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Magnesium in PDB 9dre: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)

Enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)

All present enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form):
3.6.1.13;

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form), PDB code: 9dre was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural 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) 49.19 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.873, 80.109, 115.834, 90, 90.12, 90
R / Rfree (%) 17.5 / 21.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) (pdb code 9dre). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form), PDB code: 9dre:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 9dre

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Magnesium binding site 1 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)


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 Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:64.2
occ:1.00
 O B:ALA96 2.4 32.4 1.0
O1A B:ADP301 2.5 56.5 0.4
OE2 B:GLU116 2.7 68.2 1.0
O2B B:ADP301 3.0 52.9 0.4
O B:HOH468 3.0 48.8 1.0
C B:ALA96 3.6 32.8 1.0
CD B:GLU116 3.7 65.0 1.0
O2A B:ADP301 3.8 45.9 0.6
OE1 B:GLU112 3.8 50.8 1.0
O B:HOH485 3.8 39.9 1.0
CA B:GLY97 3.9 31.7 1.0
OE2 B:GLU112 3.9 53.1 1.0
CD B:GLU112 3.9 53.1 1.0
PA B:ADP301 4.0 49.3 0.4
OE1 B:GLU116 4.2 60.6 1.0
N B:GLY97 4.2 26.9 1.0
O B:HOH493 4.3 47.6 1.0
O1A B:ADP301 4.3 43.5 0.6
PB B:ADP301 4.4 45.0 0.4
O5' B:ADP301 4.5 49.5 0.4
PA B:ADP301 4.6 51.9 0.6
O3A B:ADP301 4.7 51.6 0.4
CA B:ALA96 4.7 31.2 1.0
N B:ALA96 4.8 26.8 1.0
CG B:GLU116 4.9 62.8 1.0
CG B:GLU112 4.9 39.6 1.0

Magnesium binding site 2 out of 7 in 9dre

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Magnesium binding site 2 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)


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 Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:56.0
occ:1.00
 O C:ALA96 2.2 32.1 1.0
O C:HOH487 2.6 58.3 1.0
OE2 C:GLU116 3.0 75.2 1.0
OE1 C:GLU112 3.2 49.4 1.0
OE1 C:GLU116 3.2 66.1 1.0
O2B C:ADP301 3.2 84.6 1.0
CD C:GLU116 3.3 61.4 1.0
C C:ALA96 3.4 26.9 1.0
O1A C:ADP301 3.4 84.2 1.0
CD C:GLU112 3.9 45.1 1.0
N C:ALA96 3.9 25.1 1.0
CA C:ALA96 4.2 25.4 1.0
OE2 C:GLU112 4.4 45.3 1.0
N C:GLY97 4.4 27.3 1.0
CA C:GLY97 4.5 29.5 1.0
CG C:GLU116 4.5 53.3 1.0
PB C:ADP301 4.6 111.7 1.0
CG C:GLU112 4.7 34.8 1.0
OE2 C:GLU115 4.7 41.4 0.4
CB C:ALA96 4.8 29.1 1.0
PA C:ADP301 4.8 98.8 1.0
CB C:GLU112 4.9 31.7 1.0
OE1 C:GLN77 4.9 55.4 1.0
O3B C:ADP301 5.0 70.1 1.0

Magnesium binding site 3 out of 7 in 9dre

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Magnesium binding site 3 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:60.8
occ:1.00
 O E:ALA96 2.4 33.8 1.0
OE2 E:GLU116 2.7 75.8 1.0
O E:HOH488 2.9 60.7 1.0
O2B E:ADP301 3.0 86.2 1.0
O1A E:ADP301 3.3 81.0 1.0
C E:ALA96 3.5 36.4 1.0
CD E:GLU116 3.8 70.2 1.0
OE1 E:GLU112 3.9 56.4 1.0
NH2 E:ARG79 4.1 58.7 1.0
N E:ALA96 4.2 30.4 1.0
OE1 E:GLU116 4.2 70.7 1.0
CA E:ALA96 4.3 30.8 1.0
PB E:ADP301 4.3 101.7 1.0
N E:GLY97 4.4 34.5 1.0
CA E:GLY97 4.4 33.1 1.0
CD E:GLU112 4.5 49.3 1.0
NE2 E:GLN77 4.5 55.2 1.0
PA E:ADP301 4.6 79.2 1.0
O3B E:ADP301 4.7 50.3 1.0
CB E:ALA96 4.7 28.4 1.0
O3A E:ADP301 4.8 87.6 1.0
OE2 E:GLU112 4.8 54.8 1.0

