Cobalt in PDB 1qxo: Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Enzymatic activity of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
All present enzymatic activity of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp:
4.2.3.5;
Protein crystallography data
The structure of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp, PDB code: 1qxo
was solved by
J.Maclean,
S.Ali,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.059,
124.582,
85.163,
90.00,
115.15,
90.00
|
R / Rfree (%)
|
15.7 /
22.2
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
(pdb code 1qxo). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the
Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp, PDB code: 1qxo:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Cobalt binding site 1 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 1 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co2002
b:86.7
occ:1.00
|
CO
|
A:NCO2002
|
0.0
|
86.7
|
1.0
|
N5
|
A:NCO2002
|
1.9
|
86.2
|
1.0
|
N4
|
A:NCO2002
|
1.9
|
86.9
|
1.0
|
N2
|
A:NCO2002
|
1.9
|
86.3
|
1.0
|
N3
|
A:NCO2002
|
1.9
|
86.5
|
1.0
|
N6
|
A:NCO2002
|
2.0
|
86.4
|
1.0
|
N1
|
A:NCO2002
|
2.0
|
86.3
|
1.0
|
OD2
|
A:ASP170
|
3.5
|
53.4
|
1.0
|
OE2
|
A:GLU173
|
4.3
|
63.8
|
1.0
|
CG
|
A:ASP170
|
4.4
|
51.8
|
1.0
|
OD1
|
A:ASP170
|
4.6
|
54.0
|
1.0
|
OE1
|
A:GLU173
|
4.9
|
63.2
|
1.0
|
CD
|
A:GLU173
|
5.0
|
61.8
|
1.0
|
|
Cobalt binding site 2 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 2 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co2004
b:39.7
occ:1.00
|
CO
|
A:NCO2004
|
0.0
|
39.7
|
1.0
|
N4
|
A:NCO2004
|
1.9
|
40.7
|
1.0
|
N5
|
A:NCO2004
|
1.9
|
41.6
|
1.0
|
N2
|
A:NCO2004
|
2.0
|
42.8
|
1.0
|
N6
|
A:NCO2004
|
2.0
|
41.3
|
1.0
|
N3
|
A:NCO2004
|
2.0
|
41.8
|
1.0
|
N1
|
A:NCO2004
|
2.0
|
39.8
|
1.0
|
O
|
A:ARG120
|
3.8
|
20.6
|
1.0
|
OD1
|
A:ASP122
|
4.2
|
32.2
|
1.0
|
O
|
A:HOH5434
|
4.2
|
68.4
|
1.0
|
O
|
B:HOH5383
|
4.3
|
38.8
|
1.0
|
OE2
|
C:GLU372
|
4.6
|
31.7
|
1.0
|
O
|
C:HOH5004
|
4.7
|
10.7
|
1.0
|
O
|
A:HOH5081
|
4.7
|
27.8
|
1.0
|
O
|
C:HOH5266
|
4.8
|
54.0
|
1.0
|
O
|
A:HOH5284
|
4.9
|
35.9
|
1.0
|
CG
|
A:ASP122
|
5.0
|
31.0
|
1.0
|
|
Cobalt binding site 3 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 3 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co2007
b:80.8
occ:1.00
|
CO
|
A:NCO2007
|
0.0
|
80.8
|
1.0
|
N4
|
A:NCO2007
|
1.9
|
80.1
|
1.0
|
N5
|
A:NCO2007
|
1.9
|
80.2
|
1.0
|
N2
|
A:NCO2007
|
2.0
|
80.6
|
1.0
|
N6
|
A:NCO2007
|
2.0
|
80.7
|
1.0
|
N1
|
A:NCO2007
