Atomistry » Magnesium » PDB 7u1p-7ue5 » 7u56
Atomistry »
  Magnesium »
    PDB 7u1p-7ue5 »
      7u56 »

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 Aug 14 16:28:15 2025

Last articles

Br in 9R0Q
Br in 9J73
Br in 9BJ5
Br in 8Y72
Au in 9D33
As in 9O9I
Al in 9GSG
Zr in 1XC1
Zr in 6Y7P
Zr in 6GNL
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy