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Magnesium in PDB 3g2x: Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp

Enzymatic activity of Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp

All present enzymatic activity of Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp:
2.7.4.6;

Protein crystallography data

The structure of Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp, PDB code: 3g2x 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) 24.57 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.371, 151.492, 181.723, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp (pdb code 3g2x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp, PDB code: 3g2x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3g2x

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Magnesium binding site 1 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:56.7
occ:1.00
 O2B A:TYD201 2.7 49.4 1.0
OD2 A:ASP119 3.2 57.2 1.0
O2A A:TYD201 3.2 50.0 1.0
O A:HOH151 3.3 49.2 1.0
CG A:ASP119 3.7 57.8 1.0
CB A:ASP119 3.7 51.0 1.0
NH1 A:ARG86 4.0 50.0 1.0
PB A:TYD201 4.1 45.0 1.0
CE1 A:HIS116 4.2 44.9 1.0
NH2 A:ARG86 4.2 52.1 1.0
CZ A:ARG86 4.3 49.4 1.0
O A:ALA117 4.3 44.8 1.0
N A:ASP119 4.4 49.2 1.0
PA A:TYD201 4.5 50.1 1.0
CA A:ASP119 4.6 49.3 1.0
ND1 A:HIS116 4.7 43.6 1.0
OD1 A:ASP119 4.7 52.7 1.0
O1B A:TYD201 4.7 48.4 1.0
O A:HOH150 4.8 43.4 1.0
O3A A:TYD201 4.8 50.4 1.0

Magnesium binding site 2 out of 6 in 3g2x

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Magnesium binding site 2 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:71.0
occ:1.00
 O B:HOH144 2.8 64.0 1.0
O2B B:TYD201 2.8 59.8 1.0
O2A B:TYD201 2.8 52.6 1.0
NH2 B:ARG86 3.1 52.0 1.0
PA B:TYD201 3.6 54.4 1.0
NH1 B:ARG86 3.8 52.8 1.0
O1A B:TYD201 3.8 54.4 1.0
CZ B:ARG86 3.8 55.0 1.0
PB B:TYD201 3.8 54.4 1.0
O3A B:TYD201 4.0 56.0 1.0
OD2 B:ASP119 4.1 63.9 1.0
O3B B:TYD201 4.2 47.4 1.0
CB B:ASP119 4.4 60.7 1.0
CG B:ASP119 4.7 63.9 1.0

Magnesium binding site 3 out of 6 in 3g2x

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Magnesium binding site 3 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:55.4
occ:1.00
 O2B C:TYD201 2.7 49.1 1.0
O2A C:TYD201 2.9 46.5 1.0
NH1 C:ARG86 3.5 50.3 1.0
OD2 C:ASP119 3.6 60.8 1.0
CE1 C:HIS116 4.0 45.8 1.0
PB C:TYD201 4.1 48.2 1.0
CB C:ASP119 4.1 53.2 1.0
O C:ALA117 4.2 48.7 1.0
CG C:ASP119 4.2 58.1 1.0
CZ C:ARG86 4.2 49.7 1.0
PA C:TYD201 4.3 55.3 1.0
NH2 C:ARG86 4.4 45.2 1.0
ND1 C:HIS116 4.5 44.1 1.0
O1B C:TYD201 4.5 50.0 1.0
N C:ASP119 4.7 54.2 1.0
O3A C:TYD201 4.7 51.6 1.0
NE2 C:HIS53 4.8 56.9 1.0
CA C:ASP119 5.0 53.2 1.0
NE2 C:HIS116 5.0 44.2 1.0

Magnesium binding site 4 out of 6 in 3g2x

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Magnesium binding site 4 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:66.3
occ:1.00
 O2A D:TYD201 2.5 54.5 1.0
O2B D:TYD201 3.2 57.7 1.0
CE1 D:HIS116 3.8 46.9 1.0
NE2 D:HIS53 3.9 57.9 1.0
PA D:TYD201 4.0 60.8 1.0
PB D:TYD201 4.3 59.1 1.0
ND1 D:HIS116 4.3 48.0 1.0
O1B D:TYD201 4.4 60.6 1.0
CE2 D:TYR50 4.4 48.0 1.0
CE1 D:HIS53 4.5 58.6 1.0
O3A D:TYD201 4.6 58.6 1.0
C5' D:TYD201 4.6 58.9 1.0
OD2 D:ASP119 4.7 51.2 1.0
O5' D:TYD201 4.8 62.2 1.0
CD2 D:TYR50 4.8 47.0 1.0
CD2 D:HIS53 4.9 58.7 1.0
NE2 D:HIS116 4.9 44.4 1.0

Magnesium binding site 5 out of 6 in 3g2x

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Magnesium binding site 5 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:57.3
occ:1.00
 O2A E:TYD201 2.6 51.7 1.0
O2B E:TYD201 2.7 56.5 1.0
O E:HOH147 2.8 45.7 1.0
PA E:TYD201 3.9 52.5 1.0
PB E:TYD201 3.9 47.0 1.0
NH1 E:ARG86 4.0 57.4 1.0
CE1 E:HIS116 4.1 58.4 1.0
O3A E:TYD201 4.3 51.6 1.0
O1B E:TYD201 4.3 45.5 1.0
NE2 E:HIS53 4.5 50.9 1.0
CB E:ASP119 4.5 59.5 1.0
OD2 E:ASP119 4.5 65.5 1.0
CG E:ASP119 4.5 64.2 1.0
ND1 E:HIS116 4.6 59.6 1.0
NH2 E:ARG86 4.6 60.9 1.0
CZ E:ARG86 4.7 59.1 1.0
C5' E:TYD201 4.9 49.5 1.0
O1A E:TYD201 4.9 45.7 1.0
O E:ALA117 4.9 56.2 1.0
CE1 E:HIS53 4.9 47.7 1.0
O5' E:TYD201 5.0 48.2 1.0

Magnesium binding site 6 out of 6 in 3g2x

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Magnesium binding site 6 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:65.8
occ:1.00
 O2A F:TYD201 2.7 70.1 1.0
O2B F:TYD201 2.8 60.7 1.0
PA F:TYD201 3.4 76.6 1.0
O1A F:TYD201 3.4 62.5 1.0
NH1 F:ARG86 3.8 55.9 1.0
NH2 F:ARG86 3.8 55.6 1.0
OD2 F:ASP119 3.9 71.2 1.0
O3A F:TYD201 4.0 74.2 1.0
PB F:TYD201 4.1 63.5 1.0
CZ F:ARG86 4.2 58.2 1.0
CB F:ASP119 4.3 61.5 1.0
CG F:ASP119 4.5 66.5 1.0
NE2 F:HIS53 4.9 87.1 1.0
O5' F:TYD201 4.9 62.9 1.0
O3B F:TYD201 4.9 67.2 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: Mon Dec 14 08:09:48 2020

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