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Magnesium in PDB 9dsz: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)

Enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)

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

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound), PDB code: 9dsz 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) 72.63 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.843, 79.311, 115.827, 90, 90.3, 90
R / Rfree (%) 19.6 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound) (pdb code 9dsz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound), PDB code: 9dsz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 9dsz

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Magnesium binding site 1 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


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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 (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:53.8
occ:1.00
 OE2 A:GLU116 2.4 96.5 1.0
O A:ALA96 2.6 39.8 1.0
O1G A:DTP301 2.9 83.9 1.0
CD A:GLU116 3.3 87.4 1.0
OE1 A:GLU116 3.4 71.4 1.0
NH2 A:ARG79 3.6 49.3 1.0
C A:ALA96 3.6 37.4 1.0
PG A:DTP301 3.9 111.8 1.0
N A:ALA96 4.0 38.5 1.0
O2G A:DTP301 4.0 90.8 1.0
NE2 A:GLN77 4.0 53.5 1.0
CA A:ALA96 4.2 36.3 1.0
CB A:ALA96 4.3 35.8 1.0
O3B A:DTP301 4.3 115.8 1.0
O1A A:DTP301 4.5 110.7 1.0
N A:GLY97 4.7 32.6 1.0
CG A:GLU116 4.7 83.7 1.0
CZ A:ARG79 4.8 46.4 1.0
CD A:GLN77 4.8 52.2 1.0
OE1 A:GLN77 4.9 62.1 1.0
CA A:GLY97 4.9 36.7 1.0
OE1 A:GLU112 5.0 58.1 1.0

Magnesium binding site 2 out of 10 in 9dsz

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Magnesium binding site 2 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


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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 (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:71.8
occ:1.00
 OE2 B:GLU116 2.2 63.5 1.0
OE1 B:GLU112 2.5 56.9 1.0
O2B B:DTP301 2.8 85.0 1.0
OE1 B:GLU164 2.9 86.5 1.0
CD B:GLU116 3.0 59.9 1.0
O3A B:DTP301 3.1 102.4 1.0
PB B:DTP301 3.2 97.3 1.0
O1B B:DTP301 3.2 87.9 1.0
OE2 B:GLU164 3.3 90.3 1.0
CD B:GLU112 3.4 57.5 1.0
CD B:GLU164 3.4 95.7 1.0
CG B:GLU116 3.4 59.7 1.0
O B:HOH401 3.6 55.7 1.0
OE2 B:GLU112 3.7 61.5 1.0
O B:ALA96 3.7 45.2 1.0
O2A B:DTP301 3.8 97.7 1.0
OE1 B:GLU116 4.0 52.1 1.0
PA B:DTP301 4.1 108.0 1.0
OE2 B:GLU115 4.2 83.4 1.0
O1A B:DTP301 4.7 84.1 1.0
CG B:GLU112 4.7 47.9 1.0
O3B B:DTP301 4.8 97.0 1.0
C B:ALA96 4.9 44.2 1.0
CG B:GLU164 4.9 102.5 1.0
CB B:GLU116 4.9 54.0 1.0

Magnesium binding site 3 out of 10 in 9dsz

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Magnesium binding site 3 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


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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 (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:61.6
occ:1.00
 O C:ALA96 2.5 31.8 1.0
O2G C:DTP301 2.7 100.2 1.0
OE2 C:GLU116 3.3 94.4 1.0
C C:ALA96 3.5 29.9 1.0
O1G C:DTP301 3.7 99.0 1.0
PG C:DTP301 3.7 120.4 1.0
NH2 C:ARG79 3.8 42.6 1.0
OE1 C:GLU116 4.0 68.0 1.0
CD C:GLU116 4.0 76.0 1.0
N C:ALA96 4.1 27.2 1.0
CA C:ALA96 4.2 29.9 1.0
NE2 C:GLN77 4.3 50.2 1.0
CB C:ALA96 4.3 32.6 1.0
N C:GLY97 4.5 30.4 1.0
OE1 C:GLU112 4.5 51.4 1.0
O3B C:DTP301 4.6 117.7 1.0
CA C:GLY97 4.7 32.5 1.0
O3G C:DTP301 5.0 84.5 1.0

Magnesium binding site 4 out of 10 in 9dsz

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Magnesium binding site 4 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


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 (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:66.4
occ:1.00
 OE2 D:GLU116 2.4 87.6 1.0
OE1 D:GLU112 2.6 56.6 1.0
O3G D:DTP301 2.6 95.6 1.0
O1G D:DTP301 2.7 89.5 1.0
O D:HOH447 3.0 51.0 1.0
CD D:GLU116 3.1 84.5 1.0
PG D:DTP301 3.1 111.2 1.0
O D:ALA96 3.1 40.7 1.0
CD D:GLU112 3.5 52.9 1.0
OE1 D:GLU116 3.7 73.5 1.0
O3A D:DTP301 3.8 86.9 1.0
OE2 D:GLU112 3.8 57.1 1.0
O2B D:DTP301 3.8 77.9 1.0
O3B D:DTP301 3.9 93.6 1.0
CG D:GLU116 3.9 79.4 1.0
PB D:DTP301 4.2 77.3 1.0
OE2 D:GLU115 4.3 108.7 1.0
C D:ALA96 4.3 38.0 1.0
CA D:GLY97 4.5 43.5 1.0
O2G D:DTP301 4.5 110.5 1.0
CG D:GLU112 4.6 51.0 1.0
O1A D:DTP301 4.8 80.3 1.0
O D:HOH417 4.9 44.8 1.0
N D:GLY97 4.9 38.3 1.0
PA D:DTP301 4.9 90.4 1.0

