Magnesium in PDB 2yi9: Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
Enzymatic activity of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
All present enzymatic activity of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium:
2.7.7.48;
2.7.7.49;
Protein crystallography data
The structure of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium, PDB code: 2yi9
was solved by
S.C.Graham,
L.P.Sarin,
M.W.Bahar,
R.A.Myers,
D.I.Stuart,
D.H.Bamford,
J.M.Grimes,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.21 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
134.048,
183.874,
244.521,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16 /
18.1
|
Other elements in 2yi9:
The structure of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
(pdb code 2yi9). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium, PDB code: 2yi9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 2yi9
Go back to
Magnesium Binding Sites List in 2yi9
Magnesium binding site 1 out
of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1793
b:28.5
occ:1.00
|
O
|
A:HOH2320
|
2.0
|
28.2
|
1.0
|
OD1
|
A:ASP402
|
2.1
|
32.9
|
1.0
|
O
|
A:HOH2329
|
2.1
|
25.6
|
1.0
|
OD1
|
A:ASN389
|
2.1
|
22.2
|
1.0
|
O
|
A:HOH2321
|
2.2
|
20.4
|
1.0
|
O
|
A:HOH2319
|
2.3
|
24.4
|
1.0
|
CG
|
A:ASP402
|
3.0
|
32.2
|
1.0
|
CG
|
A:ASN389
|
3.2
|
27.6
|
1.0
|
OD2
|
A:ASP402
|
3.2
|
41.2
|
1.0
|
CB
|
A:ASN389
|
3.8
|
15.1
|
1.0
|
OG
|
A:SER400
|
4.0
|
24.6
|
1.0
|
OH
|
A:TYR391
|
4.1
|
22.9
|
1.0
|
O
|
A:HOH2418
|
4.1
|
51.8
|
1.0
|
ND2
|
A:ASN389
|
4.3
|
16.5
|
1.0
|
O
|
A:ILE401
|
4.3
|
24.1
|
1.0
|
CB
|
A:ASP402
|
4.4
|
18.8
|
1.0
|
O
|
A:HOH2330
|
4.4
|
33.6
|
1.0
|
CA
|
A:ASN389
|
4.5
|
17.0
|
1.0
|
OD2
|
A:ASP559
|
4.6
|
44.6
|
1.0
|
CZ
|
A:TYR391
|
4.8
|
24.2
|
1.0
|
CA
|
A:ASP402
|
4.9
|
17.4
|
1.0
|
C
|
A:ILE401
|
4.9
|
23.8
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 2yi9
Go back to
Magnesium Binding Sites List in 2yi9
Magnesium binding site 2 out
of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1793
b:30.1
occ:1.00
|
OD1
|
B:ASP402
|
2.0
|
28.3
|
1.0
|
O
|
B:HOH2368
|
2.1
|
30.4
|
1.0
|
OD1
|
B:ASN389
|
2.1
|
22.7
|
1.0
|
O
|
B:HOH2374
|
2.2
|
22.0
|
1.0
|
O
|
B:HOH2367
|
2.2
|
22.9
|
1.0
|
O
|
B:HOH2369
|
2.3
|
20.7
|
1.0
|
CG
|
B:ASP402
|
3.0
|
30.0
|
1.0
|
CG
|
B:ASN389
|
3.2
|
24.9
|
1.0
|
OD2
|
B:ASP402
|
3.2
|
41.2
|
1.0
|
CB
|
B:ASN389
|
3.8
|
14.8
|
1.0
|
OG
|
B:SER400
|
4.0
|
23.4
|
1.0
|
OH
|
B:TYR391
|
4.1
|
24.0
|
1.0
|
O
|
B:HOH2375
|
4.3
|
42.5
|
1.0
|
ND2
|
B:ASN389
|
4.3
|
21.3
|
1.0
|
O
|
B:ILE401
|
4.3
|
18.5
|
1.0
|
CB
|
B:ASP402
|
4.3
|
18.8
|
1.0
|
CA
|
B:ASN389
|
4.5
|
13.3
|
1.0
|
OD2
|
B:ASP559
|
4.7
|
43.4
|
1.0
|
CZ
|
B:TYR391
|
4.8
|
17.8
|
1.0
|
CA
|
B:ASP402
|
4.8
|
16.2
|
1.0
|
C
|
B:ILE401
|
4.9
|
20.0
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 2yi9
Go back to
Magnesium Binding Sites List in 2yi9
Magnesium binding site 3 out
of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1793
b:27.7
occ:1.00
|
OD1
|
C:ASP402
|
2.0
|
27.9
|
1.0
|
OD1
|
C:ASN389
|
2.1
|
21.7
|
1.0
|
O
|
C:HOH2359
|
2.1
|
25.4
|
