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Magnesium in PDB 3fbc: Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp

Enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp, PDB code: 3fbc 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) 48.11 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 80.387, 153.337, 185.384, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp (pdb code 3fbc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp, PDB code: 3fbc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3fbc

Go back to Magnesium Binding Sites List in 3fbc
Magnesium binding site 1 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp


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 Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg160

b:83.4
occ:1.00
 O2B A:TYD138 2.7 89.5 1.0
NH2 A:ARG86 3.1 66.8 1.0
O1A A:TYD138 3.6 92.2 1.0
OD2 A:ASP115 3.6 54.4 1.0
PB A:TYD138 3.8 89.0 1.0
O3B A:TYD138 3.9 73.2 1.0
CZ A:ARG86 4.0 66.3 1.0
NH1 A:ARG86 4.0 65.4 1.0
CG A:ASP115 4.4 55.0 1.0
CB A:ASP115 4.4 51.4 1.0
O3A A:TYD138 4.6 83.4 1.0
PA A:TYD138 4.7 94.2 1.0

Magnesium binding site 2 out of 6 in 3fbc

Go back to Magnesium Binding Sites List in 3fbc
Magnesium binding site 2 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp


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 Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg161

b:94.7
occ:1.00
 O1A B:TYD138 2.8 0.4 1.0
O2B B:TYD138 3.0 0.7 1.0
NE2 B:HIS53 3.6 88.0 1.0
O1B B:TYD138 3.7 89.1 1.0
PB B:TYD138 3.9 0.1 1.0
PA B:TYD138 4.1 0.4 1.0
CE1 B:HIS53 4.4 84.4 1.0
O3A B:TYD138 4.4 0.6 1.0
OD2 B:ASP115 4.5 74.4 1.0
OD1 B:ASP115 4.5 73.1 1.0
C5' B:TYD138 4.5 0.8 1.0
CD2 B:HIS53 4.6 80.8 1.0
CG B:ASP115 4.6 79.5 1.0
O5' B:TYD138 4.8 0.2 1.0
CE1 B:HIS112 4.8 61.6 1.0

Magnesium binding site 3 out of 6 in 3fbc

Go back to Magnesium Binding Sites List in 3fbc
Magnesium binding site 3 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp


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 Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg162

b:72.3
occ:1.00
 O2B C:TYD138 2.3 90.4 1.0
OD2 C:ASP115 3.0 50.9 1.0
NH2 C:ARG86 3.1 67.8 1.0
O1A C:TYD138 3.6 83.0 1.0
PB C:TYD138 3.7 86.3 1.0
CZ C:ARG86 3.8 66.3 1.0
CG C:ASP115 3.8 52.2 1.0
NH1 C:ARG86 4.0 60.6 1.0
CB C:ASP115 4.1 48.0 1.0
O3B C:TYD138 4.3 69.8 1.0
O1B C:TYD138 4.6 71.9 1.0
O3A C:TYD138 4.6 88.1 1.0
PA C:TYD138 4.7 96.8 1.0
O C:HOH148 4.7 39.2 1.0
NE C:ARG86 4.8 60.7 1.0
OD1 C:ASP115 4.8 45.7 1.0

Magnesium binding site 4 out of 6 in 3fbc

Go back to Magnesium Binding Sites List in 3fbc
Magnesium binding site 4 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp


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 Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg163

b:78.2
occ:1.00
 O1A D:TYD138 2.6 78.0 1.0
O2B D:TYD138 2.6 84.7 1.0
OD2 D:ASP115 3.1 79.5 1.0
NH2 D:ARG86 3.7 83.4 1.0
PA D:TYD138 3.8 97.6 1.0
PB D:TYD138 3.8 87.2 1.0
O3A D:TYD138 4.1 93.4 1.0
CG D:ASP115 4.3 75.3 1.0
O3B D:TYD138 4.4 82.8 1.0
CE1 D:HIS53 4.5 70.1 1.0
CZ D:ARG86 4.6 74.8 1.0
O2A D:TYD138 4.6 80.8 1.0
NH1 D:ARG86 4.7 71.1 1.0
NE2 D:HIS53 4.7 71.0 1.0

Magnesium binding site 5 out of 6 in 3fbc

Go back to Magnesium Binding Sites List in 3fbc
Magnesium binding site 5 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp


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 Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg164

b:84.3
occ:1.00
 O2B E:TYD138 2.5 0.0 1.0
O1A E:TYD138 3.3 0.9 1.0
OD2 E:ASP115 3.3 68.7 1.0
NH2 E:ARG86 3.5 76.5 1.0
PB E:TYD138 3.8 0.8 1.0
O3B E:TYD138 4.2 90.5 1.0
O3A E:TYD138 4.2 0.5 1.0
CG E:ASP115 4.2 63.4 1.0
PA E:TYD138 4.3 0.1 1.0
CZ E:ARG86 4.6 75.3 1.0
NE2 E:HIS53 4.7 71.8 1.0
CB E:ASP115 4.8 60.4 1.0
CE1 E:HIS112 4.9 47.4 1.0

Magnesium binding site 6 out of 6 in 3fbc

Go back to Magnesium Binding Sites List in 3fbc
Magnesium binding site 6 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg165

b:75.1
occ:1.00
 O2B F:TYD138 2.7 97.6 1.0
OD2 F:ASP115 2.9 67.2 1.0
NH2 F:ARG86 3.2 68.3 1.0
CG F:ASP115 3.9 64.8 1.0
O1A F:TYD138 3.9 92.8 1.0
PB F:TYD138 4.0 99.9 1.0
CZ F:ARG86 4.0 68.1 1.0
CB F:ASP115 4.2 58.4 1.0
O3B F:TYD138 4.4 76.0 1.0
NH1 F:ARG86 4.4 73.5 1.0
O3A F:TYD138 4.8 96.9 1.0
PA F:TYD138 4.9 0.6 1.0
OD1 F:ASP115 4.9 54.3 1.0
NE F:ARG86 5.0 61.1 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 13:37:49 2024

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