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Magnesium in PDB 7u56: Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp

Enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp

All present enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp, PDB code: 7u56 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.13 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.35, 115.42, 68.48, 90, 90, 90
R / Rfree (%) 16.2 / 19.9

Other elements in 7u56:

The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp (pdb code 7u56). 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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp, PDB code: 7u56:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7u56

Go back to Magnesium Binding Sites List in 7u56
Magnesium binding site 1 out of 2 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp


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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:30.4
occ:1.00
 O A:HOH512 2.0 28.0 1.0
O A:HOH613 2.1 20.9 1.0
O1P A:AMP401 2.1 28.3 1.0
O A:HOH595 2.1 36.6 1.0
O A:HOH581 2.3 28.7 1.0
O1 A:EDO403 2.4 24.8 1.0
P A:AMP401 3.5 27.8 1.0
C1 A:EDO403 3.7 27.5 1.0
ND2 A:ASN325 3.7 19.5 1.0
O2P A:AMP401 3.8 31.5 1.0
O3' A:AMP401 3.8 35.2 1.0
O A:HOH679 3.9 35.5 1.0
OD2 A:ASP313 4.0 19.6 1.0
O A:HOH523 4.1 24.2 1.0
OE1 A:GLU326 4.1 22.8 1.0
C3' A:AMP401 4.3 29.4 1.0
C5' A:AMP401 4.3 26.0 1.0
O5' A:AMP401 4.4 28.9 1.0
O3P A:AMP401 4.4 24.4 1.0
O A:HOH513 4.5 31.6 1.0
O A:HOH835 4.5 36.8 1.0
O A:HOH556 4.7 31.1 1.0
CG A:ASP313 4.8 17.3 1.0
C2 A:EDO403 4.8 21.3 1.0
C4' A:AMP401 4.9 27.3 1.0
CB A:ASP313 4.9 15.9 1.0

Magnesium binding site 2 out of 2 in 7u56

Go back to Magnesium Binding Sites List in 7u56
Magnesium binding site 2 out of 2 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp


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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:29.4
occ:1.00
 O B:HOH515 1.9 29.8 1.0
O3P B:AMP401 2.0 22.4 1.0
O B:HOH642 2.0 28.9 1.0
O B:HOH536 2.2 19.8 1.0
O2 B:EDO403 2.4 26.8 1.0
O B:HOH638 2.5 23.8 1.0
P B:AMP401 3.4 27.6 1.0
C2 B:EDO403 3.6 25.8 1.0
O3' B:AMP401 3.7 28.5 1.0
O2P B:AMP401 3.7 28.8 1.0
ND2 B:ASN325 3.8 18.8 1.0
OE1 B:GLU326 4.0 24.4 1.0
O B:HOH719 4.0 37.5 1.0
OD2 B:ASP313 4.0 18.5 1.0
C3' B:AMP401 4.2 28.5 1.0
O B:HOH537 4.2 21.7 1.0
O5' B:AMP401 4.2 26.6 1.0
C5' B:AMP401 4.3 24.7 1.0
O1P B:AMP401 4.4 24.3 1.0
O B:HOH553 4.5 26.5 1.0
O B:HOH511 4.6 32.0 1.0
O B:HOH871 4.7 36.9 1.0
C4' B:AMP401 4.8 24.3 1.0
C1 B:EDO403 4.8 21.9 1.0
CG B:ASP313 4.9 17.1 1.0

Reference:

J.Abendroth, M.J.Bolejack, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp To Be Published.
Page generated: Thu Oct 3 09:42:16 2024

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