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Magnesium in PDB 1ehi: D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides

Enzymatic activity of D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides

All present enzymatic activity of D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides:
6.3.2.4;

Protein crystallography data

The structure of D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides, PDB code: 1ehi was solved by A.P.Kuzin, T.Sun, J.Jorczak-Baillass, V.L.Healy, C.T.Walsh, J.R.Knox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.38
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.200, 90.800, 82.100, 90.00, 92.10, 90.00
R / Rfree (%) 18.4 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides (pdb code 1ehi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides, PDB code: 1ehi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1ehi

Go back to Magnesium Binding Sites List in 1ehi
Magnesium binding site 1 out of 2 in the D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg783

b:26.4
occ:1.00
O5P A:PHY782 2.2 68.1 1.0
OE1 A:GLU316 2.3 42.5 1.0
O3B A:ADP781 2.5 52.6 1.0
OD1 A:ASN318 2.5 38.1 1.0
CD A:GLU316 2.7 29.4 1.0
OE2 A:GLU316 2.8 36.9 1.0
O2B A:ADP781 3.3 59.6 1.0
P2 A:PHY782 3.4 66.5 1.0
PB A:ADP781 3.5 47.4 1.0
O4P A:PHY782 3.6 66.4 1.0
O A:HOH954 3.6 43.1 1.0
CG A:ASN318 3.7 36.6 1.0
CG A:GLU316 4.0 31.6 1.0
O A:HOH951 4.0 43.0 1.0
ND2 A:ASN318 4.3 26.0 1.0
CA A:GLY185 4.3 31.7 1.0
O3P A:PHY782 4.3 68.4 1.0
MG A:MG784 4.4 24.5 1.0
O2P A:PHY782 4.4 67.2 1.0
O3A A:ADP781 4.5 65.6 1.0
O A:GLN184 4.5 41.3 1.0
O A:PRO317 4.6 19.8 1.0
O1B A:ADP781 4.6 52.6 1.0
O2A A:ADP781 4.7 72.2 1.0
N1 A:PHY782 4.7 53.1 1.0
N A:SER186 4.7 34.0 1.0
O A:HOH837 4.8 25.5 1.0
CB A:ASN318 4.9 24.2 1.0

Magnesium binding site 2 out of 2 in 1ehi

Go back to Magnesium Binding Sites List in 1ehi
Magnesium binding site 2 out of 2 in the D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D-Alanine:D-Lactate Ligase (LMDDL2) of Vancomycin-Resistant Leuconostoc Mesenteroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg784

b:24.5
occ:1.00
O4P A:PHY782 2.2 66.4 1.0
O2B A:ADP781 2.5 59.6 1.0
OE2 A:GLU316 2.7 36.9 1.0
O2A A:ADP781 2.7 72.2 1.0
OD2 A:ASP303 3.2 26.8 1.0
O5' A:ADP781 3.4 65.3 1.0
PA A:ADP781 3.5 64.0 1.0
P2 A:PHY782 3.6 66.5 1.0
CD A:GLU316 3.7 29.4 1.0
O A:HOH819 3.9 21.4 1.0
PB A:ADP781 3.9 47.4 1.0
O3A A:ADP781 4.0 65.6 1.0
O3' A:ADP781 4.1 50.0 1.0
O A:HOH925 4.1 38.6 1.0
O3P A:PHY782 4.2 68.4 1.0
CG A:ASP303 4.2 28.5 1.0
NZ A:LYS260 4.3 18.1 1.0
OE1 A:GLU316 4.3 42.5 1.0
O5P A:PHY782 4.3 68.1 1.0
MG A:MG783 4.4 26.4 1.0
O A:HOH911 4.5 36.8 1.0
CB A:ASP303 4.5 24.7 1.0
O3B A:ADP781 4.6 52.6 1.0
C3' A:ADP781 4.6 58.7 1.0
C5' A:ADP781 4.6 61.2 1.0
ND2 A:ASN318 4.7 26.0 1.0
O1A A:ADP781 4.8 62.9 1.0
O2P A:PHY782 4.8 67.2 1.0
CG A:GLU316 4.9 31.6 1.0
CB A:GLU316 5.0 20.8 1.0
O1B A:ADP781 5.0 52.6 1.0

Reference:

A.P.Kuzin, T.Sun, J.Jorczak-Baillass, V.L.Healy, C.T.Walsh, J.R.Knox. Enzymes of Vancomycin Resistance: the Structure of D-Alanine-D-Lactate Ligase of Naturally Resistant Leuconostoc Mesenteroides. Structure Fold.Des. V. 8 463 2000.
ISSN: ISSN 0969-2126
PubMed: 10801495
DOI: 10.1016/S0969-2126(00)00129-5
Page generated: Mon Dec 14 05:52:08 2020

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