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Magnesium in PDB 3gp9: Crystal Structure of the Mimivirus Ndk Complexed with Gdp

Enzymatic activity of Crystal Structure of the Mimivirus Ndk Complexed with Gdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk Complexed with Gdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk Complexed with Gdp, PDB code: 3gp9 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) 70.53 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.482, 152.951, 183.858, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk Complexed with Gdp (pdb code 3gp9). 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 the Mimivirus Ndk Complexed with Gdp, PDB code: 3gp9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3gp9

Go back to Magnesium Binding Sites List in 3gp9
Magnesium binding site 1 out of 6 in the Crystal Structure of the Mimivirus Ndk Complexed with Gdp


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 the Mimivirus Ndk Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg140

b:36.5
occ:0.64
 O3A A:GDP138 2.6 37.7 0.6
O A:HOH376 2.7 33.5 1.0
OE1 A:GLN89 2.8 28.3 1.0
O A:ALA113 3.0 20.6 1.0
ND1 A:HIS112 3.0 25.2 1.0
N A:ALA113 3.2 19.4 1.0
NE2 A:GLN89 3.4 29.1 1.0
O1A A:GDP138 3.4 29.7 0.6
CD A:GLN89 3.5 25.0 1.0
PA A:GDP138 3.6 40.4 0.6
CE1 A:HIS112 3.6 22.4 1.0
CG A:HIS112 3.6 22.2 1.0
CA A:HIS112 3.6 20.6 1.0
NH2 A:ARG99 3.7 24.1 1.0
O1B A:GDP138 3.8 39.4 0.6
PB A:GDP138 3.8 46.1 0.6
C A:HIS112 3.9 17.6 1.0
C A:ALA113 3.9 19.9 1.0
CB A:HIS112 4.0 20.7 1.0
CA A:ALA113 4.1 18.6 1.0
NE2 A:HIS112 4.3 21.1 1.0
CD2 A:HIS112 4.3 22.6 1.0
O2A A:GDP138 4.4 40.0 0.6
O2B A:GDP138 4.5 52.1 0.6
CZ A:ARG99 4.6 25.7 1.0
O A:ILE111 4.6 20.8 1.0
O5' A:GDP138 4.7 39.8 0.6
NH1 A:ARG86 4.7 32.2 1.0
CB A:ALA113 4.8 18.9 1.0
NH1 A:ARG99 4.8 26.6 1.0
N A:HIS112 4.9 19.1 1.0
O3B A:GDP138 5.0 44.2 0.6
CG A:GLN89 5.0 20.9 1.0

Magnesium binding site 2 out of 6 in 3gp9

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Mimivirus Ndk Complexed with Gdp


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 the Mimivirus Ndk Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg140

b:36.0
occ:0.64
 O3A B:GDP138 2.6 37.2 0.6
NH2 B:ARG86 2.7 44.9 1.0
ND1 B:HIS112 2.8 26.0 1.0
N B:ALA113 3.0 18.6 1.0
OE1 B:GLN89 3.0 28.4 1.0
O B:ALA113 3.1 23.7 1.0
O3B B:GDP138 3.3 45.5 0.6
NE2 B:GLN89 3.3 29.1 1.0
CA B:HIS112 3.4 17.8 1.0
CG B:HIS112 3.4 21.7 1.0
CE1 B:HIS112 3.5 22.6 1.0
CD B:GLN89 3.5 24.9 1.0
PB B:GDP138 3.6 43.7 0.6
CZ B:ARG86 3.6 43.4 1.0
C B:HIS112 3.6 18.4 1.0
PA B:GDP138 3.7 31.1 0.6
NH2 B:ARG99 3.7 21.4 1.0
CB B:HIS112 3.7 17.7 1.0
O2A B:GDP138 3.8 26.2 0.6
NE B:ARG86 3.8 45.6 1.0
C B:ALA113 3.8 21.6 1.0
CA B:ALA113 4.0 18.4 1.0
CD2 B:HIS112 4.3 23.1 1.0
NE2 B:HIS112 4.3 24.0 1.0
O B:ILE111 4.4 20.6 1.0
O2B B:GDP138 4.6 36.2 0.6
O1A B:GDP138 4.6 33.4 0.6
O1B B:GDP138 4.6 45.6 0.6
N B:HIS112 4.6 16.4 1.0
CZ B:ARG99 4.6 22.6 1.0
NH1 B:ARG86 4.7 46.6 1.0
CB B:ALA113 4.7 18.6 1.0
O B:HIS112 4.8 17.4 1.0
O5' B:GDP138 4.9 28.8 0.6
C B:ILE111 5.0 16.3 1.0

