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Magnesium in PDB 3ejm: Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp

Enzymatic activity of Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp, PDB code: 3ejm 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) 22.96 / 1.95
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 70.153, 70.153, 104.937, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 21.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp (pdb code 3ejm). 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 Mutant Complexed with Gdp, PDB code: 3ejm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ejm

Go back to Magnesium Binding Sites List in 3ejm
Magnesium binding site 1 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp


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 Mutant Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:37.5
occ:1.00
O1A A:GDP201 2.3 32.5 1.0
O A:HOH308 2.4 27.7 1.0
O1B A:GDP201 2.4 28.4 1.0
O A:HOH240 2.6 31.1 1.0
PA A:GDP201 3.6 31.5 1.0
PB A:GDP201 3.6 30.1 1.0
O3A A:GDP201 3.9 30.9 1.0
O A:HOH214 4.0 21.1 1.0
OD2 A:ASP119 4.0 36.2 1.0
O A:HOH230 4.0 25.3 1.0
NH1 A:ARG86 4.2 24.2 1.0
O3B A:GDP201 4.2 29.1 1.0
CE1 A:HIS116 4.3 23.4 1.0
C5' A:GDP201 4.5 30.0 1.0
O5' A:GDP201 4.6 30.7 1.0
CG A:ASP119 4.6 33.3 1.0
O2A A:GDP201 4.6 33.6 1.0
NE2 A:HIS53 4.6 30.4 1.0
ND1 A:HIS116 4.7 20.7 1.0
NH2 A:ARG86 4.7 24.9 1.0
CB A:ASP119 4.7 29.7 1.0
O A:HOH251 4.7 25.8 1.0
CZ A:ARG86 4.8 23.7 1.0
O2B A:GDP201 4.8 29.4 1.0
O A:HOH234 4.9 20.7 1.0
O A:ALA117 5.0 21.3 1.0

Magnesium binding site 2 out of 2 in 3ejm

Go back to Magnesium Binding Sites List in 3ejm
Magnesium binding site 2 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp


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 Mutant Complexed with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:37.3
occ:1.00
O B:HOH322 2.4 23.4 1.0
O1A B:GDP202 2.4 23.3 1.0
O1B B:GDP202 2.5 24.6 1.0
O B:HOH306 2.7 34.5 1.0
O B:HOH279 3.5 38.1 1.0
PA B:GDP202 3.6 28.6 1.0
PB B:GDP202 3.7 23.9 1.0
O B:HOH213 3.9 21.3 1.0
O3A B:GDP202 4.0 29.2 1.0
OD2 B:ASP119 4.0 32.2 1.0
NH1 B:ARG86 4.1 22.5 1.0
O B:HOH256 4.2 24.2 1.0
CE1 B:HIS116 4.3 20.2 1.0
O3B B:GDP202 4.3 22.9 1.0
CG B:ASP119 4.5 29.0 1.0
NH2 B:ARG86 4.6 25.5 1.0
O2A B:GDP202 4.6 31.7 1.0
CZ B:ARG86 4.7 26.5 1.0
CB B:ASP119 4.7 27.4 1.0
C5' B:GDP202 4.7 29.9 1.0
ND1 B:HIS116 4.7 18.4 1.0
O5' B:GDP202 4.7 28.5 1.0
NE2 B:HIS53 4.8 28.1 1.0
O B:HOH224 4.8 24.7 1.0
O2B B:GDP202 4.9 22.3 1.0
O B:ALA117 4.9 18.5 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 08:06:28 2020

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