Atomistry » Magnesium » PDB 3efq-3eql » 3eic
Atomistry »
  Magnesium »
    PDB 3efq-3eql »
      3eic »

Magnesium in PDB 3eic: X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp

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

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

Protein crystallography data

The structure of X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp, PDB code: 3eic 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) 20.00 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 80.472, 152.726, 184.940, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp (pdb code 3eic). 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 Udp, PDB code: 3eic:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3eic

Go back to Magnesium Binding Sites List in 3eic
Magnesium binding site 1 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase 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 X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg160

b:61.2
occ:1.00
 O1A A:UDP161 2.0 45.1 1.0
O3B A:UDP161 2.1 45.5 1.0
PA A:UDP161 3.3 47.0 1.0
PB A:UDP161 3.3 45.3 1.0
O3A A:UDP161 3.6 46.6 1.0
NH2 A:ARG86 3.7 49.4 1.0
O2B A:UDP161 4.0 43.8 1.0
O2A A:UDP161 4.2 49.2 1.0
O5' A:UDP161 4.4 46.5 1.0
O1B A:UDP161 4.4 44.8 1.0
OD2 A:ASP115 4.4 45.6 1.0
C5' A:UDP161 4.5 47.0 1.0
CE1 A:HIS53 4.5 49.2 1.0
NE2 A:HIS53 4.6 48.8 1.0
CZ A:ARG86 4.6 47.7 1.0
NH1 A:ARG86 4.7 50.4 1.0

Magnesium binding site 2 out of 6 in 3eic

Go back to Magnesium Binding Sites List in 3eic
Magnesium binding site 2 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase 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 X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg161

b:72.5
occ:1.00
 O3B B:UDP162 2.1 48.3 1.0
O1A B:UDP162 2.2 49.6 1.0
PB B:UDP162 3.4 48.4 1.0
PA B:UDP162 3.5 49.5 1.0
NH2 B:ARG86 3.7 20.0 1.0
O3A B:UDP162 3.8 49.8 1.0
O2B B:UDP162 4.0 46.4 1.0
OD2 B:ASP115 4.2 53.4 1.0
NE2 B:HIS53 4.3 62.3 1.0
O1B B:UDP162 4.4 45.5 1.0
O5' B:UDP162 4.5 49.8 1.0
O2A B:UDP162 4.5 49.6 1.0
C5' B:UDP162 4.5 51.1 1.0
CE1 B:HIS53 4.6 62.1 1.0
CZ B:ARG86 4.6 20.0 1.0
NH1 B:ARG86 4.7 20.0 1.0
CG B:ASP115 4.9 53.0 1.0

Magnesium binding site 3 out of 6 in 3eic

Go back to Magnesium Binding Sites List in 3eic
Magnesium binding site 3 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase 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 X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg162

b:64.6
occ:1.00
 O3B C:UDP163 2.1 39.9 1.0
O1A C:UDP163 2.2 43.0 1.0
PB C:UDP163 3.4 42.0 1.0
PA C:UDP163 3.5 44.3 1.0
NH2 C:ARG86 3.6 46.2 1.0
O3A C:UDP163 3.8 43.1 1.0
O2B C:UDP163 4.0 40.5 1.0
NE2 C:HIS53 4.4 41.4 1.0
O5' C:UDP163 4.4 45.1 1.0
O1B C:UDP163 4.4 42.6 1.0
NH1 C:ARG86 4.4 42.0 1.0
CZ C:ARG86 4.5 44.1 1.0
OD2 C:ASP115 4.5 45.8 1.0
O2A C:UDP163 4.5 44.2 1.0
C5' C:UDP163 4.5 43.8 1.0
CE1 C:HIS53 4.5 41.5 1.0
O C:HOH195 4.8 45.4 1.0

Magnesium binding site 4 out of 6 in 3eic

Go back to Magnesium Binding Sites List in 3eic
Magnesium binding site 4 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase 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 X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg163

b:59.7
occ:1.00
 O1A D:UDP164 2.0 43.0 1.0
O3B D:UDP164 2.4 39.5 1.0
PA D:UDP164 3.4 45.0 1.0
PB D:UDP164 3.6 43.4 1.0
O3A D:UDP164 3.9 45.0 1.0
OD2 D:ASP115 4.0 45.2 1.0
NH2 D:ARG86 4.2 46.0 1.0
O2A D:UDP164 4.2 44.7 1.0
CE1 D:HIS53 4.2 47.3 1.0
O2B D:UDP164 4.4 41.2 1.0
NH1 D:ARG86 4.4 42.8 1.0
NE2 D:HIS53 4.5 46.9 1.0
O5' D:UDP164 4.5 43.2 1.0
C5' D:UDP164 4.6 43.9 1.0
O1B D:UDP164 4.7 44.5 1.0
CZ D:ARG86 4.8 44.7 1.0
CG D:ASP115 4.9 46.0 1.0

Magnesium binding site 5 out of 6 in 3eic

Go back to Magnesium Binding Sites List in 3eic
Magnesium binding site 5 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase 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 X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg164

b:64.3
occ:1.00
 O1A E:UDP165 2.0 47.5 1.0
O3B E:UDP165 2.2 48.3 1.0
PB E:UDP165 3.3 48.8 1.0
PA E:UDP165 3.3 48.2 1.0
O3A E:UDP165 3.7 47.9 1.0
O2B E:UDP165 3.8 46.1 1.0
NH2 E:ARG86 3.9 47.2 1.0
CE1 E:HIS53 4.3 51.5 1.0
O5' E:UDP165 4.3 47.6 1.0
C5' E:UDP165 4.3 46.3 1.0
O2A E:UDP165 4.3 45.8 1.0
NE2 E:HIS53 4.3 51.7 1.0
O1B E:UDP165 4.5 45.5 1.0
OD2 E:ASP115 4.6 49.7 1.0
CZ E:ARG86 4.7 47.1 1.0
NH1 E:ARG86 4.8 47.8 1.0
O E:HOH171 4.9 48.8 1.0

Magnesium binding site 6 out of 6 in 3eic

Go back to Magnesium Binding Sites List in 3eic
Magnesium binding site 6 out of 6 in the X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase 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 X-Ray Structure of Acanthamoeba Ployphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg165

b:67.4
occ:1.00
 O3B F:UDP166 2.2 52.5 1.0
O1A F:UDP166 2.2 55.0 1.0
PB F:UDP166 3.5 53.1 1.0
PA F:UDP166 3.5 57.0 1.0
NH2 F:ARG86 3.6 49.4 1.0
O F:HOH193 3.7 52.0 1.0
O3A F:UDP166 3.9 55.7 1.0
OD2 F:ASP115 4.1 50.1 1.0
O2B F:UDP166 4.2 54.0 1.0
O2A F:UDP166 4.4 55.5 1.0
CZ F:ARG86 4.5 48.4 1.0
NH1 F:ARG86 4.6 50.2 1.0
O1B F:UDP166 4.6 52.1 1.0
O5' F:UDP166 4.6 57.0 1.0
NE2 F:HIS53 4.7 56.2 1.0
C5' F:UDP166 4.7 57.2 1.0
CE1 F:HIS53 4.7 56.5 1.0
CG F:ASP115 4.9 48.2 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 20:30:29 2025

Last articles

Mg in 6I3C
Mg in 6I36
Mg in 6I2U
Mg in 6I39
Mg in 6I2R
Mg in 6I2S
Mg in 6I2I
Mg in 6I2P
Mg in 6I2Q
Mg in 6I21
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy