Magnesium in PDB 6op1: Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
Enzymatic activity of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
All present enzymatic activity of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii:
1.18.6.1;
Protein crystallography data
The structure of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii, PDB code: 6op1
was solved by
R.J.Arias,
D.C.Rees,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.93 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.191,
128.003,
107.633,
90.00,
109.15,
90.00
|
R / Rfree (%)
|
13.2 /
16.5
|
Other elements in 6op1:
The structure of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
(pdb code 6op1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii, PDB code: 6op1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6op1
Go back to
Magnesium Binding Sites List in 6op1
Magnesium binding site 1 out
of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg506
b:46.4
occ:1.00
|
O
|
A:HOH819
|
2.2
|
14.1
|
1.0
|
O
|
A:MET112
|
2.8
|
13.1
|
1.0
|
O
|
A:HOH707
|
2.8
|
11.2
|
1.0
|
O
|
A:VAL110
|
3.1
|
12.6
|
1.0
|
CA
|
A:ARG93
|
3.4
|
9.8
|
1.0
|
N
|
A:ALA94
|
3.6
|
9.9
|
1.0
|
C
|
A:MET112
|
3.6
|
11.6
|
1.0
|
O
|
A:HOH783
|
3.7
|
11.5
|
1.0
|
O
|
A:HOH744
|
3.7
|
16.7
|
1.0
|
C
|
A:THR111
|
3.7
|
9.7
|
1.0
|
NZ
|
A:LYS68
|
3.7
|
12.1
|
1.0
|
CG
|
A:ARG93
|
3.8
|
9.8
|
1.0
|
CB
|
A:ARG93
|
4.0
|
9.8
|
1.0
|
O
|
A:THR111
|
4.0
|
9.7
|
1.0
|
O
|
A:HOH659
|
4.0
|
9.6
|
1.0
|
N
|
A:MET112
|
4.0
|
9.7
|
1.0
|
C
|
A:ARG93
|
4.0
|
10.0
|
1.0
|
CA
|
A:THR111
|
4.0
|
9.7
|
1.0
|
O
|
A:SER92
|
4.0
|
12.6
|
1.0
|
C
|
A:VAL110
|
4.2
|
10.7
|
1.0
|
N
|
A:ASN113
|
4.4
|
10.6
|
1.0
|
CA
|
A:MET112
|
4.4
|
10.5
|
1.0
|
N
|
A:ARG93
|
4.5
|
10.2
|
1.0
|
CA
|
A:ASN113
|
4.6
|
9.7
|
1.0
|
N
|
A:THR111
|
4.6
|
9.8
|
1.0
|
C
|
A:SER92
|
4.7
|
11.7
|
1.0
|
CA
|
A:ALA94
|
4.7
|
11.2
|
1.0
|
CE
|
A:LYS68
|
4.7
|
12.1
|
1.0
|
O
|
A:HOH685
|
4.8
|
12.0
|
1.0
|
CB
|
A:ASN113
|
4.9
|
10.1
|
1.0
|
O
|
A:HOH849
|
4.9
|
15.3
|
1.0
|
O
|
A:HOH640
|
4.9
|
14.0
|
1.0
|
CD
|
A:ARG93
|
4.9
|
9.5
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6op1
Go back to
Magnesium Binding Sites List in 6op1
Magnesium binding site 2 out
of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg507
b:38.4
occ:1.00
|
NE1
|
A:TRP335
|
2.7
|
18.9
|
1.0
|
O
|
A:ILE328
|
2.9
|
15.5
|
1.0
|
O
|
A:HOH976
|
3.2
|
21.8
|
1.0
|
CG2
|
A:ILE328
|
3.4
|
17.2
|
1.0
|
CA
|
A:LYS332
|
3.4
|
17.4
|
1.0
|
CB
|
A:LYS332
|
3.4
|
19.9
|
1.0
|
CD1
|
A:ILE306
|
3.5
|
15.4
|
1.0
|
CE2
|
A:TRP335
|
3.6
|
18.4
|
1.0
|
N
|
A:LYS332
|
3.7
|
15.8
|
1.0
|
C
|
A:ILE328
|
3.7
|
15.4
|
1.0
|
CD1
|
A:TRP335
|
3.8
|
18.2
|
1.0
|
CZ2
|
A:TRP335
|
3.9
|
21.7
|
1.0
|
CG
|
A:LYS332
|
3.9
|
22.3
|
1.0
|
CA
|
A:ILE328
|
4.1
|
15.7
|
1.0
|
CG1
|
A:ILE306
|
4.2
|
15.9
|
1.0
|
CB
|
A:ILE328
|
4.3
|
16.3
|
1.0
|
CD
|
A:LYS332
|
4.4
|
26.4
|
1.0
|
C
|
A:TYR331
|
4.5
|
15.9
|
1.0
|
C
|
A:LYS332
|
4.8
|
17.0
|
1.0
|
CZ
|
A:PHE453
|
4.8
|
14.7
|
1.0
|
N
|
A:ALA329
|
4.9
|
14.7
|
1.0
|
CE1
|
A:PHE453
|
4.9
|
14.6
|
1.0
|
CD2
|
A:TRP335
|
4.9
|
19.2
|
1.0
|
CG
|
A:TRP335
|
4.9
|
17.4
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6op1
Go back to
Magnesium Binding Sites List in 6op1
Magnesium binding site 3 out
of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:44.2
occ:1.00
|
O
|
B:HOH1009
|
2.1
|
25.4
|
1.0
|
O
|
B:HOH986
|
3.1
|
22.0
|
1.0
|
O
|
B:HOH1201
|
3.4
|
24.1
|
1.0
|
CE
|
B:LYS365
|
3.6
|
16.2
|
1.0
|
NZ
|
B:LYS365
|
3.9
|
18.4
|
1.0
|
O
|
D:HOH1005
|
4.0
|
21.6
|
1.0
|
O
|
B:HOH1081
|
4.0
|
32.0
|
1.0
|
CZ3
|
B:TRP361
|
4.1
|
12.2
|
1.0
|
CG2
|
B:ILE501
|
4.1
|
11.7
|
1.0
|
O
|
B:HOH1167
|
4.2
|
23.5
|
1.0
|
CE3
|
B:TRP361
|
4.2
|
12.3
|
1.0
|
CD1
|
B:LEU505
|
4.4
|
11.6
|
1.0
|
CD2
|
B:LEU505
|
4.4
|
12.8
|
1.0
|
CB
|
B:LEU505
|
4.5
|
11.2
|
1.0
|
CG
|
B:LEU505
|
4.7
|
11.4
|
1.0
|
O
|
B:ILE501
|
5.0
|
10.6
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6op1
Go back to
Magnesium Binding Sites List in 6op1
Magnesium binding site 4 out
of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg604
b:44.1
occ:1.00
|
O
|
D:HOH781
|
2.6
|
16.3
|
1.0
|
CE
|
D:LYS9
|
3.5
|
18.9
|
1.0
|
CG
|
D:PRO13
|
4.0
|
12.7
|
1.0
|
CB
|
D:PRO13
|
4.2
|
11.7
|
1.0
|
CD
|
D:LYS9
|
4.3
|
15.8
|
1.0
|
O
|
D:HOH1188
|
4.3
|
34.9
|
1.0
|
OD1
|
D:ASP17
|
4.5
|
15.0
|
1.0
|
NZ
|
D:LYS9
|
4.6
|
20.1
|
1.0
|
O
|
D:PRO13
|
4.7
|
10.8
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6op1
Go back to
Magnesium Binding Sites List in 6op1
Magnesium binding site 5 out
of 5 in the Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Selenium Incorporated, Carbon Monoxide Inhibited Femo-Cofactor of Azotobacter Vinelandii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg605
b:54.2
occ:1.00
|
O
|
C:HOH784
|
2.4
|
22.3
|
1.0
|
O
|
D:HOH1111
|
2.5
|
16.6
|
1.0
|
O
|
C:HOH826
|
2.8
|
11.3
|
1.0
|
O
|
C:HOH929
|
3.5
|
13.9
|
1.0
|
CE1
|
D:TYR98
|
3.5
|
12.4
|
1.0
|
CD1
|
D:TYR98
|
3.7
|
13.0
|
1.0
|
C4
|
C:HCA501
|
3.9
|
10.2
|
1.0
|
O2
|
C:HCA501
|
3.9
|
13.9
|
1.0
|
O
|
D:HOH819
|
4.0
|
12.5
|
1.0
|
NH2
|
D:ARG105
|
4.1
|
12.7
|
1.0
|
C2
|
C:HCA501
|
4.1
|
10.7
|
1.0
|
NH1
|
D:ARG105
|
4.2
|
12.4
|
1.0
|
O
|
D:HOH739
|
4.3
|
12.6
|
1.0
|
C1
|
C:HCA501
|
4.3
|
13.0
|
1.0
|
O
|
C:HOH711
|
4.4
|
14.2
|
1.0
|
C3
|
C:HCA501
|
4.6
|
10.7
|
1.0
|
CZ
|
D:ARG105
|
4.6
|
11.6
|
1.0
|
CB
|
D:SER101
|
4.7
|
12.7
|
1.0
|
OG
|
D:SER101
|
4.7
|
15.6
|
1.0
|
CZ
|
D:TYR98
|
4.7
|
11.6
|
1.0
|
O
|
C:TYR91
|
4.8
|
11.0
|
1.0
|
O6
|
C:HCA501
|
4.9
|
9.9
|
1.0
|
|
Reference:
J.T.Henthorn,
R.J.Arias,
S.Koroidov,
T.Kroll,
D.Sokaras,
U.Bergmann,
D.C.Rees,
S.Debeer.
Localized Electronic Structure of Nitrogenase Femoco Revealed By Selenium K-Edge High Resolution X-Ray Absorption Spectroscopy. J.Am.Chem.Soc. V. 141 13676 2019.
ISSN: ESSN 1520-5126
PubMed: 31356071
DOI: 10.1021/JACS.9B06988
Page generated: Mon Dec 14 23:44:09 2020
|