|
2.0
|
80.6
|
1.0
|
N3
|
A:NCO2007
|
2.0
|
80.6
|
1.0
|
O
|
A:ASN387
|
3.9
|
24.0
|
1.0
|
O
|
A:HOH5407
|
4.0
|
53.1
|
1.0
|
O
|
A:HOH5436
|
4.2
|
57.8
|
1.0
|
O
|
A:HOH5373
|
4.4
|
54.0
|
1.0
|
O
|
B:HOH5148
|
4.8
|
44.8
|
1.0
|
|
Cobalt binding site 4 out
of 9 in 1qxo
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Cobalt Binding Sites List in 1qxo
Cobalt binding site 4 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co2003
b:41.1
occ:1.00
|
CO
|
B:NCO2003
|
0.0
|
41.1
|
1.0
|
N4
|
B:NCO2003
|
1.9
|
41.6
|
1.0
|
N3
|
B:NCO2003
|
1.9
|
41.1
|
1.0
|
N6
|
B:NCO2003
|
1.9
|
41.4
|
1.0
|
N5
|
B:NCO2003
|
1.9
|
41.2
|
1.0
|
N1
|
B:NCO2003
|
2.0
|
41.0
|
1.0
|
N2
|
B:NCO2003
|
2.0
|
42.4
|
1.0
|
OD1
|
B:ASP154
|
3.7
|
35.4
|
1.0
|
O
|
B:HOH5446
|
4.7
|
53.9
|
1.0
|
CG
|
B:ASP154
|
4.8
|
35.2
|
1.0
|
O
|
B:HOH5205
|
4.9
|
49.2
|
1.0
|
O
|
B:GLU152
|
5.0
|
22.0
|
1.0
|
O
|
B:ALA151
|
5.0
|
22.6
|
1.0
|
|
Cobalt binding site 5 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 5 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co2008
b:73.7
occ:1.00
|
CO
|
B:NCO2008
|
0.0
|
73.7
|
1.0
|
N4
|
B:NCO2008
|
1.9
|
74.5
|
1.0
|
N3
|
B:NCO2008
|
1.9
|
74.5
|
1.0
|
N6
|
B:NCO2008
|
1.9
|
74.9
|
1.0
|
N5
|
B:NCO2008
|
1.9
|
73.9
|
1.0
|
N2
|
B:NCO2008
|
1.9
|
74.4
|
1.0
|
N1
|
B:NCO2008
|
2.0
|
74.0
|
1.0
|
O
|
B:ASN387
|
3.8
|
21.1
|
1.0
|
O
|
B:HOH5476
|
3.8
|
50.0
|
1.0
|
O
|
B:TYR388
|
4.9
|
22.9
|
1.0
|
O
|
B:HOH5212
|
4.9
|
34.0
|
1.0
|
O
|
A:HOH5225
|
4.9
|
46.6
|
1.0
|
C
|
B:ASN387
|
4.9
|
22.2
|
1.0
|
O
|
B:HOH5475
|
5.0
|
40.4
|
1.0
|
O
|
B:HOH5062
|
5.0
|
25.4
|
1.0
|
|
Cobalt binding site 6 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 6 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co2001
b:34.2
occ:1.00
|
CO
|
C:NCO2001
|
0.0
|
34.2
|
1.0
|
N3
|
C:NCO2001
|
1.9
|
35.0
|
1.0
|
N2
|
C:NCO2001
|
1.9
|
35.4
|
1.0
|
N5
|
C:NCO2001
|
1.9
|
34.4
|
1.0
|
N4
|
C:NCO2001
|
2.0
|
36.2
|
1.0
|
N1
|
C:NCO2001
|
2.0
|
35.4
|
1.0
|
N6
|
C:NCO2001
|
2.0
|
34.6
|
1.0
|
O
|
C:HOH5429
|
3.9
|
47.0
|
1.0
|
O
|
C:ASN387
|
4.0
|
25.4
|
1.0
|
O
|
C:HOH5309
|
4.4
|
46.7
|
1.0
|
O
|
C:TYR388
|
4.6
|
28.1
|
1.0
|
O
|
C:HOH5288
|
4.7
|
66.6
|
1.0
|
O
|
C:HOH5335
|
4.9
|
58.7
|
1.0
|
O
|
C:HOH5328
|
5.0
|
33.1
|
1.0
|
|
Cobalt binding site 7 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 7 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co2005
b:52.8
occ:1.00
|
CO
|
C:NCO2005
|
0.0
|
52.8
|
1.0
|
N5
|
C:NCO2005
|
1.9
|
53.7
|
1.0
|
N4
|
