Atomistry » Magnesium » PDB 3fzn-3g8c » 3g2x
Atomistry »
  Magnesium »
    PDB 3fzn-3g8c »
      3g2x »

Magnesium in PDB 3g2x: Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp

Enzymatic activity of Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp

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

Protein crystallography data

The structure of Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp, PDB code: 3g2x 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) 24.57 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.371, 151.492, 181.723, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp (pdb code 3g2x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp, PDB code: 3g2x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3g2x

Go back to Magnesium Binding Sites List in 3g2x
Magnesium binding site 1 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L Double 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:56.7
occ:1.00
 O2B A:TYD201 2.7 49.4 1.0
OD2 A:ASP119 3.2 57.2 1.0
O2A A:TYD201 3.2 50.0 1.0
O A:HOH151 3.3 49.2 1.0
CG A:ASP119 3.7 57.8 1.0
CB A:ASP119 3.7 51.0 1.0
NH1 A:ARG86 4.0 50.0 1.0
PB A:TYD201 4.1 45.0 1.0
CE1 A:HIS116 4.2 44.9 1.0
NH2 A:ARG86 4.2 52.1 1.0
CZ A:ARG86 4.3 49.4 1.0
O A:ALA117 4.3 44.8 1.0
N A:ASP119 4.4 49.2 1.0
PA A:TYD201 4.5 50.1 1.0
CA A:ASP119 4.6 49.3 1.0
ND1 A:HIS116 4.7 43.6 1.0
OD1 A:ASP119 4.7 52.7 1.0
O1B A:TYD201 4.7 48.4 1.0
O A:HOH150 4.8 43.4 1.0
O3A A:TYD201 4.8 50.4 1.0

Magnesium binding site 2 out of 6 in 3g2x

Go back to Magnesium Binding Sites List in 3g2x
Magnesium binding site 2 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L Double 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:71.0
occ:1.00
 O B:HOH144 2.8 64.0 1.0
O2B B:TYD201 2.8 59.8 1.0
O2A B:TYD201 2.8 52.6 1.0
NH2 B:ARG86 3.1 52.0 1.0
PA B:TYD201 3.6 54.4 1.0
NH1 B:ARG86 3.8 52.8 1.0
O1A B:TYD201 3.8 54.4 1.0
CZ B:ARG86 3.8 55.0 1.0
PB B:TYD201 3.8 54.4 1.0
O3A B:TYD201 4.0 56.0 1.0
OD2 B:ASP119 4.1 63.9 1.0
O3B B:TYD201 4.2 47.4 1.0
CB B:ASP119 4.4 60.7 1.0
CG B:ASP119 4.7 63.9 1.0

Magnesium binding site 3 out of 6 in 3g2x

Go back to Magnesium Binding Sites List in 3g2x
Magnesium binding site 3 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L Double 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:55.4
occ:1.00
 O2B C:TYD201 2.7 49.1 1.0
O2A C:TYD201 2.9 46.5 1.0
NH1 C:ARG86 3.5 50.3 1.0
OD2 C:ASP119 3.6 60.8 1.0
CE1 C:HIS116 4.0 45.8 1.0
PB C:TYD201 4.1 48.2 1.0
CB C:ASP119 4.1 53.2 1.0
O C:ALA117 4.2 48.7 1.0
CG C:ASP119 4.2 58.1 1.0
CZ C:ARG86 4.2 49.7 1.0
PA C:TYD201 4.3 55.3 1.0
NH2 C:ARG86 4.4 45.2 1.0
ND1 C:HIS116 4.5 44.1 1.0
O1B C:TYD201 4.5 50.0 1.0
N C:ASP119 4.7 54.2 1.0
O3A C:TYD201 4.7 51.6 1.0
NE2 C:HIS53 4.8 56.9 1.0
CA C:ASP119 5.0 53.2 1.0
NE2 C:HIS116 5.0 44.2 1.0

