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Magnesium in PDB 3fbe: Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp

Enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp, PDB code: 3fbe 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) 28.53 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.243, 152.897, 183.785, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp (pdb code 3fbe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Gdp, PDB code: 3fbe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3fbe

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Magnesium binding site 1 out of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg160

b:54.0
occ:1.00
 OH A:TYR50 2.7 41.4 1.0
NZ A:LYS9 2.9 35.4 1.0
ND1 A:HIS112 3.0 33.4 1.0
O3' A:GDP138 3.1 57.9 1.0
O1B A:GDP138 3.2 71.1 1.0
CB A:HIS112 3.3 34.1 1.0
CG A:HIS112 3.6 35.9 1.0
CE A:LYS9 3.6 34.0 1.0
CZ A:TYR50 3.6 49.6 1.0
CE2 A:TYR50 3.6 46.4 1.0
NH2 A:ARG99 3.8 38.3 1.0
O2B A:GDP138 3.9 76.0 1.0
PB A:GDP138 3.9 84.0 1.0
CA A:HIS112 3.9 29.9 1.0
O3A A:GDP138 4.1 97.2 1.0
C4' A:GDP138 4.1 72.8 1.0
CE1 A:HIS112 4.1 35.3 1.0
C3' A:GDP138 4.2 65.5 1.0
O A:ILE111 4.4 30.8 1.0
O2' A:GDP138 4.6 66.7 1.0
N A:HIS112 4.7 31.3 1.0
O4' A:GDP138 4.8 71.3 1.0
CD2 A:HIS112 4.8 32.7 1.0
C A:ILE111 4.9 30.6 1.0
CE1 A:TYR50 5.0 52.0 1.0
CD2 A:TYR50 5.0 49.3 1.0
C2' A:GDP138 5.0 65.2 1.0

Magnesium binding site 2 out of 5 in 3fbe

Go back to Magnesium Binding Sites List in 3fbe
Magnesium binding site 2 out of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg162

b:70.5
occ:1.00
 O3A C:GDP138 2.8 94.8 1.0
O2A C:GDP138 3.1 77.7 1.0
PA C:GDP138 3.3 94.2 1.0
O2B C:GDP138 3.3 70.6 1.0
PB C:GDP138 3.5 71.2 1.0
NH2 C:ARG86 3.6 61.6 1.0
O1A C:GDP138 3.6 92.3 1.0
O1B C:GDP138 3.8 67.7 1.0
CE1 C:HIS112 4.1 40.1 1.0
NE2 C:HIS53 4.2 48.2 1.0
OD2 C:ASP115 4.3 55.1 1.0
O C:HOH147 4.3 40.4 1.0
ND1 C:HIS112 4.4 38.8 1.0
O C:HOH163 4.6 34.2 1.0
CE1 C:HIS53 4.8 47.1 1.0
O3B C:GDP138 4.9 62.5 1.0
O5' C:GDP138 4.9 80.1 1.0
CZ C:ARG86 4.9 58.7 1.0
CG C:ASP115 4.9 51.5 1.0
CE2 C:TYR50 5.0 41.9 1.0

Magnesium binding site 3 out of 5 in 3fbe

Go back to Magnesium Binding Sites List in 3fbe
Magnesium binding site 3 out of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg163

b:60.0
occ:1.00
 ND1 D:HIS112 2.9 50.4 1.0
OH D:TYR50 2.9 52.3 1.0
O3' D:GDP138 3.2 59.2 1.0
O1B D:GDP138 3.3 72.9 1.0
O2B D:GDP138 3.3 77.3 1.0
CB D:HIS112 3.4 43.9 1.0
CE2 D:TYR50 3.4 52.9 1.0
NZ D:LYS9 3.5 44.9 1.0
CG D:HIS112 3.5 44.0 1.0
CZ D:TYR50 3.6 53.1 1.0
C4' D:GDP138 3.8 68.8 1.0
NH2 D:ARG99 4.0 49.8 1.0
PB D:GDP138 4.0 89.9 1.0
CE1 D:HIS112 4.0 49.4 1.0
CA D:HIS112 4.0 43.5 1.0
CE D:LYS9 4.1 38.3 1.0
C3' D:GDP138 4.1 66.0 1.0
O D:ILE111 4.6 43.2 1.0
C5' D:GDP138 4.6 73.4 1.0
CD2 D:TYR50 4.7 55.4 1.0
O5' D:GDP138 4.7 81.8 1.0
CD2 D:HIS112 4.8 46.3 1.0
O2' D:GDP138 4.9 57.5 1.0
O4' D:GDP138 4.9 72.5 1.0
N D:HIS112 4.9 43.6 1.0
O2A D:GDP138 4.9 91.2 1.0
CE1 D:TYR50 4.9 56.6 1.0
NE2 D:HIS112 5.0 47.6 1.0
NE2 D:GLN89 5.0 49.1 1.0

Magnesium binding site 4 out of 5 in 3fbe

Go back to Magnesium Binding Sites List in 3fbe
Magnesium binding site 4 out of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg164

b:78.2
occ:1.00
 OD2 E:ASP115 2.9 60.7 1.0
NH2 E:ARG86 3.0 59.5 1.0
NH1 E:ARG86 3.2 51.6 1.0
O2B E:GDP138 3.2 78.1 1.0
CZ E:ARG86 3.2 62.4 1.0
CB E:ASP115 3.3 50.8 1.0
CG E:ASP115 3.4 54.8 1.0
O3A E:GDP138 3.8 96.8 1.0
PB E:GDP138 4.0 80.5 1.0
O1A E:GDP138 4.0 0.7 1.0
NE E:ARG86 4.2 55.8 1.0
PA E:GDP138 4.3 0.2 1.0
O1B E:GDP138 4.3 76.9 1.0
OD1 E:ASP115 4.5 49.9 1.0
O2A E:GDP138 4.5 96.2 1.0
CA E:ASP115 4.7 44.4 1.0
O E:HOH152 5.0 36.8 1.0

Magnesium binding site 5 out of 5 in 3fbe

Go back to Magnesium Binding Sites List in 3fbe
Magnesium binding site 5 out of 5 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 N62L-R107G Double Mutant Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg165

b:77.2
occ:1.00
 O3A F:GDP138 3.1 0.6 1.0
NH2 F:ARG86 3.1 64.1 1.0
OD2 F:ASP115 3.2 58.6 1.0
O1B F:GDP138 3.4 77.0 1.0
CG F:ASP115 3.7 57.6 1.0
PB F:GDP138 3.8 91.8 1.0
CZ F:ARG86 3.9 64.7 1.0
CB F:ASP115 3.9 53.6 1.0
NH1 F:ARG86 4.0 63.2 1.0
O2A F:GDP138 4.2 0.7 1.0
PA F:GDP138 4.3 0.2 1.0
O3B F:GDP138 4.5 76.1 1.0
OD1 F:ASP115 4.6 49.9 1.0
O F:HOH154 4.8 44.5 1.0
NE F:ARG86 5.0 58.1 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 20:54:14 2025

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