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

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

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

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp, PDB code: 3fbb 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) 28.55 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.676, 152.899, 184.534, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp (pdb code 3fbb). 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 N62L-R107G Double Mutant Complexed with Udp, PDB code: 3fbb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3fbb

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:59.1
occ:1.00
 O3B A:UDP201 2.5 52.8 1.0
O A:HOH171 2.5 46.6 1.0
O1A A:UDP201 2.7 46.2 1.0
NH2 A:ARG86 3.5 47.2 1.0
OD2 A:ASP115 3.7 44.1 1.0
PB A:UDP201 3.9 50.0 1.0
PA A:UDP201 4.0 55.4 1.0
O3A A:UDP201 4.4 54.7 1.0
CZ A:ARG86 4.5 51.4 1.0
CG A:ASP115 4.6 44.2 1.0
CE1 A:HIS53 4.6 45.8 1.0
O2B A:UDP201 4.7 48.2 1.0
NE2 A:HIS53 4.7 44.5 1.0
O1B A:UDP201 4.7 51.2 1.0
NH1 A:ARG86 4.8 53.7 1.0
O2A A:UDP201 5.0 60.7 1.0
O A:HOH141 5.0 40.0 1.0
C5' A:UDP201 5.0 49.8 1.0

Magnesium binding site 2 out of 6 in 3fbb

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:73.3
occ:1.00
 O3B B:UDP201 2.6 60.1 1.0
O1A B:UDP201 2.7 59.9 1.0
OD2 B:ASP115 3.9 60.1 1.0
NH2 B:ARG86 3.9 59.4 1.0
PB B:UDP201 4.0 59.7 1.0
NE2 B:HIS53 4.0 57.5 1.0
PA B:UDP201 4.0 68.9 1.0
O B:HOH178 4.2 42.4 1.0
O3A B:UDP201 4.4 70.0 1.0
C5' B:UDP201 4.4 58.0 1.0
O B:HOH173 4.5 41.8 1.0
O2B B:UDP201 4.5 55.7 1.0
CE1 B:HIS53 4.6 51.5 1.0
CG B:ASP115 4.6 54.8 1.0
CE1 B:HIS112 4.7 41.2 1.0
O5' B:UDP201 4.8 62.8 1.0
O1B B:UDP201 5.0 50.9 1.0

Magnesium binding site 3 out of 6 in 3fbb

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:62.5
occ:1.00
 O3B C:UDP201 2.4 51.3 1.0
O1A C:UDP201 2.8 49.0 1.0
OD2 C:ASP115 3.4 52.5 1.0
NH2 C:ARG86 3.4 48.4 1.0
PB C:UDP201 3.8 48.0 1.0
O C:HOH181 3.9 38.8 1.0
PA C:UDP201 4.1 52.2 1.0
NH1 C:ARG86 4.1 36.8 1.0
CZ C:ARG86 4.1 45.8 1.0
CG C:ASP115 4.2 45.9 1.0
O3A C:UDP201 4.3 52.9 1.0
O2B C:UDP201 4.4 43.2 1.0
CB C:ASP115 4.6 37.9 1.0
O1B C:UDP201 4.7 45.3 1.0
NE2 C:HIS53 4.8 39.2 1.0
O2A C:UDP201 5.0 58.1 1.0

Magnesium binding site 4 out of 6 in 3fbb

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:58.6
occ:1.00
 O1A D:UDP201 2.5 51.3 1.0
O3B D:UDP201 2.5 47.7 1.0
OD2 D:ASP115 3.5 54.2 1.0
PA D:UDP201 3.8 53.5 1.0
PB D:UDP201 3.9 51.3 1.0
NH2 D:ARG86 3.9 53.5 1.0
O3A D:UDP201 4.3 62.1 1.0
NH1 D:ARG86 4.4 46.5 1.0
CG D:ASP115 4.5 52.8 1.0
CE1 D:HIS53 4.5 47.9 1.0
CZ D:ARG86 4.5 52.5 1.0
NE2 D:HIS53 4.6 51.8 1.0
O2B D:UDP201 4.7 47.9 1.0
O1B D:UDP201 4.7 53.7 1.0
O5' D:UDP201 4.8 51.1 1.0
O2A D:UDP201 4.9 56.3 1.0
C5' D:UDP201 4.9 48.9 1.0

Magnesium binding site 5 out of 6 in 3fbb

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:62.7
occ:1.00
 O3B E:UDP201 2.5 53.5 1.0
O1A E:UDP201 2.6 53.1 1.0
OD2 E:ASP115 3.4 55.1 1.0
NH2 E:ARG86 3.6 52.6 1.0
PB E:UDP201 3.8 56.4 1.0
PA E:UDP201 3.9 57.2 1.0
NH1 E:ARG86 4.2 50.0 1.0
CZ E:ARG86 4.3 52.1 1.0
CG E:ASP115 4.3 47.4 1.0
O3A E:UDP201 4.3 63.4 1.0
O2B E:UDP201 4.5 52.2 1.0
CB E:ASP115 4.7 41.3 1.0
O2A E:UDP201 4.8 54.5 1.0
O E:HOH151 4.8 35.5 1.0
O1B E:UDP201 4.8 55.1 1.0
NE2 E:HIS53 5.0 51.1 1.0

Magnesium binding site 6 out of 6 in 3fbb

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant 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 Crystal Structure of the Mimivirus Ndk N62L-R107G Double Mutant Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:60.9
occ:1.00
 O3B F:UDP201 2.6 69.5 1.0
O1A F:UDP201 3.0 64.2 1.0
OD2 F:ASP115 3.1 56.7 1.0
NH2 F:ARG86 3.3 54.4 1.0
CG F:ASP115 3.9 50.6 1.0
NH1 F:ARG86 3.9 56.9 1.0
CZ F:ARG86 3.9 55.5 1.0
PB F:UDP201 4.0 60.4 1.0
CB F:ASP115 4.1 44.2 1.0
PA F:UDP201 4.2 75.0 1.0
O3A F:UDP201 4.6 69.2 1.0
O1B F:UDP201 4.6 63.9 1.0
OD1 F:ASP115 4.8 44.8 1.0
O2B F:UDP201 4.9 59.6 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: Wed Aug 14 13:37:29 2024

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