Magnesium in PDB 1sja: X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Acetylmethionine
Protein crystallography data
The structure of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Acetylmethionine, PDB code: 1sja
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 /
2.30
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
215.300,
215.300,
259.100,
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-Acetylmethionine
(pdb code 1sja). 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-Acetylmethionine, PDB code: 1sja:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1sja
Go back to
Magnesium Binding Sites List in 1sja
Magnesium binding site 1 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Acetylmethionine
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-Acetylmethionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:41.1
occ:1.00
|
O
|
A:HOH673
|
2.0
|
38.3
|
1.0
|
O
|
A:AME600
|
2.1
|
69.7
|
1.0
|
OD2
|
A:ASP239
|
2.4
|
46.0
|
1.0
|
OE2
|
A:GLU214
|
2.5
|
59.7
|
1.0
|
OD2
|
A:ASP189
|
2.5
|
39.2
|
1.0
|
OD1
|
A:ASP189
|
3.0
|
65.6
|
1.0
|
C
|
A:AME600
|
3.0
|
88.5
|
1.0
|
CG
|
A:ASP189
|
3.1
|
44.5
|
1.0
|
CD
|
A:GLU214
|
3.2
|
40.0
|
1.0
|
OXT
|
A:AME600
|
3.3
|
62.7
|
1.0
|
ND2
|
A:ASN191
|
3.4
|
56.8
|
1.0
|
CG
|
A:ASP239
|
3.5
|
27.0
|
1.0
|
OE1
|
A:GLU240
|
3.6
|
53.5
|
1.0
|
CB
|
A:ASP239
|
3.6
|
28.4
|
1.0
|
CG
|
A:GLU214
|
3.8
|
47.7
|
1.0
|
OE1
|
A:GLU214
|
4.0
|
0.0
|
1.0
|
CG
|
A:ASN191
|
4.0
|
50.8
|
1.0
|
NZ
|
A:LYS263
|
4.1
|
55.0
|
1.0
|
OD1
|
A:ASN191
|
4.2
|
52.4
|
1.0
|
CB
|
A:AME600
|
4.3
|
79.4
|
1.0
|
CA
|
A:AME600
|
4.3
|
0.0
|
1.0
|
CB
|
A:ASP189
|
4.5
|
20.9
|
1.0
|
OD1
|
A:ASP239
|
4.6
|
49.7
|
1.0
|
CD
|
A:GLU240
|
4.6
|
41.5
|
1.0
|
CB
|
A:GLU214
|
4.6
|
27.8
|
1.0
|
NZ
|
A:LYS163
|
4.6
|
33.5
|
1.0
|
ND2
|
A:ASN261
|
4.8
|
30.5
|
1.0
|
CE2
|
A:TYR55
|
4.9
|
72.1
|
1.0
|
CB
|
A:GLN215
|
4.9
|
27.4
|
1.0
|
CA
|
A:ASN191
|
4.9
|
49.8
|
1.0
|
CE
|
A:LYS263
|
5.0
|
32.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1sja
Go back to
Magnesium Binding Sites List in 1sja
Magnesium binding site 2 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Acetylmethionine
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-Acetylmethionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg701
b:35.5
occ:1.00
|
O
|
B:AME700
|
2.0
|
80.0
|
1.0
|
O
|
B:HOH775
|
2.0
|
42.4
|
1.0
|
OE2
|
B:GLU214
|
2.2
|
33.7
|
1.0
|
OD2
|
B:ASP239
|
2.3
|
42.2
|
1.0
|
OD2
|
B:ASP189
|
2.6
|
44.4
|
1.0
|
CD
|
B:GLU214
|
3.1
|
47.0
|
1.0
|
C
|
B:AME700
|
3.2
|
38.0
|
1.0
|
CG
|
B:ASP189
|
3.3
|
37.6
|
1.0
|
OD1
|
B:ASP189
|
3.4
|
35.7
|
1.0
|
CG
|
B:ASP239
|
3.4
|
55.1
|
1.0
|
ND2
|
B:ASN191
|
3.5
|
79.4
|
1.0
|
CB
|
B:ASP239
|
3.6
|
29.8
|
1.0
|
OXT
|
B:AME700
|
3.7
|
80.0
|
1.0
|
OE1
|
B:GLU214
|
3.7
|
34.1
|
1.0
|
CG
|
B:GLU214
|
4.0
|
14.2
|
1.0
|
CB
|
B:AME700
|
4.0
|
63.0
|
1.0
|
OE1
|
B:GLU240
|
4.1
|
42.2
|
1.0
|
NZ
|
B:LYS161
|
4.1
|
45.1
|
1.0
|
NZ
|
B:LYS263
|
4.2
|
34.9
|
1.0
|
NZ
|
B:LYS163
|
4.3
|
57.9
|
1.0
|
CA
|
B:AME700
|
4.3
|
43.2
|
1.0
|
ND2
|
B:ASN261
|
4.4
|
21.5
|
1.0
|
CG
|
B:ASN191
|
4.5
|
48.9
|
1.0
|
CB
|
B:ASP189
|
4.5
|
30.5
|
1.0
|
OD1
|
B:ASP239
|
4.5
|
39.0
|
1.0
|
CE
|
B:LYS263
|
4.6
|
36.6
|
1.0
|
CB
|
B:GLU214
|
4.6
|
65.6
|
1.0
|
OD1
|
B:ASN191
|
4.8
|
31.3
|
1.0
|
CE2
|
B:TYR55
|
4.9
|
36.5
|
1.0
|
CD
|
B:GLU240
|
4.9
|
27.0
|
1.0
|
CG
|
B:AME700
|
4.9
|
54.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1sja
Go back to
Magnesium Binding Sites List in 1sja
Magnesium binding site 3 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Acetylmethionine
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-Acetylmethionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg801
b:49.5
occ:1.00
|
O
|
C:AME800
|
1.7
|
0.0
|
1.0
|
O
|
C:HOH871
|
2.0
|
40.4
|
1.0
|
OD2
|
C:ASP189
|
2.1
|
41.3
|
1.0
|
OD2
|
C:ASP239
|
2.4
|
52.9
|
1.0
|
OE2
|
C:GLU214
|
2.4
|
35.6
|
1.0
|
C
|
C:AME800
|
3.0
|
26.7
|
1.0
|
CG
|
C:ASP189
|
3.0
|
38.8
|
1.0
|
OD1
|
C:ASP189
|
3.0
|
48.1
|
1.0
|
CD
|
C:GLU214
|
3.2
|
33.4
|
1.0
|
CG
|
C:ASP239
|
3.5
|
40.3
|
1.0
|
ND2
|
C:ASN191
|
3.5
|
38.2
|
1.0
|
OXT
|
C:AME800
|
3.6
|
0.0
|
1.0
|
CB
|
C:ASP239
|
3.7
|
51.5
|
1.0
|
OE1
|
C:GLU214
|
3.8
|
39.8
|
1.0
|
OE1
|
C:GLU240
|
4.0
|
23.5
|
1.0
|
CB
|
C:AME800
|
4.0
|
75.2
|
1.0
|
CG
|
C:GLU214
|
4.1
|
35.9
|
1.0
|
NZ
|
C:LYS263
|
4.1
|
41.9
|
1.0
|
CA
|
C:AME800
|
4.1
|
97.9
|
1.0
|
NZ
|
C:LYS161
|
4.2
|
47.7
|
1.0
|
CG
|
C:ASN191
|
4.3
|
39.5
|
1.0
|
CB
|
C:ASP189
|
4.4
|
25.8
|
1.0
|
NZ
|
C:LYS163
|
4.4
|
63.6
|
1.0
|
OD1
|
C:ASN191
|
4.6
|
38.8
|
1.0
|
CB
|
C:GLU214
|
4.6
|
39.6
|
1.0
|
OD1
|
C:ASP239
|
4.6
|
60.3
|
1.0
|
CE
|
C:LYS263
|
4.7
|
29.2
|
1.0
|
CD
|
C:GLU240
|
4.8
|
26.3
|
1.0
|
CE2
|
C:TYR55
|
4.8
|
29.1
|
1.0
|
ND2
|
C:ASN261
|
4.9
|
22.2
|
1.0
|
OE2
|
C:GLU240
|
4.9
|
29.0
|
1.0
|
CE
|
C:LYS161
|
4.9
|
31.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1sja
Go back to
Magnesium Binding Sites List in 1sja
Magnesium binding site 4 out
of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Acetylmethionine
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-Acetylmethionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg901
b:54.2
occ:1.00
|
OXT
|
D:AME900
|
1.7
|
83.2
|
1.0
|
O
|
D:HOH970
|
1.9
|
44.8
|
1.0
|
OD2
|
D:ASP239
|
2.3
|
34.0
|
1.0
|
OE2
|
D:GLU214
|
2.5
|
42.5
|
1.0
|
OD2
|
D:ASP189
|
2.6
|
40.1
|
1.0
|
C
|
D:AME900
|
2.9
|
61.4
|
1.0
|
ND2
|
D:ASN191
|
3.3
|
56.6
|
1.0
|
CD
|
D:GLU214
|
3.3
|
0.0
|
1.0
|
CG
|
D:ASP189
|
3.3
|
39.7
|
1.0
|
OD1
|
D:ASP189
|
3.4
|
46.0
|
1.0
|
CG
|
D:ASP239
|
3.4
|
99.9
|
1.0
|
CB
|
D:AME900
|
3.4
|
40.6
|
1.0
|
OE1
|
D:GLU240
|
3.6
|
62.6
|
1.0
|
O
|
D:AME900
|
3.7
|
72.7
|
1.0
|
CB
|
D:ASP239
|
3.7
|
65.9
|
1.0
|
CA
|
D:AME900
|
3.8
|
0.0
|
1.0
|
CG
|
D:GLU214
|
3.8
|
30.9
|
1.0
|
NZ
|
D:LYS263
|
4.0
|
50.5
|
1.0
|
CG
|
D:ASN191
|
4.0
|
0.0
|
1.0
|
OE1
|
D:GLU214
|
4.1
|
41.4
|
1.0
|
OD1
|
D:ASN191
|
4.2
|
54.2
|
1.0
|
CD
|
D:GLU240
|
4.4
|
54.7
|
1.0
|
OD1
|
D:ASP239
|
4.5
|
37.0
|
1.0
|
NZ
|
D:LYS161
|
4.5
|
32.3
|
1.0
|
CE2
|
D:TYR55
|
4.7
|
69.1
|
1.0
|
OE2
|
D:GLU240
|
4.7
|
58.9
|
1.0
|
CB
|
D:ASP189
|
4.7
|
22.4
|
1.0
|
CG
|
D:AME900
|
4.8
|
91.6
|
1.0
|
N
|
D:AME900
|
4.9
|
0.0
|
1.0
|
CB
|
D:GLU214
|
4.9
|
41.0
|
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 13:44:45 2024
|