D:GLU346
|
3.7
|
35.7
|
1.0
|
CB
|
D:SER391
|
3.8
|
36.2
|
1.0
|
CG
|
D:GLU346
|
3.9
|
35.6
|
1.0
|
C
|
D:SER391
|
3.9
|
36.3
|
1.0
|
CA
|
D:ASN392
|
4.0
|
38.2
|
1.0
|
CB
|
D:ASN301
|
4.0
|
34.3
|
1.0
|
CA
|
D:SER391
|
4.0
|
36.4
|
1.0
|
N
|
D:HIS303
|
4.0
|
38.2
|
1.0
|
O
|
D:HOH938
|
4.0
|
36.4
|
1.0
|
N
|
D:ALA302
|
4.1
|
35.0
|
1.0
|
CA
|
D:ALA302
|
4.3
|
37.1
|
1.0
|
CA
|
D:HIS303
|
4.3
|
38.8
|
1.0
|
CA
|
D:ASN301
|
4.4
|
35.0
|
1.0
|
OE2
|
D:GLU346
|
4.5
|
34.4
|
1.0
|
CG2
|
D:THR393
|
4.5
|
40.7
|
1.0
|
N
|
D:THR393
|
4.7
|
40.0
|
1.0
|
O
|
D:HOH918
|
4.7
|
28.5
|
1.0
|
CB
|
D:ASN392
|
4.8
|
38.0
|
1.0
|
O
|
D:SER391
|
4.8
|
36.2
|
1.0
|
ND2
|
D:ASN301
|
4.8
|
35.4
|
1.0
|
NZ
|
D:LYS332
|
4.9
|
30.2
|
1.0
|
|
Reference:
A.C.Price,
C.O.Rock,
S.W.White.
The 1.3-Angstrom-Resolution Crystal Structure of Beta-Ketoacyl-Acyl Carrier Protein Synthase II From Streptococcus Pneumoniae. J.Bacteriol. V. 185 4136 2003.
ISSN: ISSN 0021-9193
PubMed: 12837788
DOI: 10.1128/JB.185.14.4136-4143.2003
Page generated: Tue Aug 13 10:44:19 2024
|