Magnesium in PDB 3fbe: Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
Enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
All present enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp:
2.7.4.6;
Protein crystallography data
The structure of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp, PDB code: 3fbe
was solved by
S.Jeudy,
A.Lartigue,
J.M.Claverie,
C.Abergel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.53 /
2.40
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.243,
152.897,
183.785,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
23
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
(pdb code 3fbe). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp, PDB code: 3fbe:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 3fbe
Go back to
Magnesium Binding Sites List in 3fbe
Magnesium binding site 1 out
of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg160
b:54.0
occ:1.00
|
OH
|
A:TYR50
|
2.7
|
41.4
|
1.0
|
NZ
|
A:LYS9
|
2.9
|
35.4
|
1.0
|
ND1
|
A:HIS112
|
3.0
|
33.4
|
1.0
|
O3'
|
A:GDP138
|
3.1
|
57.9
|
1.0
|
O1B
|
A:GDP138
|
3.2
|
71.1
|
1.0
|
CB
|
A:HIS112
|
3.3
|
34.1
|
1.0
|
CG
|
A:HIS112
|
3.6
|
35.9
|
1.0
|
CE
|
A:LYS9
|
3.6
|
34.0
|
1.0
|
CZ
|
A:TYR50
|
3.6
|
49.6
|
1.0
|
CE2
|
A:TYR50
|
3.6
|
46.4
|
1.0
|
NH2
|
A:ARG99
|
3.8
|
38.3
|
1.0
|
O2B
|
A:GDP138
|
3.9
|
76.0
|
1.0
|
PB
|
A:GDP138
|
3.9
|
84.0
|
1.0
|
CA
|
A:HIS112
|
3.9
|
29.9
|
1.0
|
O3A
|
A:GDP138
|
4.1
|
97.2
|
1.0
|
C4'
|
A:GDP138
|
4.1
|
72.8
|
1.0
|
CE1
|
A:HIS112
|
4.1
|
35.3
|
1.0
|
C3'
|
A:GDP138
|
4.2
|
65.5
|
1.0
|
O
|
A:ILE111
|
4.4
|
30.8
|
1.0
|
O2'
|
A:GDP138
|
4.6
|
66.7
|
1.0
|
N
|
A:HIS112
|
4.7
|
31.3
|
1.0
|
O4'
|
A:GDP138
|
4.8
|
71.3
|
1.0
|
CD2
|
A:HIS112
|
4.8
|
32.7
|
1.0
|
C
|
A:ILE111
|
4.9
|
30.6
|
1.0
|
CE1
|
A:TYR50
|
5.0
|
52.0
|
1.0
|
CD2
|
A:TYR50
|
5.0
|
49.3
|
1.0
|
C2'
|
A:GDP138
|
5.0
|
65.2
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 3fbe
Go back to
Magnesium Binding Sites List in 3fbe
Magnesium binding site 2 out
of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg162
b:70.5
occ:1.00
|
O3A
|
C:GDP138
|
2.8
|
94.8
|
1.0
|
O2A
|
C:GDP138
|
3.1
|
77.7
|
1.0
|
PA
|
C:GDP138
|
3.3
|
94.2
|
1.0
|
O2B
|
C:GDP138
|
3.3
|
70.6
|
1.0
|
PB
|
C:GDP138
|
3.5
|
71.2
|
1.0
|
NH2
|
C:ARG86
|
3.6
|
61.6
|
1.0
|
O1A
|
C:GDP138
|
3.6
|
92.3
|
1.0
|
O1B
|
C:GDP138
|
3.8
|
67.7
|
1.0
|
CE1
|
C:HIS112
|
4.1
|
40.1
|
1.0
|
NE2
|
C:HIS53
|
4.2
|
48.2
|
1.0
|
OD2
|
C:ASP115
|
4.3
|
55.1
|
1.0
|
O
|
C:HOH147
|
4.3
|
40.4
|
1.0
|
ND1
|
C:HIS112
|
4.4
|
38.8
|
1.0
|
O
|
C:HOH163
|
4.6
|
34.2
|
1.0
|
CE1
|
C:HIS53
|
4.8
|
47.1
|
1.0
|
O3B
|
C:GDP138
|
4.9
|
62.5
|
1.0
|
O5'
|
C:GDP138
|
4.9
|
80.1
|
1.0
|
CZ
|
C:ARG86
|
4.9
|
58.7
|
1.0
|
CG
|
C:ASP115
|
4.9
|
51.5
|
1.0
|
CE2
|
C:TYR50
|
5.0
|
41.9
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 3fbe
Go back to
Magnesium Binding Sites List in 3fbe
