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Magnesium in PDB 3elh: X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp

Enzymatic activity of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp

All present enzymatic activity of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp:
2.7.4.6;

Protein crystallography data

The structure of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp, PDB code: 3elh 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) 19.87 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 80.717, 153.576, 185.795, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp (pdb code 3elh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp, PDB code: 3elh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3elh

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Magnesium binding site 1 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:57.5
occ:1.00
 O3B A:DUD160 2.3 45.9 1.0
O1A A:DUD160 2.6 44.9 1.0
NH2 A:ARG86 3.4 57.9 1.0
PB A:DUD160 3.7 46.9 1.0
PA A:DUD160 3.9 48.5 1.0
OD2 A:ASP115 3.9 50.8 1.0
O3A A:DUD160 4.3 50.0 1.0
O2B A:DUD160 4.3 44.9 1.0
CZ A:ARG86 4.3 48.6 1.0
NE2 A:HIS53 4.4 44.0 1.0
NH1 A:ARG86 4.5 44.1 1.0
C5' A:DUD160 4.7 45.6 1.0
CG A:ASP115 4.7 48.1 1.0
CE1 A:HIS53 4.7 43.5 1.0
O A:HOH165 4.8 44.2 1.0
O5' A:DUD160 4.8 46.2 1.0
O1B A:DUD160 4.9 47.9 1.0

Magnesium binding site 2 out of 6 in 3elh

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Magnesium binding site 2 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg162

b:72.1
occ:1.00
 O3B B:DUD161 2.4 65.5 1.0
O1A B:DUD161 2.6 68.2 1.0
OD2 B:ASP115 3.8 59.6 1.0
NH2 B:ARG86 3.8 54.2 1.0
PB B:DUD161 3.8 57.7 1.0
PA B:DUD161 4.0 60.0 1.0
CG B:ASP115 4.2 66.3 1.0
O3A B:DUD161 4.3 63.8 1.0
NE2 B:HIS53 4.4 63.2 1.0
O2B B:DUD161 4.5 47.0 1.0
CZ B:ARG86 4.7 51.8 1.0
OD1 B:ASP115 4.8 66.8 1.0
CB B:ASP115 4.8 60.0 1.0
O2A B:DUD161 4.8 59.3 1.0
NH1 B:ARG86 4.9 60.1 1.0
CE1 B:HIS53 4.9 58.7 1.0
O1B B:DUD161 4.9 54.0 1.0

Magnesium binding site 3 out of 6 in 3elh

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Magnesium binding site 3 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg163

b:61.1
occ:1.00
 O3B C:DUD162 2.3 51.9 1.0
O1A C:DUD162 2.5 45.5 1.0
NH2 C:ARG86 3.5 56.8 1.0
PB C:DUD162 3.7 41.8 1.0
OD2 C:ASP115 3.7 57.2 1.0
PA C:DUD162 3.9 47.7 1.0
CZ C:ARG86 4.2 52.5 1.0
NH1 C:ARG86 4.3 46.0 1.0
O3A C:DUD162 4.3 47.3 1.0
O2B C:DUD162 4.4 43.2 1.0
O C:HOH201 4.4 51.9 1.0
CG C:ASP115 4.4 48.3 1.0
NE2 C:HIS53 4.6 42.3 1.0
O1B C:DUD162 4.8 49.0 1.0
CE1 C:HIS53 4.8 39.8 1.0
O2A C:DUD162 4.9 44.3 1.0
CB C:ASP115 4.9 44.1 1.0
O5' C:DUD162 5.0 46.6 1.0

Magnesium binding site 4 out of 6 in 3elh

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Magnesium binding site 4 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg164

b:55.7
occ:1.00
 O1A D:DUD163 2.4 47.5 1.0
O3B D:DUD163 2.5 52.3 1.0
OD2 D:ASP115 3.7 48.9 1.0
PA D:DUD163 3.7 48.2 1.0
PB D:DUD163 3.9 46.4 1.0
O3A D:DUD163 4.1 54.7 1.0
NH2 D:ARG86 4.2 52.3 1.0
NH1 D:ARG86 4.4 44.2 1.0
CE1 D:HIS53 4.5 45.0 1.0
O2A D:DUD163 4.5 50.4 1.0
CG D:ASP115 4.7 48.4 1.0
CZ D:ARG86 4.7 49.2 1.0
O2B D:DUD163 4.8 49.6 1.0
O5' D:DUD163 4.9 50.9 1.0
NE2 D:HIS53 4.9 47.8 1.0
O1B D:DUD163 4.9 54.1 1.0

Magnesium binding site 5 out of 6 in 3elh

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Magnesium binding site 5 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg165

b:66.2
occ:1.00
 O3B E:DUD164 2.4 58.7 1.0
O1A E:DUD164 2.5 57.0 1.0
NH2 E:ARG86 3.6 55.7 1.0
PB E:DUD164 3.6 56.8 1.0
PA E:DUD164 3.8 57.2 1.0
OD2 E:ASP115 4.1 59.8 1.0
O2B E:DUD164 4.1 45.3 1.0
O3A E:DUD164 4.1 60.2 1.0
CZ E:ARG86 4.4 54.5 1.0
NH1 E:ARG86 4.4 46.0 1.0
CE1 E:HIS53 4.6 48.3 1.0
NE2 E:HIS53 4.6 46.9 1.0
CG E:ASP115 4.7 53.1 1.0
C5' E:DUD164 4.8 48.9 1.0
O2A E:DUD164 4.9 49.4 1.0
O5' E:DUD164 4.9 54.3 1.0
O1B E:DUD164 4.9 47.8 1.0
O E:HOH175 5.0 43.9 1.0

Magnesium binding site 6 out of 6 in 3elh

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Magnesium binding site 6 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dudp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg166

b:64.8
occ:1.00
 O3B F:DUD165 2.5 58.9 1.0
O1A F:DUD165 2.6 60.3 1.0
NH2 F:ARG86 3.2 64.5 1.0
OD2 F:ASP115 3.7 58.8 1.0
PB F:DUD165 3.9 58.7 1.0
PA F:DUD165 4.0 66.8 1.0
O3A F:DUD165 4.4 68.5 1.0
CZ F:ARG86 4.5 52.5 1.0
CG F:ASP115 4.5 52.2 1.0
O2B F:DUD165 4.7 56.0 1.0
CE1 F:HIS53 4.7 61.7 1.0
NE2 F:HIS53 4.7 57.3 1.0
O2A F:DUD165 4.9 58.9 1.0
O1B F:DUD165 4.9 55.8 1.0
CB F:ASP115 5.0 47.7 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: Sun Aug 10 20:31:45 2025

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