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Magnesium in PDB 3ee3: Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp

Enzymatic activity of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp

All present enzymatic activity of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp, PDB code: 3ee3 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 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.419, 154.419, 187.039, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp (pdb code 3ee3). 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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp, PDB code: 3ee3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ee3

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Magnesium binding site 1 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:60.0
occ:1.00
 O1A A:CDP160 2.1 46.7 1.0
O3B A:CDP160 2.1 46.0 1.0
PB A:CDP160 3.4 46.0 1.0
PA A:CDP160 3.4 47.7 1.0
NH1 A:ARG86 3.7 38.7 1.0
O3A A:CDP160 3.8 48.4 1.0
O A:HOH192 3.9 48.5 1.0
O2B A:CDP160 4.2 43.9 1.0
NH2 A:ARG86 4.3 42.9 1.0
CZ A:ARG86 4.4 42.7 1.0
OD2 A:ASP115 4.4 46.5 1.0
C5' A:CDP160 4.4 45.9 1.0
O5' A:CDP160 4.4 44.5 1.0
O2A A:CDP160 4.5 47.9 1.0
O1B A:CDP160 4.5 48.2 1.0
NE2 A:HIS53 4.7 51.3 1.0
CE1 A:HIS53 4.8 51.0 1.0

Magnesium binding site 2 out of 6 in 3ee3

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Magnesium binding site 2 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg162

b:70.4
occ:1.00
 O3B B:CDP161 1.9 62.0 1.0
O1A B:CDP161 2.3 59.0 1.0
PB B:CDP161 3.3 60.4 1.0
PA B:CDP161 3.5 59.1 1.0
NH2 B:ARG86 3.6 54.6 1.0
O3A B:CDP161 3.8 61.5 1.0
O1B B:CDP161 4.2 58.5 1.0
O2B B:CDP161 4.2 57.5 1.0
O2A B:CDP161 4.2 56.8 1.0
OD2 B:ASP115 4.4 58.1 1.0
CZ B:ARG86 4.5 54.8 1.0
NH1 B:ARG86 4.6 55.6 1.0
O5' B:CDP161 4.7 57.5 1.0
NE2 B:HIS53 4.7 75.2 1.0
CE1 B:HIS53 4.9 74.6 1.0
C5' B:CDP161 5.0 58.5 1.0

Magnesium binding site 3 out of 6 in 3ee3

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Magnesium binding site 3 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg163

b:54.2
occ:1.00
 O3B C:CDP162 2.2 47.5 1.0
O1A C:CDP162 2.2 44.6 1.0
PB C:CDP162 3.5 44.3 1.0
PA C:CDP162 3.6 45.0 1.0
O C:HOH195 3.7 45.0 1.0
NH2 C:ARG86 3.8 49.8 1.0
O3A C:CDP162 3.9 46.0 1.0
O2B C:CDP162 4.3 47.2 1.0
NE2 C:HIS53 4.4 45.4 1.0
OD2 C:ASP115 4.4 49.6 1.0
O2A C:CDP162 4.6 43.8 1.0
O5' C:CDP162 4.6 44.5 1.0
O1B C:CDP162 4.6 47.6 1.0
C5' C:CDP162 4.6 43.9 1.0
CZ C:ARG86 4.6 48.5 1.0
NH1 C:ARG86 4.7 46.1 1.0
CE1 C:HIS53 4.8 45.6 1.0
O C:HOH179 4.8 48.4 1.0

Magnesium binding site 4 out of 6 in 3ee3

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Magnesium binding site 4 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg164

b:59.0
occ:1.00
 O1A D:CDP163 2.1 47.2 1.0
O3B D:CDP163 2.5 48.1 1.0
PA D:CDP163 3.5 49.3 1.0
PB D:CDP163 3.8 48.4 1.0
OD2 D:ASP115 3.8 53.1 1.0
O3A D:CDP163 4.0 49.5 1.0
NH2 D:ARG86 4.1 51.4 1.0
O D:HOH184 4.2 47.9 1.0
O D:HOH173 4.3 35.7 1.0
O2A D:CDP163 4.5 47.7 1.0
CE1 D:HIS53 4.6 50.9 1.0
NH1 D:ARG86 4.6 49.4 1.0
O5' D:CDP163 4.6 46.8 1.0
O1B D:CDP163 4.7 49.9 1.0
O2B D:CDP163 4.8 48.9 1.0
CZ D:ARG86 4.8 50.0 1.0
CG D:ASP115 4.9 52.8 1.0
C5' D:CDP163 4.9 48.3 1.0
NE2 D:HIS53 4.9 51.0 1.0

Magnesium binding site 5 out of 6 in 3ee3

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Magnesium binding site 5 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg165

b:63.2
occ:1.00
 O3B E:CDP164 2.1 51.2 1.0
O1A E:CDP164 2.2 49.6 1.0
PB E:CDP164 3.3 50.1 1.0
PA E:CDP164 3.5 51.4 1.0
NH2 E:ARG86 3.7 46.3 1.0
O3A E:CDP164 3.8 52.0 1.0
O2B E:CDP164 3.9 48.8 1.0
C5' E:CDP164 4.3 48.9 1.0
O5' E:CDP164 4.4 50.0 1.0
CE1 E:HIS53 4.5 52.6 1.0
NE2 E:HIS53 4.5 51.5 1.0
CZ E:ARG86 4.5 46.2 1.0
O1B E:CDP164 4.6 49.5 1.0
NH1 E:ARG86 4.6 44.6 1.0
O2A E:CDP164 4.6 49.6 1.0
OD2 E:ASP115 4.6 51.5 1.0

Magnesium binding site 6 out of 6 in 3ee3

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Magnesium binding site 6 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg166

b:65.9
occ:1.00
 O1A F:CDP165 2.1 54.8 1.0
O3B F:CDP165 2.3 51.6 1.0
PA F:CDP165 3.5 57.6 1.0
PB F:CDP165 3.6 54.4 1.0
NH2 F:ARG86 3.7 58.5 1.0
O F:HOH185 3.8 49.3 1.0
O3A F:CDP165 3.9 57.9 1.0
OD2 F:ASP115 4.0 56.9 1.0
O2B F:CDP165 4.3 54.6 1.0
O2A F:CDP165 4.4 54.7 1.0
O5' F:CDP165 4.6 58.2 1.0
C5' F:CDP165 4.6 60.0 1.0
CZ F:ARG86 4.7 58.0 1.0
O1B F:CDP165 4.8 53.9 1.0
CE1 F:HIS53 4.9 62.1 1.0
CG F:ASP115 4.9 55.2 1.0
NE2 F:HIS53 5.0 62.0 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 20:28:17 2025

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