Magnesium binding site 4 out of 7 in 9dre

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Magnesium binding site 4 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:45.3
occ:1.00
 O E:HOH492 2.2 36.4 1.0
O F:HOH487 2.2 49.0 1.0
O F:HOH489 2.4 50.3 1.0
OD2 F:ASP186 2.5 26.2 1.0
O F:GLY183 2.6 26.4 1.0
CG F:ASP186 3.3 26.1 1.0
O F:HOH472 3.4 45.9 1.0
C F:GLY183 3.6 28.9 1.0
CB F:ASP186 3.8 24.0 1.0
CA F:GLY183 3.9 27.6 1.0
O F:HOH456 4.0 41.2 1.0
NH1 E:ARG140 4.1 26.6 1.0
OD1 F:ASP186 4.3 25.3 1.0
O F:HOH435 4.4 47.4 1.0
NH2 E:ARG140 4.4 22.4 1.0
O F:HOH495 4.4 53.0 1.0
O F:HOH433 4.4 29.8 1.0
CZ E:ARG140 4.6 23.6 1.0
O E:HOH468 4.7 29.2 1.0
N F:LYS184 4.8 22.5 1.0
O E:SER129 4.8 22.7 1.0

Magnesium binding site 5 out of 7 in 9dre

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Magnesium binding site 5 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:54.2
occ:1.00
 OE2 F:GLU116 2.4 70.1 1.0
O F:ALA96 2.5 32.2 1.0
O1A F:ADP301 3.2 53.5 0.4
O F:HOH464 3.3 45.4 1.0
CD F:GLU116 3.3 67.4 1.0
O2B F:ADP301 3.3 51.9 0.4
O F:HOH417 3.4 44.2 1.0
OE1 F:GLU116 3.4 56.3 1.0
C F:ALA96 3.5 33.1 1.0
NH2 F:ARG79 4.0 49.7 1.0
O1A F:ADP301 4.0 55.1 0.6
N F:ALA96 4.1 27.5 1.0
O2A F:ADP301 4.2 44.4 0.6
CA F:ALA96 4.2 28.6 1.0
OE1 F:GLU112 4.4 52.6 1.0
NE2 F:GLN77 4.5 46.6 1.0
CB F:ALA96 4.5 28.1 1.0
N F:GLY97 4.5 28.1 1.0
PA F:ADP301 4.6 43.1 0.6
O F:HOH403 4.6 46.8 1.0
PA F:ADP301 4.7 52.8 0.4
PB F:ADP301 4.7 57.4 0.4
CA F:GLY97 4.7 33.2 1.0
CG F:GLU116 4.7 60.4 1.0
OE1 F:GLN77 5.0 49.1 1.0

Magnesium binding site 6 out of 7 in 9dre

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Magnesium binding site 6 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:53.7
occ:1.00
 OE2 G:GLU116 2.1 73.2 1.0
O2B G:ADP301 2.1 81.6 1.0
O G:ALA96 2.3 31.6 1.0
CD G:GLU116 2.9 66.5 1.0
OE1 G:GLU116 3.2 42.4 1.0
C G:ALA96 3.3 29.8 1.0
O G:HOH454 3.4 52.8 1.0
O1A G:ADP301 3.5 85.6 1.0
PB G:ADP301 3.6 105.4 1.0
OE1 G:GLU112 4.0 54.1 1.0
N G:ALA96 4.1 28.1 1.0
CA G:ALA96 4.2 25.2 1.0
NH2 G:ARG79 4.2 52.2 1.0
CG G:GLU116 4.2 61.1 1.0
N G:GLY97 4.3 25.2 1.0
CA G:GLY97 4.3 26.9 1.0
O3B G:ADP301 4.4 62.8 1.0
O1B G:ADP301 4.4 87.4 1.0
CD G:GLU112 4.5 51.2 1.0
CB G:ALA96 4.5 26.6 1.0
O3A G:ADP301 4.5 89.5 1.0
PA G:ADP301 4.6 96.6 1.0
NE2 G:GLN77 4.6 51.9 1.0
OE2 G:GLU112 4.9 54.9 1.0

Magnesium binding site 7 out of 7 in 9dre

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Magnesium binding site 7 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:48.6
occ:1.00
 O G:HOH476 2.1 36.5 1.0
O H:HOH481 2.4 50.4 1.0
OD2 H:ASP186 2.5 28.7 1.0
O H:GLY183 2.6 28.3 1.0
O H:HOH468 2.7 44.8 1.0
CG H:ASP186 3.3 27.2 1.0
C H:GLY183 3.6 30.7 1.0
CB H:ASP186 3.7 24.4 1.0
CA H:GLY183 3.8 28.8 1.0
NH1 G:ARG140 4.1 23.9 1.0
OD1 H:ASP186 4.3 26.7 1.0
NH2 G:ARG140 4.4 22.8 1.0
O G:HOH474 4.5 28.5 1.0
O G:SER129 4.6 24.2 1.0
CZ G:ARG140 4.7 23.4 1.0
O H:HOH441 4.8 31.9 1.0
N H:LYS184 4.8 24.5 1.0

Reference:

L.Liu, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Bound, P21 Form) To Be Published.
Page generated: Thu Oct 31 22:27:21 2024

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