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Magnesium in PDB 2b8q: X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp

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

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

Protein crystallography data

The structure of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp, PDB code: 2b8q was solved by S.Jeudy, J.M.Claverie, C.Abergel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 80.390, 153.352, 185.491, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 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 Tdp (pdb code 2b8q). 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 Tdp, PDB code: 2b8q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 1 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:65.8
occ:1.00
 O1A A:TYD160 2.5 52.2 1.0
O2B A:TYD160 2.7 52.0 1.0
PA A:TYD160 3.7 53.8 1.0
NE2 A:HIS53 3.8 53.9 1.0
PB A:TYD160 3.8 50.0 1.0
NH2 A:ARG86 3.9 52.9 1.0
C5' A:TYD160 4.0 51.5 1.0
O1B A:TYD160 4.0 49.4 1.0
CE1 A:HIS53 4.1 53.4 1.0
O3A A:TYD160 4.2 52.0 1.0
O5' A:TYD160 4.3 51.7 1.0
OD2 A:ASP115 4.6 48.1 1.0
O A:HOH205 4.6 46.5 1.0
CE1 A:HIS112 4.7 37.0 1.0
CD2 A:HIS53 5.0 53.2 1.0

Magnesium binding site 2 out of 6 in 2b8q

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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 Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:66.8
occ:1.00
 O1A B:TYD161 2.5 57.3 1.0
O2B B:TYD161 2.6 57.4 1.0
PA B:TYD161 3.8 57.6 1.0
OD2 B:ASP115 4.0 64.1 1.0
NH2 B:ARG86 4.0 51.3 1.0
PB B:TYD161 4.1 54.8 1.0
CG B:ASP115 4.2 64.1 1.0
O3A B:TYD161 4.2 58.3 1.0
OD1 B:ASP115 4.5 66.4 1.0
NE2 B:HIS53 4.6 69.3 1.0
O2A B:TYD161 4.6 56.5 1.0
CB B:ASP115 4.8 59.6 1.0
O1B B:TYD161 4.9 54.6 1.0
CZ B:ARG86 5.0 50.6 1.0

Magnesium binding site 3 out of 6 in 2b8q

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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 Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:71.7
occ:1.00
 O2B C:TYD162 2.5 46.8 1.0
O1A C:TYD162 2.6 45.1 1.0
PB C:TYD162 3.6 44.4 1.0
PA C:TYD162 3.8 46.7 1.0
NH2 C:ARG86 3.8 47.5 1.0
O1B C:TYD162 3.8 45.0 1.0
O C:HOH1040 3.9 41.0 1.0
OD2 C:ASP115 4.1 52.1 1.0
NE2 C:HIS53 4.1 45.0 1.0
O3A C:TYD162 4.2 47.2 1.0
C5' C:TYD162 4.2 49.0 1.0
O C:HOH1029 4.3 32.9 1.0
O C:HOH1014 4.3 34.6 1.0
CE1 C:HIS112 4.3 37.5 1.0
O5' C:TYD162 4.4 47.2 1.0
ND1 C:HIS112 4.6 37.2 1.0
CE1 C:HIS53 4.7 43.5 1.0
CG C:ASP115 4.9 48.4 1.0
CZ C:ARG86 4.9 44.8 1.0

Magnesium binding site 4 out of 6 in 2b8q

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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 Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:72.0
occ:1.00
 O1A D:TYD163 2.5 51.3 1.0
O2B D:TYD163 2.5 52.0 1.0
OD2 D:ASP115 3.2 51.7 1.0
NH2 D:ARG86 3.7 48.6 1.0
PA D:TYD163 3.9 52.9 1.0
PB D:TYD163 4.1 50.0 1.0
CG D:ASP115 4.3 49.8 1.0
O3A D:TYD163 4.3 53.0 1.0
CZ D:ARG86 4.5 47.1 1.0
NH1 D:ARG86 4.6 46.9 1.0
CE1 D:HIS53 4.7 53.0 1.0
CB D:ASP115 4.7 47.8 1.0
NE2 D:HIS53 4.8 52.8 1.0
O2A D:TYD163 4.8 52.5 1.0
O D:HOH209 4.8 47.9 1.0
O1B D:TYD163 4.9 49.8 1.0
O5' D:TYD163 5.0 53.5 1.0

Magnesium binding site 5 out of 6 in 2b8q

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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 Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg206

b:61.2
occ:1.00
 O1A E:TYD164 2.5 57.4 1.0
O2B E:TYD164 2.6 58.2 1.0
PB E:TYD164 3.7 56.3 1.0
NH2 E:ARG86 3.8 50.8 1.0
PA E:TYD164 3.8 57.5 1.0
O1B E:TYD164 4.0 55.0 1.0
O E:HOH216 4.1 38.4 1.0
NE2 E:HIS53 4.2 54.3 1.0
O3A E:TYD164 4.2 58.0 1.0
CE1 E:HIS112 4.4 34.1 1.0
C5' E:TYD164 4.4 58.0 1.0
O5' E:TYD164 4.6 57.3 1.0
CE1 E:HIS53 4.7 54.0 1.0
ND1 E:HIS112 4.7 35.7 1.0
O E:HOH214 4.8 44.5 1.0
OD2 E:ASP115 4.9 54.3 1.0
CZ E:ARG86 4.9 49.8 1.0

Magnesium binding site 6 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 6 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


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 Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:78.0
occ:1.00
 O1A F:TYD165 2.5 65.8 1.0
O2B F:TYD165 2.6 63.1 1.0
OD2 F:ASP115 3.0 58.2 1.0
NH2 F:ARG86 3.6 57.7 1.0
PA F:TYD165 3.9 66.7 1.0
CG F:ASP115 4.1 56.1 1.0
PB F:TYD165 4.2 60.9 1.0
O3A F:TYD165 4.3 64.8 1.0
O2A F:TYD165 4.6 66.8 1.0
CB F:ASP115 4.6 53.1 1.0
NE2 F:HIS53 4.8 58.0 1.0
CE1 F:HIS53 4.8 58.1 1.0
CZ F:ARG86 4.9 55.8 1.0
O F:HOH217 4.9 34.6 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 09:56:46 2025

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