Atomistry » Magnesium » PDB 2b2x-2bhc » 2b8q
Atomistry »
  Magnesium »
    PDB 2b2x-2bhc »
      2b8q »

Magnesium in PDB 2b8q: X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp

Enzymatic activity of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp

All present enzymatic activity of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp:
2.7.4.6;

Protein crystallography data

The structure of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp, PDB code: 2b8q was solved by S.Jeudy, J.M.Claverie, C.Abergel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 80.390, 153.352, 185.491, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp (pdb code 2b8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp, PDB code: 2b8q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 1 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:65.8
occ:1.00
O1A A:TYD160 2.5 52.2 1.0
O2B A:TYD160 2.7 52.0 1.0
PA A:TYD160 3.7 53.8 1.0
NE2 A:HIS53 3.8 53.9 1.0
PB A:TYD160 3.8 50.0 1.0
NH2 A:ARG86 3.9 52.9 1.0
C5' A:TYD160 4.0 51.5 1.0
O1B A:TYD160 4.0 49.4 1.0
CE1 A:HIS53 4.1 53.4 1.0
O3A A:TYD160 4.2 52.0 1.0
O5' A:TYD160 4.3 51.7 1.0
OD2 A:ASP115 4.6 48.1 1.0
O A:HOH205 4.6 46.5 1.0
CE1 A:HIS112 4.7 37.0 1.0
CD2 A:HIS53 5.0 53.2 1.0

Magnesium binding site 2 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 2 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:66.8
occ:1.00
O1A B:TYD161 2.5 57.3 1.0
O2B B:TYD161 2.6 57.4 1.0
PA B:TYD161 3.8 57.6 1.0
OD2 B:ASP115 4.0 64.1 1.0
NH2 B:ARG86 4.0 51.3 1.0
PB B:TYD161 4.1 54.8 1.0
CG B:ASP115 4.2 64.1 1.0
O3A B:TYD161 4.2 58.3 1.0
OD1 B:ASP115 4.5 66.4 1.0
NE2 B:HIS53 4.6 69.3 1.0
O2A B:TYD161 4.6 56.5 1.0
CB B:ASP115 4.8 59.6 1.0
O1B B:TYD161 4.9 54.6 1.0
CZ B:ARG86 5.0 50.6 1.0

Magnesium binding site 3 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 3 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:71.7
occ:1.00
O2B C:TYD162 2.5 46.8 1.0
O1A C:TYD162 2.6 45.1 1.0
PB C:TYD162 3.6 44.4 1.0
PA C:TYD162 3.8 46.7 1.0
NH2 C:ARG86 3.8 47.5 1.0
O1B C:TYD162 3.8 45.0 1.0
O C:HOH1040 3.9 41.0 1.0
OD2 C:ASP115 4.1 52.1 1.0
NE2 C:HIS53 4.1 45.0 1.0
O3A C:TYD162 4.2 47.2 1.0
C5' C:TYD162 4.2 49.0 1.0
O C:HOH1029 4.3 32.9 1.0
O C:HOH1014 4.3 34.6 1.0
CE1 C:HIS112 4.3 37.5 1.0
O5' C:TYD162 4.4 47.2 1.0
ND1 C:HIS112 4.6 37.2 1.0
CE1 C:HIS53 4.7 43.5 1.0
CG C:ASP115 4.9 48.4 1.0
CZ C:ARG86 4.9 44.8 1.0

Magnesium binding site 4 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 4 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:72.0
occ:1.00
O1A D:TYD163 2.5 51.3 1.0
O2B D:TYD163 2.5 52.0 1.0
OD2 D:ASP115 3.2 51.7 1.0
NH2 D:ARG86 3.7 48.6 1.0
PA D:TYD163 3.9 52.9 1.0
PB D:TYD163 4.1 50.0 1.0
CG D:ASP115 4.3 49.8 1.0
O3A D:TYD163 4.3 53.0 1.0
CZ D:ARG86 4.5 47.1 1.0
NH1 D:ARG86 4.6 46.9 1.0
CE1 D:HIS53 4.7 53.0 1.0
CB D:ASP115 4.7 47.8 1.0
NE2 D:HIS53 4.8 52.8 1.0
O2A D:TYD163 4.8 52.5 1.0
O D:HOH209 4.8 47.9 1.0
O1B D:TYD163 4.9 49.8 1.0
O5' D:TYD163 5.0 53.5 1.0

Magnesium binding site 5 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 5 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg206

b:61.2
occ:1.00
O1A E:TYD164 2.5 57.4 1.0
O2B E:TYD164 2.6 58.2 1.0
PB E:TYD164 3.7 56.3 1.0
NH2 E:ARG86 3.8 50.8 1.0
PA E:TYD164 3.8 57.5 1.0
O1B E:TYD164 4.0 55.0 1.0
O E:HOH216 4.1 38.4 1.0
NE2 E:HIS53 4.2 54.3 1.0
O3A E:TYD164 4.2 58.0 1.0
CE1 E:HIS112 4.4 34.1 1.0
C5' E:TYD164 4.4 58.0 1.0
O5' E:TYD164 4.6 57.3 1.0
CE1 E:HIS53 4.7 54.0 1.0
ND1 E:HIS112 4.7 35.7 1.0
O E:HOH214 4.8 44.5 1.0
OD2 E:ASP115 4.9 54.3 1.0
CZ E:ARG86 4.9 49.8 1.0

Magnesium binding site 6 out of 6 in 2b8q

Go back to Magnesium Binding Sites List in 2b8q
Magnesium binding site 6 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Tdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:78.0
occ:1.00
O1A F:TYD165 2.5 65.8 1.0
O2B F:TYD165 2.6 63.1 1.0
OD2 F:ASP115 3.0 58.2 1.0
NH2 F:ARG86 3.6 57.7 1.0
PA F:TYD165 3.9 66.7 1.0
CG F:ASP115 4.1 56.1 1.0
PB F:TYD165 4.2 60.9 1.0
O3A F:TYD165 4.3 64.8 1.0
O2A F:TYD165 4.6 66.8 1.0
CB F:ASP115 4.6 53.1 1.0
NE2 F:HIS53 4.8 58.0 1.0
CE1 F:HIS53 4.8 58.1 1.0
CZ F:ARG86 4.9 55.8 1.0
O F:HOH217 4.9 34.6 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: Mon Dec 14 07:16:16 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