1.0
|
O
|
C:HOH2350
|
2.1
|
24.6
|
1.0
|
O
|
C:HOH2349
|
2.2
|
25.2
|
1.0
|
O
|
C:HOH2351
|
2.2
|
25.8
|
1.0
|
CG
|
C:ASP402
|
3.0
|
28.9
|
1.0
|
CG
|
C:ASN389
|
3.2
|
25.0
|
1.0
|
OD2
|
C:ASP402
|
3.2
|
47.9
|
1.0
|
CB
|
C:ASN389
|
3.8
|
13.8
|
1.0
|
OG
|
C:SER400
|
4.0
|
24.6
|
1.0
|
OH
|
C:TYR391
|
4.1
|
21.4
|
1.0
|
ND2
|
C:ASN389
|
4.3
|
19.7
|
1.0
|
O
|
C:HOH2360
|
4.3
|
42.0
|
1.0
|
O
|
C:ILE401
|
4.3
|
20.8
|
1.0
|
CB
|
C:ASP402
|
4.3
|
19.2
|
1.0
|
CA
|
C:ASN389
|
4.5
|
12.2
|
1.0
|
OD2
|
C:ASP559
|
4.6
|
42.9
|
1.0
|
CZ
|
C:TYR391
|
4.8
|
22.3
|
1.0
|
CA
|
C:ASP402
|
4.8
|
17.2
|
1.0
|
C
|
C:ILE401
|
4.9
|
20.8
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 2yi9
Go back to
Magnesium Binding Sites List in 2yi9
Magnesium binding site 4 out
of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1793
b:24.6
occ:1.00
|
OD1
|
D:ASP402
|
2.0
|
25.2
|
1.0
|
O
|
D:HOH2394
|
2.1
|
21.9
|
1.0
|
O
|
D:HOH2387
|
2.1
|
30.3
|
1.0
|
OD1
|
D:ASN389
|
2.1
|
17.1
|
1.0
|
O
|
D:HOH2385
|
2.1
|
21.4
|
1.0
|
O
|
D:HOH2386
|
2.2
|
17.1
|
1.0
|
CG
|
D:ASP402
|
3.0
|
26.0
|
1.0
|
CG
|
D:ASN389
|
3.2
|
20.5
|
1.0
|
OD2
|
D:ASP402
|
3.2
|
42.3
|
1.0
|
CB
|
D:ASN389
|
3.8
|
9.4
|
1.0
|
OG
|
D:SER400
|
4.0
|
28.2
|
1.0
|
OH
|
D:TYR391
|
4.1
|
22.6
|
1.0
|
ND2
|
D:ASN389
|
4.3
|
18.3
|
1.0
|
O
|
D:HOH2395
|
4.3
|
38.7
|
1.0
|
O
|
D:ILE401
|
4.3
|
17.2
|
1.0
|
CB
|
D:ASP402
|
4.4
|
15.8
|
1.0
|
CA
|
D:ASN389
|
4.5
|
13.1
|
1.0
|
OD2
|
D:ASP559
|
4.7
|
40.4
|
1.0
|
CZ
|
D:TYR391
|
4.8
|
19.3
|
1.0
|
CA
|
D:ASP402
|
4.8
|
13.9
|
1.0
|
C
|
D:ILE401
|
4.9
|
19.0
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 2yi9
Go back to
Magnesium Binding Sites List in 2yi9
Magnesium binding site 5 out
of 5 in the Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of the Rna Polymerase VP1 From Infectious Pancreatic Necrosis Virus in Complex with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1793
b:26.1
occ:1.00
|
OD1
|
E:ASP402
|
2.0
|
31.8
|
1.0
|
O
|
E:HOH2406
|
2.0
|
28.3
|
1.0
|
OD1
|
E:ASN389
|
2.1
|
19.0
|
1.0
|
O
|
E:HOH2405
|
2.1
|
15.8
|
1.0
|
O
|
E:HOH2414
|
2.2
|
20.6
|
1.0
|
O
|
E:HOH2407
|
2.3
|
15.0
|
1.0
|
CG
|
E:ASP402
|
3.0
|
32.8
|
1.0
|
CG
|
E:ASN389
|
3.2
|
24.6
|
1.0
|
OD2
|
E:ASP402
|
3.2
|
48.3
|
1.0
|
CB
|
E:ASN389
|
3.8
|
13.0
|
1.0
|
OG
|
E:SER400
|
4.0
|
18.1
|
1.0
|
O
|
E:HOH2402
|
4.1
|
43.8
|
1.0
|
OH
|
E:TYR391
|
4.1
|
18.3
|
1.0
|
O
|
E:HOH2415
|
4.2
|
27.7
|
1.0
|
ND2
|
E:ASN389
|
4.2
|
15.0
|
1.0
|
O
|
E:HOH2520
|
4.3
|
44.9
|
1.0
|
O
|
E:ILE401
|
4.3
|
17.5
|
1.0
|
CB
|
E:ASP402
|
4.4
|
17.7
|
1.0
|
CA
|
E:ASN389
|
4.4
|
10.8
|
1.0
|
OD2
|
E:ASP559
|
4.7
|
37.1
|
1.0
|
CZ
|
E:TYR391
|
4.8
|
17.3
|
1.0
|
CA
|
E:ASP402
|
4.8
|
15.8
|
1.0
|
C
|
E:ILE401
|
4.9
|
18.4
|
1.0
|
|
Reference:
S.C.Graham,
L.P.Sarin,
M.W.Bahar,
R.A.Myers,
D.I.Stuart,
D.H.Bamford,
J.M.Grimes.
The N-Terminus of the Rna Polymerase From Infectious Pancreatic Necrosis Virus Is the Determinant of Genome Attachment. Plos Pathog. V. 7 2085 2011.
ISSN: ISSN 1553-7366
PubMed: 21731487
DOI: 10.1371/JOURNAL.PPAT.1002085
Page generated: Wed Aug 14 07:32:20 2024
|