Magnesium binding site 3 out of 6 in 3gp9

Go back to Magnesium Binding Sites List in 3gp9
Magnesium binding site 3 out of 6 in the Crystal Structure of the Mimivirus Ndk Complexed with Gdp


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 the Mimivirus Ndk Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg140

b:36.5
occ:0.64
 O1A C:GDP138 2.6 43.9 0.6
O1B C:GDP138 2.7 44.6 0.6
NH2 C:ARG86 3.0 46.7 1.0
ND1 C:HIS112 3.0 24.9 1.0
OE1 C:GLN89 3.2 28.7 1.0
NE2 C:GLN89 3.2 32.3 1.0
N C:ALA113 3.2 19.2 1.0
O C:ALA113 3.2 22.2 1.0
PA C:GDP138 3.5 36.4 0.6
CD C:GLN89 3.6 24.9 1.0
CA C:HIS112 3.6 21.8 1.0
O3A C:GDP138 3.7 35.1 0.6
CE1 C:HIS112 3.7 23.4 1.0
CG C:HIS112 3.7 22.6 1.0
PB C:GDP138 3.7 41.9 0.6
NH2 C:ARG99 3.7 22.9 1.0
C C:HIS112 3.9 18.7 1.0
CZ C:ARG86 4.0 42.5 1.0
O2A C:GDP138 4.0 25.6 0.6
CB C:HIS112 4.0 21.1 1.0
C C:ALA113 4.0 20.7 1.0
NE C:ARG86 4.1 43.9 1.0
CA C:ALA113 4.2 19.6 1.0
O2B C:GDP138 4.3 49.0 0.6
O C:ILE111 4.5 18.7 1.0
NE2 C:HIS112 4.5 22.6 1.0
CZ C:ARG99 4.5 22.1 1.0
CD2 C:HIS112 4.5 21.4 1.0
NH1 C:ARG99 4.7 23.7 1.0
N C:HIS112 4.8 18.6 1.0
CB C:ALA113 4.9 20.9 1.0
O5' C:GDP138 5.0 35.7 0.6

Magnesium binding site 4 out of 6 in 3gp9

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Mimivirus Ndk Complexed with Gdp


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 the Mimivirus Ndk Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg140

b:38.3
occ:0.64
 O1B D:GDP138 2.9 43.1 0.6
O3A D:GDP138 2.9 42.4 0.6
NE2 D:GLN89 3.0 26.5 1.0
OE1 D:GLN89 3.1 35.3 1.0
ND1 D:HIS112 3.2 28.6 1.0
N D:ALA113 3.3 21.3 1.0
O2A D:GDP138 3.3 43.6 0.6
O D:ALA113 3.3 25.3 1.0
PB D:GDP138 3.4 41.0 0.6
PA D:GDP138 3.5 52.5 0.6
CD D:GLN89 3.5 28.1 1.0
NH2 D:ARG99 3.7 24.0 1.0
CA D:HIS112 3.7 22.5 1.0
O1A D:GDP138 3.8 55.7 0.6
CG D:HIS112 3.8 26.3 1.0
CE1 D:HIS112 3.8 26.2 1.0
C D:HIS112 4.0 22.0 1.0
O2B D:GDP138 4.0 28.4 0.6
CB D:HIS112 4.1 24.6 1.0
C D:ALA113 4.1 22.8 1.0
CA D:ALA113 4.3 24.2 1.0
CZ D:ARG99 4.4 26.0 1.0
O D:ILE111 4.5 22.7 1.0
NH1 D:ARG99 4.6 24.8 1.0
NE D:ARG86 4.6 46.0 1.0
NE2 D:HIS112 4.6 27.6 1.0
CD2 D:HIS112 4.7 25.1 1.0
CZ D:ARG86 4.7 50.9 1.0
O3B D:GDP138 4.8 45.4 0.6
N D:HIS112 4.9 20.9 1.0
NH2 D:ARG86 4.9 56.0 1.0
CG D:GLN89 5.0 23.6 1.0
O5' D:GDP138 5.0 49.0 0.6
CB D:ALA113 5.0 24.0 1.0

Magnesium binding site 5 out of 6 in 3gp9

Go back to Magnesium Binding Sites List in 3gp9
Magnesium binding site 5 out of 6 in the Crystal Structure of the Mimivirus Ndk Complexed with Gdp