Magnesium binding site 3 out
of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg163
b:60.0
occ:1.00
|
ND1
|
D:HIS112
|
2.9
|
50.4
|
1.0
|
OH
|
D:TYR50
|
2.9
|
52.3
|
1.0
|
O3'
|
D:GDP138
|
3.2
|
59.2
|
1.0
|
O1B
|
D:GDP138
|
3.3
|
72.9
|
1.0
|
O2B
|
D:GDP138
|
3.3
|
77.3
|
1.0
|
CB
|
D:HIS112
|
3.4
|
43.9
|
1.0
|
CE2
|
D:TYR50
|
3.4
|
52.9
|
1.0
|
NZ
|
D:LYS9
|
3.5
|
44.9
|
1.0
|
CG
|
D:HIS112
|
3.5
|
44.0
|
1.0
|
CZ
|
D:TYR50
|
3.6
|
53.1
|
1.0
|
C4'
|
D:GDP138
|
3.8
|
68.8
|
1.0
|
NH2
|
D:ARG99
|
4.0
|
49.8
|
1.0
|
PB
|
D:GDP138
|
4.0
|
89.9
|
1.0
|
CE1
|
D:HIS112
|
4.0
|
49.4
|
1.0
|
CA
|
D:HIS112
|
4.0
|
43.5
|
1.0
|
CE
|
D:LYS9
|
4.1
|
38.3
|
1.0
|
C3'
|
D:GDP138
|
4.1
|
66.0
|
1.0
|
O
|
D:ILE111
|
4.6
|
43.2
|
1.0
|
C5'
|
D:GDP138
|
4.6
|
73.4
|
1.0
|
CD2
|
D:TYR50
|
4.7
|
55.4
|
1.0
|
O5'
|
D:GDP138
|
4.7
|
81.8
|
1.0
|
CD2
|
D:HIS112
|
4.8
|
46.3
|
1.0
|
O2'
|
D:GDP138
|
4.9
|
57.5
|
1.0
|
O4'
|
D:GDP138
|
4.9
|
72.5
|
1.0
|
N
|
D:HIS112
|
4.9
|
43.6
|
1.0
|
O2A
|
D:GDP138
|
4.9
|
91.2
|
1.0
|
CE1
|
D:TYR50
|
4.9
|
56.6
|
1.0
|
NE2
|
D:HIS112
|
5.0
|
47.6
|
1.0
|
NE2
|
D:GLN89
|
5.0
|
49.1
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 3fbe
Go back to
Magnesium Binding Sites List in 3fbe
Magnesium binding site 4 out
of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg164
b:78.2
occ:1.00
|
OD2
|
E:ASP115
|
2.9
|
60.7
|
1.0
|
NH2
|
E:ARG86
|
3.0
|
59.5
|
1.0
|
NH1
|
E:ARG86
|
3.2
|
51.6
|
1.0
|
O2B
|
E:GDP138
|
3.2
|
78.1
|
1.0
|
CZ
|
E:ARG86
|
3.2
|
62.4
|
1.0
|
CB
|
E:ASP115
|
3.3
|
50.8
|
1.0
|
CG
|
E:ASP115
|
3.4
|
54.8
|
1.0
|
O3A
|
E:GDP138
|
3.8
|
96.8
|
1.0
|
PB
|
E:GDP138
|
4.0
|
80.5
|
1.0
|
O1A
|
E:GDP138
|
4.0
|
0.7
|
1.0
|
NE
|
E:ARG86
|
4.2
|
55.8
|
1.0
|
PA
|
E:GDP138
|
4.3
|
0.2
|
1.0
|
O1B
|
E:GDP138
|
4.3
|
76.9
|
1.0
|
OD1
|
E:ASP115
|
4.5
|
49.9
|
1.0
|
O2A
|
E:GDP138
|
4.5
|
96.2
|
1.0
|
CA
|
E:ASP115
|
4.7
|
44.4
|
1.0
|
O
|
E:HOH152
|
5.0
|
36.8
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 3fbe
Go back to
Magnesium Binding Sites List in 3fbe
Magnesium binding site 5 out
of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg165
b:77.2
occ:1.00
|
O3A
|
F:GDP138
|
3.1
|
0.6
|
1.0
|
NH2
|
F:ARG86
|
3.1
|
64.1
|
1.0
|
OD2
|
F:ASP115
|
3.2
|
58.6
|
1.0
|
O1B
|
F:GDP138
|
3.4
|
77.0
|
1.0
|
CG
|
F:ASP115
|
3.7
|
57.6
|
1.0
|
PB
|
F:GDP138
|
3.8
|
91.8
|
1.0
|
CZ
|
F:ARG86
|
3.9
|
64.7
|
1.0
|
CB
|
F:ASP115
|
3.9
|
53.6
|
1.0
|
NH1
|
F:ARG86
|
4.0
|
63.2
|
1.0
|
O2A
|
F:GDP138
|
4.2
|
0.7
|
1.0
|
PA
|
F:GDP138
|
4.3
|
0.2
|
1.0
|
O3B
|
F:GDP138
|
4.5
|
76.1
|
1.0
|
OD1
|
F:ASP115
|
4.6
|
49.9
|
1.0
|
O
|
F:HOH154
|
4.8
|
44.5
|
1.0
|
NE
|
F:ARG86
|
5.0
|
58.1
|
1.0
|
|
Reference:
S.Jeudy,
A.Lartigue,
J.M.Claverie,
C.Abergel.
Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase. J.Virol. V. 83 7142 2009.
ISSN: ISSN 0022-538X
PubMed: 19439473
DOI: 10.1128/JVI.00511-09
Page generated: Wed Aug 14 13:38:16 2024
|