Magnesium in PDB 1sjc: X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine
Protein crystallography data
The structure of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine, PDB code: 1sjc
was solved by
J.B.Thoden,
E.A.Taylor-Ringia,
J.B.Garrett,
J.A.Gerlt,
H.M.Holden,
I.Rayment,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.10
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
215.700,
215.700,
259.000,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
n/a /
n/a
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine
(pdb code 1sjc). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine, PDB code: 1sjc:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1sjc
Go back to
Magnesium Binding Sites List in 1sjc
Magnesium binding site 1 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1001
b:47.8
occ:1.00
|
O12
|
A:SMG1000
|
2.1
|
70.1
|
1.0
|
OD2
|
A:ASP189
|
2.1
|
33.5
|
1.0
|
O
|
A:HOH1186
|
2.3
|
39.8
|
1.0
|
OE2
|
A:GLU214
|
2.4
|
45.7
|
1.0
|
OD2
|
A:ASP239
|
2.4
|
39.1
|
1.0
|
C2
|
A:SMG1000
|
2.7
|
39.4
|
1.0
|
O11
|
A:SMG1000
|
2.7
|
73.8
|
1.0
|
CD
|
A:GLU214
|
2.9
|
35.6
|
1.0
|
CG
|
A:ASP189
|
3.0
|
40.0
|
1.0
|
OD1
|
A:ASP189
|
3.3
|
39.5
|
1.0
|
OE1
|
A:GLU214
|
3.4
|
77.7
|
1.0
|
NZ
|
A:LYS161
|
3.5
|
33.9
|
1.0
|
CG
|
A:ASP239
|
3.6
|
27.5
|
1.0
|
CG
|
A:GLU214
|
3.7
|
40.5
|
1.0
|
ND2
|
A:ASN191
|
3.8
|
40.2
|
1.0
|
CB
|
A:ASP239
|
3.9
|
33.5
|
1.0
|
NZ
|
A:LYS163
|
4.0
|
47.2
|
1.0
|
C1
|
A:SMG1000
|
4.0
|
0.0
|
1.0
|
NZ
|
A:LYS263
|
4.1
|
62.1
|
1.0
|
ND2
|
A:ASN261
|
4.2
|
35.5
|
1.0
|
CB
|
A:ASP189
|
4.2
|
26.2
|
1.0
|
CG
|
A:ASN191
|
4.4
|
51.1
|
1.0
|
OD1
|
A:ASN191
|
4.4
|
45.9
|
1.0
|
OE1
|
A:GLU240
|
4.4
|
44.0
|
1.0
|
CE
|
A:LYS263
|
4.4
|
40.6
|
1.0
|
CE
|
A:LYS161
|
4.5
|
28.5
|
1.0
|
O
|
A:HOH1008
|
4.6
|
28.2
|
1.0
|
OD1
|
A:ASP239
|
4.6
|
41.2
|
1.0
|
CB
|
A:GLU214
|
4.7
|
31.0
|
1.0
|
CB
|
A:SMG1000
|
4.9
|
57.1
|
1.0
|
N1
|
A:SMG1000
|
4.9
|
57.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1sjc
Go back to
Magnesium Binding Sites List in 1sjc
Magnesium binding site 2 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1101
b:33.2
occ:1.00
|
OE2
|
B:GLU214
|
2.2
|
36.5
|
1.0
|
O12
|
B:SMG1100
|
2.2
|
50.9
|
1.0
|
O11
|
B:SMG1100
|
2.3
|
51.5
|
1.0
|
OD2
|
B:ASP239
|
2.4
|
30.1
|
1.0
|
O
|
B:HOH1113
|
2.4
|
30.8
|
1.0
|
OD2
|
B:ASP189
|
2.6
|
36.7
|
1.0
|
C2
|
B:SMG1100
|
2.6
|
32.7
|
1.0
|
CD
|
B:GLU214
|
3.0
|
30.9
|
1.0
|
CG
|
B:ASP189
|
3.3
|
28.5
|
1.0
|
OD1
|
B:ASP189
|
3.4
|
42.2
|
1.0
|
CG
|
B:ASP239
|
3.5
|
34.5
|
1.0
|
ND2
|
B:ASN191
|
3.6
|
46.5
|
1.0
|
CB
|
B:ASP239
|
3.7
|
29.9
|
1.0
|
OE1
|
B:GLU214
|
3.7
|
33.5
|
1.0
|
CG
|
B:GLU214
|
3.7
|
29.5
|
1.0
|
NZ
|
B:LYS161
|
3.8
|
26.3
|
1.0
|
NZ
|
B:LYS263
|
3.8
|
51.5
|
1.0
|
NZ
|
B:LYS163
|
3.9
|
49.8
|
1.0
|
C1
|
B:SMG1100
|
4.1
|
31.2
|
1.0
|
OE1
|
B:GLU240
|
4.2
|
30.7
|
1.0
|
O
|
B:HOH1176
|
4.3
|
49.6
|
1.0
|
ND2
|
B:ASN261
|
4.4
|
35.4
|
1.0
|
CG
|
B:ASN191
|
4.4
|
33.0
|
1.0
|
OD1
|
B:ASP239
|
4.6
|
37.4
|
1.0
|
CB
|
B:ASP189
|
4.6
|
29.8
|
1.0
|
OD1
|
B:ASN191
|
4.7
|
28.9
|
1.0
|
CE
|
B:LYS263
|
4.8
|
28.0
|
1.0
|
CE2
|
B:TYR55
|
4.8
|
29.3
|
1.0
|
CB
|
B:SMG1100
|
4.9
|
45.2
|
1.0
|
CE
|
B:LYS161
|
4.9
|
28.6
|
1.0
|
N1
|
B:SMG1100
|
4.9
|
43.0
|
1.0
|
CB
|
B:GLU214
|
4.9
|
28.7
|
1.0
|
CD
|
B:GLU240
|
5.0
|
35.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1sjc
Go back to
Magnesium Binding Sites List in 1sjc
Magnesium binding site 3 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1201
b:47.6
occ:1.00
|
OD2
|
C:ASP239
|
2.1
|
51.4
|
1.0
|
O
|
C:HOH1386
|
2.1
|
36.0
|
1.0
|
OD2
|
C:ASP189
|
2.2
|
33.6
|
1.0
|
OE2
|
C:GLU214
|
2.4
|
41.7
|
1.0
|
O11
|
C:SMG1200
|
2.6
|
38.7
|
1.0
|
O12
|
C:SMG1200
|
2.7
|
34.8
|
1.0
|
CG
|
C:ASP189
|
3.0
|
35.0
|
1.0
|
C2
|
C:SMG1200
|
3.0
|
0.0
|
1.0
|
OD1
|
C:ASP189
|
3.1
|
41.6
|
1.0
|
CD
|
C:GLU214
|
3.2
|
21.3
|
1.0
|
CG
|
C:ASP239
|
3.2
|
70.0
|
1.0
|
CB
|
C:ASP239
|
3.7
|
36.0
|
1.0
|
NZ
|
C:LYS161
|
3.8
|
39.1
|
1.0
|
OE1
|
C:GLU214
|
3.8
|
58.6
|
1.0
|
NZ
|
C:LYS263
|
3.9
|
50.2
|
1.0
|
ND2
|
C:ASN191
|
3.9
|
43.7
|
1.0
|
CG
|
C:GLU214
|
4.0
|
32.5
|
1.0
|
OE1
|
C:GLU240
|
4.1
|
38.9
|
1.0
|
OD1
|
C:ASP239
|
4.3
|
34.3
|
1.0
|
OD1
|
C:ASN191
|
4.3
|
34.6
|
1.0
|
CB
|
C:ASP189
|
4.4
|
29.2
|
1.0
|
CG
|
C:ASN191
|
4.4
|
40.2
|
1.0
|
NZ
|
C:LYS163
|
4.5
|
51.8
|
1.0
|
C1
|
C:SMG1200
|
4.5
|
37.6
|
1.0
|
CE
|
C:LYS263
|
4.6
|
40.0
|
1.0
|
ND2
|
C:ASN261
|
4.7
|
32.1
|
1.0
|
CB
|
C:GLU214
|
4.7
|
46.9
|
1.0
|
O
|
C:HOH1280
|
4.7
|
47.0
|
1.0
|
OE2
|
C:GLU240
|
4.8
|
37.6
|
1.0
|
CD
|
C:GLU240
|
4.8
|
33.1
|
1.0
|
CE
|
C:LYS161
|
4.8
|
22.2
|
1.0
|
CE1
|
C:TYR55
|
4.9
|
50.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1sjc
Go back to
Magnesium Binding Sites List in 1sjc
Magnesium binding site 4 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1301
b:66.7
occ:1.00
|
O12
|
D:SMG1300
|
1.9
|
78.8
|
1.0
|
OE2
|
D:GLU214
|
2.1
|
43.3
|
1.0
|
OD2
|
D:ASP239
|
2.3
|
38.1
|
1.0
|
O
|
D:HOH1437
|
2.4
|
47.6
|
1.0
|
OD2
|
D:ASP189
|
2.4
|
62.0
|
1.0
|
C2
|
D:SMG1300
|
2.7
|
59.0
|
1.0
|
O11
|
D:SMG1300
|
2.7
|
0.0
|
1.0
|
CD
|
D:GLU214
|
2.8
|
67.2
|
1.0
|
CG
|
D:ASP189
|
3.3
|
49.1
|
1.0
|
NZ
|
D:LYS161
|
3.4
|
39.6
|
1.0
|
OE1
|
D:GLU214
|
3.5
|
35.5
|
1.0
|
OD1
|
D:ASP189
|
3.5
|
45.9
|
1.0
|
CG
|
D:ASP239
|
3.5
|
62.2
|
1.0
|
CG
|
D:GLU214
|
3.6
|
37.5
|
1.0
|
ND2
|
D:ASN191
|
3.7
|
42.0
|
1.0
|
NZ
|
D:LYS263
|
3.7
|
42.6
|
1.0
|
CB
|
D:ASP239
|
3.8
|
49.9
|
1.0
|
C1
|
D:SMG1300
|
4.1
|
90.5
|
1.0
|
O
|
D:HOH1421
|
4.1
|
49.4
|
1.0
|
OE1
|
D:GLU240
|
4.2
|
55.4
|
1.0
|
CE
|
D:LYS161
|
4.3
|
60.9
|
1.0
|
ND2
|
D:ASN261
|
4.3
|
27.1
|
1.0
|
CG
|
D:ASN191
|
4.4
|
59.6
|
1.0
|
OD1
|
D:ASP239
|
4.5
|
37.6
|
1.0
|
OD1
|
D:ASN191
|
4.5
|
46.1
|
1.0
|
NZ
|
D:LYS163
|
4.6
|
42.0
|
1.0
|
CB
|
D:ASP189
|
4.6
|
33.0
|
1.0
|
CE
|
D:LYS263
|
4.6
|
41.1
|
1.0
|
CB
|
D:GLU214
|
4.7
|
29.8
|
1.0
|
CE2
|
D:TYR55
|
4.9
|
67.9
|
1.0
|
CB
|
D:SMG1300
|
4.9
|
55.5
|
1.0
|
N1
|
D:SMG1300
|
4.9
|
51.5
|
1.0
|
|
Reference:
J.B.Thoden,
E.A.Taylor-Ringia,
J.B.Garrett,
J.A.Gerlt,
H.M.Holden,
I.Rayment.
Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous O-Succinylbenzoate Synthase From Amycolatopsis Biochemistry V. 43 5716 2004.
ISSN: ISSN 0006-2960
PubMed: 15134446
DOI: 10.1021/BI0497897
Page generated: Tue Aug 13 13:44:46 2024
|