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 the Mimivirus Ndk Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg140

b:37.1
occ:0.64
 O3A E:GDP138 2.6 42.4 0.6
NH2 E:ARG86 2.7 41.3 1.0
ND1 E:HIS112 2.9 26.4 1.0
N E:ALA113 3.0 19.8 1.0
NE2 E:GLN89 3.0 27.9 1.0
OE1 E:GLN89 3.1 32.3 1.0
O E:ALA113 3.2 23.5 1.0
CA E:HIS112 3.4 18.4 1.0
CD E:GLN89 3.4 27.5 1.0
O1A E:GDP138 3.5 29.1 0.6
CZ E:ARG86 3.5 41.3 1.0
CG E:HIS112 3.5 22.1 1.0
NH2 E:ARG99 3.6 22.3 1.0
PA E:GDP138 3.6 39.1 0.6
CE1 E:HIS112 3.6 25.6 1.0
O1B E:GDP138 3.7 52.1 0.6
C E:HIS112 3.7 21.1 1.0
PB E:GDP138 3.7 55.2 0.6
CB E:HIS112 3.8 20.8 1.0
C E:ALA113 4.0 22.8 1.0
NE E:ARG86 4.0 40.0 1.0
CA E:ALA113 4.1 20.4 1.0
NH1 E:ARG86 4.3 42.6 1.0
O E:ILE111 4.4 19.9 1.0
CD2 E:HIS112 4.4 19.5 1.0
NE2 E:HIS112 4.4 23.5 1.0
CZ E:ARG99 4.5 25.4 1.0
O2A E:GDP138 4.5 40.1 0.6
O3B E:GDP138 4.6 48.7 0.6
N E:HIS112 4.6 16.8 1.0
O5' E:GDP138 4.7 38.8 0.6
NH1 E:ARG99 4.8 25.0 1.0
CB E:ALA113 4.8 18.7 1.0
O2B E:GDP138 4.8 59.5 0.6
O E:HIS112 4.9 17.1 1.0
C E:ILE111 4.9 17.2 1.0
CG E:GLN89 4.9 19.6 1.0

Magnesium binding site 6 out of 6 in 3gp9

Go back to Magnesium Binding Sites List in 3gp9
Magnesium binding site 6 out of 6 in the Crystal Structure of the Mimivirus Ndk Complexed with Gdp


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 the Mimivirus Ndk Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg140

b:37.2
occ:0.64
 O3A F:GDP138 2.7 36.7 0.6
ND1 F:HIS112 2.8 29.1 1.0
OE1 F:GLN89 2.9 32.5 1.0
N F:ALA113 3.1 21.9 1.0
NH2 F:ARG86 3.1 49.7 1.0
O F:ALA113 3.2 23.0 1.0
NE2 F:GLN89 3.4 32.4 1.0
O1B F:GDP138 3.5 45.8 0.6
CA F:HIS112 3.5 23.5 1.0
CG F:HIS112 3.5 22.8 1.0
CE1 F:HIS112 3.5 28.1 1.0
CD F:GLN89 3.6 28.4 1.0
PB F:GDP138 3.7 50.7 0.6
NH2 F:ARG99 3.7 24.1 1.0
O1A F:GDP138 3.7 27.3 0.6
C F:HIS112 3.8 19.6 1.0
PA F:GDP138 3.8 37.3 0.6
CB F:HIS112 3.8 22.8 1.0
CZ F:ARG86 3.9 44.3 1.0
C F:ALA113 4.0 21.4 1.0
CA F:ALA113 4.1 21.3 1.0
NE F:ARG86 4.3 44.2 1.0
NE2 F:HIS112 4.3 25.2 1.0
CD2 F:HIS112 4.3 26.2 1.0
O2B F:GDP138 4.4 57.1 0.6
O F:ILE111 4.5 22.4 1.0
O2A F:GDP138 4.6 45.0 0.6
CZ F:ARG99 4.6 27.2 1.0
NH1 F:ARG86 4.6 50.7 1.0
N F:HIS112 4.7 20.7 1.0
CB F:ALA113 4.8 23.6 1.0
NH1 F:ARG99 4.9 24.1 1.0
O3B F:GDP138 4.9 54.9 0.6
O5' F:GDP138 5.0 45.8 0.6
O F:HIS112 5.0 18.0 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 21:45:50 2025

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