Magnesium binding site 4 out of 6 in 3g2x

Go back to Magnesium Binding Sites List in 3g2x
Magnesium binding site 4 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L Double 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:66.3
occ:1.00
 O2A D:TYD201 2.5 54.5 1.0
O2B D:TYD201 3.2 57.7 1.0
CE1 D:HIS116 3.8 46.9 1.0
NE2 D:HIS53 3.9 57.9 1.0
PA D:TYD201 4.0 60.8 1.0
PB D:TYD201 4.3 59.1 1.0
ND1 D:HIS116 4.3 48.0 1.0
O1B D:TYD201 4.4 60.6 1.0
CE2 D:TYR50 4.4 48.0 1.0
CE1 D:HIS53 4.5 58.6 1.0
O3A D:TYD201 4.6 58.6 1.0
C5' D:TYD201 4.6 58.9 1.0
OD2 D:ASP119 4.7 51.2 1.0
O5' D:TYD201 4.8 62.2 1.0
CD2 D:TYR50 4.8 47.0 1.0
CD2 D:HIS53 4.9 58.7 1.0
NE2 D:HIS116 4.9 44.4 1.0

Magnesium binding site 5 out of 6 in 3g2x

Go back to Magnesium Binding Sites List in 3g2x
Magnesium binding site 5 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L Double 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:57.3
occ:1.00
 O2A E:TYD201 2.6 51.7 1.0
O2B E:TYD201 2.7 56.5 1.0
O E:HOH147 2.8 45.7 1.0
PA E:TYD201 3.9 52.5 1.0
PB E:TYD201 3.9 47.0 1.0
NH1 E:ARG86 4.0 57.4 1.0
CE1 E:HIS116 4.1 58.4 1.0
O3A E:TYD201 4.3 51.6 1.0
O1B E:TYD201 4.3 45.5 1.0
NE2 E:HIS53 4.5 50.9 1.0
CB E:ASP119 4.5 59.5 1.0
OD2 E:ASP119 4.5 65.5 1.0
CG E:ASP119 4.5 64.2 1.0
ND1 E:HIS116 4.6 59.6 1.0
NH2 E:ARG86 4.6 60.9 1.0
CZ E:ARG86 4.7 59.1 1.0
C5' E:TYD201 4.9 49.5 1.0
O1A E:TYD201 4.9 45.7 1.0
O E:ALA117 4.9 56.2 1.0
CE1 E:HIS53 4.9 47.7 1.0
O5' E:TYD201 5.0 48.2 1.0

Magnesium binding site 6 out of 6 in 3g2x

Go back to Magnesium Binding Sites List in 3g2x
Magnesium binding site 6 out of 6 in the Structure of Mimivirus Ndk +Kpn - N62L Double 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 Structure of Mimivirus Ndk +Kpn - N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:65.8
occ:1.00
 O2A F:TYD201 2.7 70.1 1.0
O2B F:TYD201 2.8 60.7 1.0
PA F:TYD201 3.4 76.6 1.0
O1A F:TYD201 3.4 62.5 1.0
NH1 F:ARG86 3.8 55.9 1.0
NH2 F:ARG86 3.8 55.6 1.0
OD2 F:ASP119 3.9 71.2 1.0
O3A F:TYD201 4.0 74.2 1.0
PB F:TYD201 4.1 63.5 1.0
CZ F:ARG86 4.2 58.2 1.0
CB F:ASP119 4.3 61.5 1.0
CG F:ASP119 4.5 66.5 1.0
NE2 F:HIS53 4.9 87.1 1.0
O5' F:TYD201 4.9 62.9 1.0
O3B F:TYD201 4.9 67.2 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 21:09:44 2025

Last articles

Mg in 7BOD
Mg in 7BNR
Mg in 7BNK
Mg in 7BMC
Mg in 7BM9
Mg in 7BM8
Mg in 7BM6
Mg in 7BL4
Mg in 7BL6
Mg in 7BL5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy