Atomistry » Magnesium » PDB 3f2t-3fcv » 3fbf
Atomistry »
  Magnesium »
    PDB 3f2t-3fcv »
      3fbf »

Magnesium in PDB 3fbf: Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp

Enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp, PDB code: 3fbf 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) 28.62 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 80.241, 152.680, 185.248, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.4

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 3fbf

Go back to Magnesium Binding Sites List in 3fbf
Magnesium binding site 1 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp


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 Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg160

b:62.5
occ:1.00
 O2B A:TYD138 2.5 57.6 1.0
O1A A:TYD138 2.5 57.1 1.0
O A:HOH167 2.9 51.8 1.0
NH2 A:ARG86 3.5 51.6 1.0
OD2 A:ASP115 3.8 53.5 1.0
PA A:TYD138 3.9 62.0 1.0
PB A:TYD138 4.0 50.9 1.0
O3A A:TYD138 4.3 57.8 1.0
CZ A:ARG86 4.5 49.5 1.0
CE1 A:HIS53 4.6 42.7 1.0
NH1 A:ARG86 4.7 53.2 1.0
O3B A:TYD138 4.7 54.8 1.0
CG A:ASP115 4.8 48.6 1.0
NE2 A:HIS53 4.8 43.0 1.0
O2A A:TYD138 4.8 57.1 1.0
O1B A:TYD138 5.0 48.7 1.0

Magnesium binding site 2 out of 6 in 3fbf

Go back to Magnesium Binding Sites List in 3fbf
Magnesium binding site 2 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp


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 Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg161

b:75.2
occ:1.00
 O2B B:TYD138 2.6 70.9 1.0
O1A B:TYD138 2.8 75.1 1.0
OD2 B:ASP115 4.0 71.2 1.0
PB B:TYD138 4.1 65.9 1.0
NE2 B:HIS53 4.1 71.1 1.0
PA B:TYD138 4.2 76.3 1.0
CG B:ASP115 4.3 75.6 1.0
NH2 B:ARG86 4.4 20.0 1.0
NH1 B:ARG86 4.5 20.0 1.0
CE1 B:HIS53 4.6 66.5 1.0
O3A B:TYD138 4.6 72.5 1.0
OD1 B:ASP115 4.6 71.1 1.0
O1B B:TYD138 4.8 65.4 1.0
CB B:ASP115 4.8 60.4 1.0
CZ B:ARG86 5.0 20.0 1.0

Magnesium binding site 3 out of 6 in 3fbf

Go back to Magnesium Binding Sites List in 3fbf
Magnesium binding site 3 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp


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 Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg162

b:68.3
occ:1.00
 O2B C:TYD138 2.6 63.4 1.0
O1A C:TYD138 2.9 56.2 1.0
OD2 C:ASP115 3.4 59.3 1.0
NH2 C:ARG86 3.5 54.4 1.0
PB C:TYD138 3.9 53.0 1.0
CG C:ASP115 4.1 46.9 1.0
CZ C:ARG86 4.1 48.0 1.0
NH1 C:ARG86 4.2 47.0 1.0
O3B C:TYD138 4.2 50.5 1.0
PA C:TYD138 4.2 63.3 1.0
CB C:ASP115 4.5 41.1 1.0
O3A C:TYD138 4.5 56.5 1.0
NE2 C:HIS53 4.9 42.8 1.0
OD1 C:ASP115 4.9 42.0 1.0

Magnesium binding site 4 out of 6 in 3fbf

Go back to Magnesium Binding Sites List in 3fbf
Magnesium binding site 4 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp


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 Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg163

b:59.0
occ:1.00
 O2B D:TYD138 2.6 64.7 1.0
O1A D:TYD138 2.6 60.7 1.0
OD2 D:ASP115 3.2 47.2 1.0
O D:HOH167 3.2 46.5 1.0
PB D:TYD138 4.0 55.7 1.0
PA D:TYD138 4.0 71.8 1.0
NH2 D:ARG86 4.2 60.3 1.0
CG D:ASP115 4.2 52.9 1.0
NH1 D:ARG86 4.4 52.5 1.0
O3A D:TYD138 4.5 68.1 1.0
CE1 D:HIS53 4.5 55.1 1.0
CZ D:ARG86 4.7 59.0 1.0
O3B D:TYD138 4.7 59.1 1.0
NE2 D:HIS53 4.7 52.9 1.0
CB D:ASP115 4.9 51.9 1.0

Magnesium binding site 5 out of 6 in 3fbf

Go back to Magnesium Binding Sites List in 3fbf
Magnesium binding site 5 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp


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 Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg164

b:78.0
occ:1.00
 O2B E:TYD138 2.5 71.0 1.0
O1A E:TYD138 2.6 73.0 1.0
NH2 E:ARG86 3.7 61.4 1.0
OD2 E:ASP115 3.8 63.0 1.0
PB E:TYD138 3.9 66.6 1.0
PA E:TYD138 4.0 72.3 1.0
CG E:ASP115 4.4 53.7 1.0
O3A E:TYD138 4.4 69.8 1.0
O1B E:TYD138 4.6 57.8 1.0
NE2 E:HIS53 4.7 53.4 1.0
CZ E:ARG86 4.7 55.2 1.0
CB E:ASP115 4.9 48.6 1.0
CE1 E:HIS53 5.0 55.5 1.0
NH1 E:ARG86 5.0 50.4 1.0
O3B E:TYD138 5.0 60.8 1.0

Magnesium binding site 6 out of 6 in 3fbf

Go back to Magnesium Binding Sites List in 3fbf
Magnesium binding site 6 out of 6 in the Crystal Structure of the Mimivirus Ndk N62L Mutant Complexed with Dtdp


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 Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg165

b:70.0
occ:1.00
 O2B F:TYD138 2.6 69.0 1.0
O1A F:TYD138 2.8 77.5 1.0
NH2 F:ARG86 3.3 57.8 1.0
OD2 F:ASP115 3.3 55.4 1.0
PB F:TYD138 4.1 69.0 1.0
CG F:ASP115 4.2 53.7 1.0
PA F:TYD138 4.2 84.0 1.0
CZ F:ARG86 4.4 55.5 1.0
O3A F:TYD138 4.6 77.3 1.0
O1B F:TYD138 4.6 62.9 1.0
CB F:ASP115 4.7 49.9 1.0
NH1 F:ARG86 4.8 55.7 1.0
O F:HOH144 4.8 39.2 1.0
NE2 F:HIS53 4.9 62.8 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: Mon Dec 14 08:08:05 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy