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Magnesium in PDB 3fc9: Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp

Enzymatic activity of Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp, PDB code: 3fc9 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) 29.47 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.586, 153.043, 184.786, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp (pdb code 3fc9). 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 +Kpn-N62L Double Mutant Complexed with Cdp, PDB code: 3fc9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3fc9

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Magnesium binding site 1 out of 5 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant 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 the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg142

b:30.7
occ:1.00
 O1A B:CDP143 2.4 24.6 1.0
O2B B:CDP143 2.5 31.8 1.0
O B:HOH156 2.5 26.9 1.0
PA B:CDP143 3.9 28.0 1.0
PB B:CDP143 3.9 23.0 1.0
OD2 B:ASP119 4.0 43.6 1.0
NE2 B:HIS53 4.2 27.8 1.0
NH2 B:ARG86 4.2 29.7 1.0
CE1 B:HIS53 4.3 28.8 1.0
O3A B:CDP143 4.3 31.3 1.0
NH1 B:ARG86 4.6 32.0 1.0
O1B B:CDP143 4.7 24.9 1.0
C5' B:CDP143 4.7 24.6 1.0
CG B:ASP119 4.8 39.3 1.0
CZ B:ARG86 4.8 29.4 1.0
O5' B:CDP143 4.8 26.9 1.0
O2A B:CDP143 4.9 28.6 1.0
O3B B:CDP143 4.9 28.6 1.0

Magnesium binding site 2 out of 5 in 3fc9

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Magnesium binding site 2 out of 5 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant 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 the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg142

b:37.0
occ:1.00
 O1A C:CDP143 2.4 32.7 1.0
O2B C:CDP143 2.4 34.6 1.0
OD2 C:ASP119 3.5 33.8 1.0
PA C:CDP143 3.7 30.8 1.0
PB C:CDP143 3.9 30.7 1.0
NH1 C:ARG86 4.1 26.7 1.0
NH2 C:ARG86 4.2 32.1 1.0
O3A C:CDP143 4.2 34.7 1.0
O2A C:CDP143 4.4 31.1 1.0
CZ C:ARG86 4.5 29.6 1.0
CG C:ASP119 4.6 29.7 1.0
CE1 C:HIS53 4.7 32.3 1.0
NE2 C:HIS53 4.8 31.3 1.0
O1B C:CDP143 4.8 30.7 1.0
O3B C:CDP143 4.8 32.7 1.0
O5' C:CDP143 4.9 23.5 1.0

Magnesium binding site 3 out of 5 in 3fc9

Go back to Magnesium Binding Sites List in 3fc9
Magnesium binding site 3 out of 5 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant 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 the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg142

b:27.1
occ:1.00
 O2B D:CDP143 2.4 35.4 1.0
O1A D:CDP143 2.5 23.3 1.0
OD2 D:ASP119 3.7 43.0 1.0
PA D:CDP143 3.8 30.6 1.0
PB D:CDP143 3.9 21.5 1.0
NH2 D:ARG86 4.1 32.4 1.0
O3A D:CDP143 4.3 29.8 1.0
NE2 D:HIS53 4.3 29.9 1.0
CE1 D:HIS53 4.5 27.2 1.0
O1B D:CDP143 4.6 23.6 1.0
CG D:ASP119 4.7 40.0 1.0
CZ D:ARG86 4.7 29.4 1.0
NH1 D:ARG86 4.8 26.2 1.0
O2A D:CDP143 4.8 25.0 1.0
O5' D:CDP143 4.9 28.4 1.0
C5' D:CDP143 4.9 27.3 1.0
O3B D:CDP143 4.9 23.9 1.0

Magnesium binding site 4 out of 5 in 3fc9

Go back to Magnesium Binding Sites List in 3fc9
Magnesium binding site 4 out of 5 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant 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 the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg142

b:24.9
occ:1.00
 O1A E:CDP143 2.4 27.5 1.0
O2B E:CDP143 2.5 29.5 1.0
NH2 E:ARG86 3.7 31.6 1.0
PA E:CDP143 3.8 27.1 1.0
OD2 E:ASP119 3.9 36.7 1.0
PB E:CDP143 4.0 25.2 1.0
O3A E:CDP143 4.3 32.5 1.0
NE2 E:HIS53 4.5 32.2 1.0
CG E:ASP119 4.6 36.7 1.0
CZ E:ARG86 4.6 27.1 1.0
CE1 E:HIS53 4.7 33.8 1.0
NH1 E:ARG86 4.8 26.7 1.0
O2A E:CDP143 4.8 24.6 1.0
O5' E:CDP143 4.8 28.4 1.0
O1B E:CDP143 4.8 27.1 1.0
C5' E:CDP143 4.9 30.8 1.0
CB E:ASP119 4.9 28.7 1.0
O3B E:CDP143 5.0 26.7 1.0

Magnesium binding site 5 out of 5 in 3fc9

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Magnesium binding site 5 out of 5 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant 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 the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg142

b:32.4
occ:1.00
 O2B F:CDP143 2.3 36.5 1.0
O1A F:CDP143 2.7 34.8 1.0
NH2 F:ARG86 3.1 34.9 1.0
PB F:CDP143 3.8 27.3 1.0
PA F:CDP143 3.9 37.6 1.0
OD2 F:ASP119 4.1 38.6 1.0
CZ F:ARG86 4.1 32.1 1.0
O3A F:CDP143 4.2 38.9 1.0
CG F:ASP119 4.3 40.2 1.0
NH1 F:ARG86 4.4 27.4 1.0
CB F:ASP119 4.5 36.0 1.0
O3B F:CDP143 4.5 26.6 1.0
O2A F:CDP143 4.5 32.8 1.0
O1B F:CDP143 4.8 34.9 1.0
OD1 F:ASP119 4.8 40.5 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 13:40:34 2024

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