Atomistry » Magnesium » PDB 3efq-3eql » 3em1
Atomistry »
  Magnesium »
    PDB 3efq-3eql »
      3em1 »

Magnesium in PDB 3em1: Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp

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

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

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp, PDB code: 3em1 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) 29.23 / 1.50
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 70.343, 70.343, 104.137, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp (pdb code 3em1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp, PDB code: 3em1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3em1

Go back to Magnesium Binding Sites List in 3em1
Magnesium binding site 1 out of 2 in the Crystal Structure of the 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 Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg142

b:26.3
occ:1.00
O2B A:TYD143 2.3 14.9 1.0
O2A A:TYD143 2.3 15.1 1.0
O A:HOH177 2.4 20.9 1.0
O A:HOH180 2.7 23.7 1.0
PB A:TYD143 3.5 12.2 1.0
PA A:TYD143 3.6 13.9 1.0
O3A A:TYD143 3.8 12.7 1.0
O A:HOH251 3.8 31.7 1.0
O A:HOH154 3.9 12.8 1.0
O1B A:TYD143 4.1 13.3 1.0
O A:HOH169 4.1 18.6 1.0
NH1 A:ARG86 4.2 14.4 1.0
CE1 A:HIS116 4.3 14.7 1.0
OD2 A:ASP119 4.5 33.8 1.0
C5' A:TYD143 4.5 14.1 1.0
O5' A:TYD143 4.5 13.3 1.0
NE2 A:HIS53 4.7 21.0 1.0
ND1 A:HIS116 4.7 12.6 1.0
O1A A:TYD143 4.7 17.4 1.0
O A:HOH191 4.7 17.4 1.0
O A:HOH173 4.8 14.3 1.0
O3B A:TYD143 4.8 14.2 1.0
NH2 A:ARG86 4.8 16.9 1.0
CZ A:ARG86 4.8 14.2 1.0
CG A:ASP119 4.9 26.2 1.0
CB A:ASP119 4.9 20.5 1.0
O A:ALA117 5.0 14.8 1.0

Magnesium binding site 2 out of 2 in 3em1

Go back to Magnesium Binding Sites List in 3em1
Magnesium binding site 2 out of 2 in the Crystal Structure of the 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 Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg142

b:25.7
occ:1.00
O2A B:TYD143 2.3 15.2 1.0
O2B B:TYD143 2.3 17.1 1.0
O B:HOH353 2.4 32.2 1.0
O B:HOH258 2.4 18.7 1.0
O B:HOH343 2.6 24.1 1.0
PA B:TYD143 3.5 15.0 1.0
O B:HOH304 3.5 28.2 1.0
PB B:TYD143 3.5 14.0 1.0
O3A B:TYD143 3.8 14.0 1.0
O B:HOH240 3.9 14.7 1.0
O1B B:TYD143 4.1 14.1 1.0
NH1 B:ARG86 4.2 15.6 1.0
O B:HOH284 4.3 17.7 1.0
CE1 B:HIS116 4.4 12.5 1.0
C5' B:TYD143 4.4 14.1 1.0
OD2 B:ASP119 4.5 29.8 1.0
O5' B:TYD143 4.5 13.7 1.0
NE2 B:HIS53 4.6 18.3 1.0
O1A B:TYD143 4.6 18.1 1.0
O B:HOH351 4.6 31.9 1.0
ND1 B:HIS116 4.7 12.8 1.0
NH2 B:ARG86 4.8 20.6 1.0
O B:HOH350 4.8 27.5 1.0
O3B B:TYD143 4.8 14.9 1.0
O B:HOH235 4.8 13.3 1.0
O B:HOH253 4.8 15.4 1.0
CZ B:ARG86 4.8 15.5 1.0
CG B:ASP119 4.9 24.4 1.0
CB B:ASP119 4.9 20.8 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: Wed Aug 14 13:07:09 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy