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Magnesium in PDB 3hav: Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex

Protein crystallography data

The structure of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex, PDB code: 3hav was solved by P.G.Young, E.N.Baker, S.B.Vakulenko, C.A.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.78 / 2.45
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 128.620, 128.620, 57.870, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex (pdb code 3hav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex, PDB code: 3hav:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3hav

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Magnesium binding site 1 out of 3 in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:79.5
occ:1.00
OD2 A:ASP210 2.7 67.2 1.0
O1G A:ATP401 2.7 65.4 0.6
O2B A:ATP401 2.7 60.5 0.6
O2A A:ATP401 2.7 49.2 1.0
O A:HOH352 2.8 69.3 1.0
CG A:ASP210 2.9 66.5 1.0
O A:HOH321 3.0 53.0 1.0
OD1 A:ASP210 3.3 71.4 1.0
CB A:ASP210 3.6 56.4 1.0
PG A:ATP401 3.9 65.3 0.6
PB A:ATP401 4.0 58.5 0.6
O3G A:ATP401 4.1 60.8 0.6
PA A:ATP401 4.1 62.4 1.0
O A:HOH370 4.3 57.9 1.0
CA A:ASP210 4.4 42.5 1.0
O3B A:ATP401 4.4 83.8 0.6
O3A A:ATP401 4.5 56.9 1.0
NZ A:LYS42 4.7 64.0 1.0
O A:HOH309 4.8 50.8 1.0

Magnesium binding site 2 out of 3 in 3hav

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Magnesium binding site 2 out of 3 in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:0.2
occ:1.00
O2B B:ATP401 2.7 95.2 1.0
OD2 B:ASP210 2.9 88.2 1.0
O1G B:ATP401 2.9 84.1 1.0
CG B:ASP210 3.2 81.6 1.0
OD1 B:ASP210 3.3 87.3 1.0
O2A B:ATP401 3.4 83.0 1.0
O B:HOH320 3.5 67.1 1.0
O B:HOH348 3.6 70.9 1.0
PG B:ATP401 3.9 85.1 1.0
O3G B:ATP401 4.0 83.2 1.0
PB B:ATP401 4.0 91.2 1.0
NC1 B:SRY403 4.2 88.2 0.5
CB B:ASP210 4.2 65.8 1.0
O3B B:ATP401 4.2 0.3 1.0
NB1 B:SRY403 4.3 89.9 0.5
O B:HOH337 4.5 58.0 1.0
CA1 B:SRY403 4.5 88.4 0.5
PA B:ATP401 4.7 86.6 1.0
O3A B:ATP401 4.8 1.0 1.0
O B:HOH357 4.9 54.8 1.0
OD1 B:ASN197 5.0 54.9 1.0

Magnesium binding site 3 out of 3 in 3hav

Go back to Magnesium Binding Sites List in 3hav
Magnesium binding site 3 out of 3 in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:38.1
occ:1.00
O2B C:ATP401 2.3 56.0 1.0
O1G C:ATP401 2.4 36.9 1.0
OD2 C:ASP210 2.5 49.4 1.0
OD1 C:ASP210 2.5 48.4 1.0
O2A C:ATP401 2.5 56.5 1.0
CG C:ASP210 2.7 49.4 1.0
PB C:ATP401 3.6 59.3 1.0
PG C:ATP401 3.7 61.8 1.0
PA C:ATP401 3.9 48.5 1.0
O3B C:ATP401 4.0 0.4 1.0
CB C:ASP210 4.1 51.3 1.0
O C:HOH339 4.2 60.2 1.0
O3A C:ATP401 4.2 45.4 1.0
O3G C:ATP401 4.3 62.7 1.0
O C:HOH303 4.3 28.4 1.0
O C:HOH322 4.5 46.0 1.0
O5' C:ATP401 4.6 41.0 1.0
NZ C:LYS42 4.8 34.3 1.0
O1B C:ATP401 4.8 72.3 1.0
O2G C:ATP401 4.9 59.9 1.0

Reference:

P.G.Young, R.Walanj, V.Lakshmi, L.J.Byrnes, P.Metcalf, E.N.Baker, S.B.Vakulenko, C.A.Smith. The Crystal Structures of Substrate and Nucleotide Complexes of Enterococcus Faecium Aminoglycoside-2''-Phosphotransferase-Iia [Aph(2'')-Iia] Provide Insights Into Substrate Selectivity in the Aph(2'') Subfamily. J.Bacteriol. V. 191 4133 2009.
ISSN: ISSN 0021-9193
PubMed: 19429619
DOI: 10.1128/JB.00149-09
Page generated: Mon Dec 14 08:13:19 2020

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