C:NCO2005
|
1.9
|
53.9
|
1.0
|
N6
|
C:NCO2005
|
1.9
|
53.8
|
1.0
|
N3
|
C:NCO2005
|
1.9
|
53.8
|
1.0
|
N2
|
C:NCO2005
|
2.0
|
53.1
|
1.0
|
N1
|
C:NCO2005
|
2.0
|
52.3
|
1.0
|
O
|
C:HOH5099
|
3.6
|
55.6
|
1.0
|
O
|
C:HOH5262
|
3.7
|
50.9
|
1.0
|
O
|
C:HOH5455
|
3.7
|
72.7
|
1.0
|
OE1
|
C:GLU168
|
4.0
|
35.6
|
1.0
|
OE1
|
C:GLU263
|
4.1
|
36.5
|
1.0
|
O
|
C:HOH5159
|
4.3
|
46.6
|
1.0
|
O2
|
D:FMN4006
|
4.5
|
49.8
|
1.0
|
OE2
|
C:GLU168
|
4.6
|
37.8
|
1.0
|
CD
|
C:GLU168
|
4.6
|
35.9
|
1.0
|
|
Cobalt binding site 8 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 8 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 8 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co2006
b:48.3
occ:1.00
|
CO
|
D:NCO2006
|
0.0
|
48.3
|
1.0
|
N4
|
D:NCO2006
|
1.9
|
47.9
|
1.0
|
N3
|
D:NCO2006
|
1.9
|
47.3
|
1.0
|
N5
|
D:NCO2006
|
2.0
|
47.5
|
1.0
|
N6
|
D:NCO2006
|
2.0
|
47.7
|
1.0
|
N2
|
D:NCO2006
|
2.0
|
47.3
|
1.0
|
N1
|
D:NCO2006
|
2.0
|
47.3
|
1.0
|
O
|
C:HOH5231
|
3.7
|
49.9
|
1.0
|
O
|
D:HOH5215
|
3.9
|
37.4
|
1.0
|
O
|
D:HOH5260
|
4.0
|
71.3
|
1.0
|
O
|
D:HOH5385
|
4.0
|
57.6
|
1.0
|
OE1
|
D:GLU263
|
4.0
|
33.1
|
1.0
|
OE1
|
D:GLU168
|
4.2
|
36.7
|
1.0
|
O2P
|
C:FMN4005
|
4.3
|
62.8
|
1.0
|
O
|
C:HOH5233
|
4.4
|
73.2
|
1.0
|
OE2
|
D:GLU168
|
4.5
|
39.0
|
1.0
|
O2
|
C:FMN4005
|
4.6
|
46.2
|
1.0
|
O
|
D:HOH5351
|
4.7
|
54.2
|
1.0
|
CD
|
D:GLU168
|
4.7
|
37.6
|
1.0
|
C5'
|
C:FMN4005
|
4.8
|
61.7
|
1.0
|
O
|
D:HOH5450
|
4.9
|
48.6
|
1.0
|
|
Cobalt binding site 9 out
of 9 in 1qxo
Go back to
Cobalt Binding Sites List in 1qxo
Cobalt binding site 9 out
of 9 in the Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 9 of Crystal Structure of Chorismate Synthase Complexed with Oxidized Fmn and Epsp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co2009
b:26.9
occ:1.00
|
CO
|
D:NCO2009
|
0.0
|
26.9
|
1.0
|
N5
|
D:NCO2009
|
1.9
|
29.1
|
1.0
|
N4
|
D:NCO2009
|
1.9
|
27.7
|
1.0
|
N6
|
D:NCO2009
|
1.9
|
28.7
|
1.0
|
N2
|
D:NCO2009
|
1.9
|
26.7
|
1.0
|
N3
|
D:NCO2009
|
2.0
|
25.0
|
1.0
|
N1
|
D:NCO2009
|
2.0
|
26.7
|
1.0
|
O
|
D:ASN387
|
4.2
|
19.9
|
1.0
|
O
|
D:HOH5409
|
4.5
|
42.6
|
1.0
|
O
|
D:TYR388
|
4.7
|
22.1
|
1.0
|
O
|
D:HOH5435
|
4.7
|
37.7
|
1.0
|
O
|
D:HOH5404
|
5.0
|
61.8
|
1.0
|
|
Reference:
J.Maclean,
S.Ali.
The Structure of Chorismate Synthase Reveals A Novel Flavin Binding Site Fundamental to A Unique Chemical Reaction Structure V. 11 1499 2003.
ISSN: ISSN 0969-2126
PubMed: 14656434
DOI: 10.1016/J.STR.2003.11.005
Page generated: Tue Jul 30 14:32:16 2024
|