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

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

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

Protein crystallography data

The structure of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp, PDB code: 3eic 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) 20.00 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 80.472, 152.726, 184.940, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp (pdb code 3eic). 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 Udp, PDB code: 3eic:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3eic

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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 Udp


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

b:61.2
occ:1.00
 O1A A:UDP161 2.0 45.1 1.0
O3B A:UDP161 2.1 45.5 1.0
PA A:UDP161 3.3 47.0 1.0
PB A:UDP161 3.3 45.3 1.0
O3A A:UDP161 3.6 46.6 1.0
NH2 A:ARG86 3.7 49.4 1.0
O2B A:UDP161 4.0 43.8 1.0
O2A A:UDP161 4.2 49.2 1.0
O5' A:UDP161 4.4 46.5 1.0
O1B A:UDP161 4.4 44.8 1.0
OD2 A:ASP115 4.4 45.6 1.0
C5' A:UDP161 4.5 47.0 1.0
CE1 A:HIS53 4.5 49.2 1.0
NE2 A:HIS53 4.6 48.8 1.0
CZ A:ARG86 4.6 47.7 1.0
NH1 A:ARG86 4.7 50.4 1.0

Magnesium binding site 2 out of 6 in 3eic

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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 Udp


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

b:72.5
occ:1.00
 O3B B:UDP162 2.1 48.3 1.0
O1A B:UDP162 2.2 49.6 1.0
PB B:UDP162 3.4 48.4 1.0
PA B:UDP162 3.5 49.5 1.0
NH2 B:ARG86 3.7 20.0 1.0
O3A B:UDP162 3.8 49.8 1.0
O2B B:UDP162 4.0 46.4 1.0
OD2 B:ASP115 4.2 53.4 1.0
NE2 B:HIS53 4.3 62.3 1.0
O1B B:UDP162 4.4 45.5 1.0
O5' B:UDP162 4.5 49.8 1.0
O2A B:UDP162 4.5 49.6 1.0
C5' B:UDP162 4.5 51.1 1.0
CE1 B:HIS53 4.6 62.1 1.0
CZ B:ARG86 4.6 20.0 1.0
NH1 B:ARG86 4.7 20.0 1.0
CG B:ASP115 4.9 53.0 1.0

Magnesium binding site 3 out of 6 in 3eic

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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 Udp


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

b:64.6
occ:1.00
 O3B C:UDP163 2.1 39.9 1.0
O1A C:UDP163 2.2 43.0 1.0
PB C:UDP163 3.4 42.0 1.0
PA C:UDP163 3.5 44.3 1.0
NH2 C:ARG86 3.6 46.2 1.0
O3A C:UDP163 3.8 43.1 1.0
O2B C:UDP163 4.0 40.5 1.0
NE2 C:HIS53 4.4 41.4 1.0
O5' C:UDP163 4.4 45.1 1.0
O1B C:UDP163 4.4 42.6 1.0
NH1 C:ARG86 4.4 42.0 1.0
CZ C:ARG86 4.5 44.1 1.0
OD2 C:ASP115 4.5 45.8 1.0
O2A C:UDP163 4.5 44.2 1.0
C5' C:UDP163 4.5 43.8 1.0
CE1 C:HIS53 4.5 41.5 1.0
O C:HOH195 4.8 45.4 1.0

Magnesium binding site 4 out of 6 in 3eic

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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 Udp


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

b:59.7
occ:1.00
 O1A D:UDP164 2.0 43.0 1.0
O3B D:UDP164 2.4 39.5 1.0
PA D:UDP164 3.4 45.0 1.0
PB D:UDP164 3.6 43.4 1.0
O3A D:UDP164 3.9 45.0 1.0
OD2 D:ASP115 4.0 45.2 1.0
NH2 D:ARG86 4.2 46.0 1.0
O2A D:UDP164 4.2 44.7 1.0
CE1 D:HIS53 4.2 47.3 1.0
O2B D:UDP164 4.4 41.2 1.0
NH1 D:ARG86 4.4 42.8 1.0
NE2 D:HIS53 4.5 46.9 1.0
O5' D:UDP164 4.5 43.2 1.0
C5' D:UDP164 4.6 43.9 1.0
O1B D:UDP164 4.7 44.5 1.0
CZ D:ARG86 4.8 44.7 1.0
CG D:ASP115 4.9 46.0 1.0

Magnesium binding site 5 out of 6 in 3eic

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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 Udp


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

b:64.3
occ:1.00
 O1A E:UDP165 2.0 47.5 1.0
O3B E:UDP165 2.2 48.3 1.0
PB E:UDP165 3.3 48.8 1.0
PA E:UDP165 3.3 48.2 1.0
O3A E:UDP165 3.7 47.9 1.0
O2B E:UDP165 3.8 46.1 1.0
NH2 E:ARG86 3.9 47.2 1.0
CE1 E:HIS53 4.3 51.5 1.0
O5' E:UDP165 4.3 47.6 1.0
C5' E:UDP165 4.3 46.3 1.0
O2A E:UDP165 4.3 45.8 1.0
NE2 E:HIS53 4.3 51.7 1.0
O1B E:UDP165 4.5 45.5 1.0
OD2 E:ASP115 4.6 49.7 1.0
CZ E:ARG86 4.7 47.1 1.0
NH1 E:ARG86 4.8 47.8 1.0
O E:HOH171 4.9 48.8 1.0

Magnesium binding site 6 out of 6 in 3eic

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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 Udp


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 Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg165

b:67.4
occ:1.00
 O3B F:UDP166 2.2 52.5 1.0
O1A F:UDP166 2.2 55.0 1.0
PB F:UDP166 3.5 53.1 1.0
PA F:UDP166 3.5 57.0 1.0
NH2 F:ARG86 3.6 49.4 1.0
O F:HOH193 3.7 52.0 1.0
O3A F:UDP166 3.9 55.7 1.0
OD2 F:ASP115 4.1 50.1 1.0
O2B F:UDP166 4.2 54.0 1.0
O2A F:UDP166 4.4 55.5 1.0
CZ F:ARG86 4.5 48.4 1.0
NH1 F:ARG86 4.6 50.2 1.0
O1B F:UDP166 4.6 52.1 1.0
O5' F:UDP166 4.6 57.0 1.0
NE2 F:HIS53 4.7 56.2 1.0
C5' F:UDP166 4.7 57.2 1.0
CE1 F:HIS53 4.7 56.5 1.0
CG F:ASP115 4.9 48.2 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: Wed Aug 14 13:04:43 2024

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