Magnesium binding site 5 out of 10 in 9dsz

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Magnesium binding site 5 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


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 (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:60.4
occ:1.00
 O E:ALA96 2.7 48.4 1.0
OE2 E:GLU116 2.7 90.2 1.0
O1B E:DTP301 3.2 99.9 1.0
OE1 E:GLU116 3.3 74.0 1.0
CD E:GLU116 3.4 87.9 1.0
NH2 E:ARG79 3.5 64.2 1.0
N E:ALA96 3.6 43.8 1.0
C E:ALA96 3.6 45.0 1.0
NE2 E:GLN77 3.8 60.4 1.0
O2B E:DTP301 3.9 98.7 1.0
CA E:ALA96 4.0 48.7 1.0
PB E:DTP301 4.0 122.1 1.0
CB E:ALA96 4.1 36.4 1.0
O3A E:DTP301 4.6 115.8 1.0
CD E:GLN77 4.7 56.1 1.0
O E:MET94 4.7 46.0 1.0
C E:VAL95 4.7 43.6 1.0
N E:GLY97 4.8 41.3 1.0
OE1 E:GLN77 4.8 56.1 1.0
CZ E:ARG79 4.8 56.4 1.0
CG E:GLU116 4.9 81.5 1.0
OE1 E:GLU112 5.0 67.8 1.0
CA E:VAL95 5.0 39.5 1.0

Magnesium binding site 6 out of 10 in 9dsz

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Magnesium binding site 6 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


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 (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:46.0
occ:1.00
 O F:HOH473 2.2 45.0 1.0
O E:HOH451 2.3 36.2 1.0
O F:HOH445 2.3 40.9 1.0
OD2 F:ASP186 2.5 34.1 1.0
O F:GLY183 2.6 29.0 1.0
CG F:ASP186 3.2 32.3 1.0
C F:GLY183 3.5 30.2 1.0
CB F:ASP186 3.6 25.7 1.0
CA F:GLY183 3.9 33.1 1.0
O F:HOH458 4.0 45.2 1.0
NH1 E:ARG140 4.1 26.9 1.0
OD1 F:ASP186 4.2 29.9 1.0
NH2 E:ARG140 4.3 27.6 1.0
O E:HOH457 4.4 34.5 1.0
O F:HOH434 4.5 28.7 1.0
O E:SER129 4.5 31.5 1.0
CZ E:ARG140 4.6 31.8 1.0
N F:LYS184 4.7 24.0 1.0

Magnesium binding site 7 out of 10 in 9dsz

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Magnesium binding site 7 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


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 (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:60.0
occ:1.00
 O F:ALA96 2.4 42.0 1.0
OE2 F:GLU116 2.6 81.6 1.0
O F:HOH407 3.2 48.4 1.0
O2G F:DTP301 3.2 80.5 1.0
C F:ALA96 3.4 39.4 1.0
CD F:GLU116 3.4 72.5 1.0
OE1 F:GLU116 3.5 54.4 1.0
O3B F:DTP301 3.6 93.3 1.0
O3A F:DTP301 3.8 92.8 1.0
NH2 F:ARG79 3.8 46.8 1.0
N F:ALA96 4.0 36.9 1.0
PG F:DTP301 4.0 97.8 1.0
CA F:ALA96 4.1 39.0 1.0
CB F:ALA96 4.2 33.9 1.0
OE1 F:GLN77 4.3 53.1 1.0
N F:GLY97 4.4 38.0 1.0
PB F:DTP301 4.4 86.0 1.0
CA F:GLY97 4.6 41.9 1.0
OE1 F:GLU112 4.6 61.1 1.0
O1G F:DTP301 4.7 86.7 1.0
O1A F:DTP301 4.7 87.1 1.0
PA F:DTP301 4.7 103.9 1.0
CG F:GLU116 4.8 56.4 1.0
CZ F:ARG79 5.0 41.1 1.0

Magnesium binding site 8 out of 10 in 9dsz

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Magnesium binding site 8 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:37.5
occ:1.00
 O G:HOH409 2.2 34.5 1.0
OE2 G:GLU116 2.3 32.5 1.0
O G:ALA96 2.3 24.7 1.0
O G:HOH488 2.4 40.4 1.0
O G:HOH451 2.5 26.2 1.0
O G:HOH415 2.5 38.4 1.0
CD G:GLU116 3.1 36.9 1.0
OE1 G:GLU116 3.2 34.3 1.0
C G:ALA96 3.4 29.0 1.0
MG G:MG302 3.5 34.9 1.0
NH2 G:ARG79 3.9 41.6 1.0
OE2 G:GLU164 4.0 49.8 1.0
N G:ALA96 4.0 27.1 1.0
CA G:ALA96 4.1 23.8 1.0
NE2 G:GLN77 4.1 42.2 1.0
OE1 G:GLU112 4.3 37.3 1.0
N G:GLY97 4.3 24.5 1.0
CB G:ALA96 4.4 25.2 1.0
O G:HOH472 4.4 41.5 1.0
CA G:GLY97 4.5 24.4 1.0
CG G:GLU116 4.6 32.7 1.0
O G:HOH493 4.6 35.5 1.0
OE1 G:GLN77 4.6 38.5 1.0
CD G:GLN77 4.8 32.5 1.0
CZ G:ARG79 4.9 40.3 1.0
CD G:GLU112 5.0 35.1 1.0

Magnesium binding site 9 out of 10 in 9dsz

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Magnesium binding site 9 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:34.9
occ:1.00
 O G:HOH451 2.1 26.2 1.0
OE1 G:GLU112 2.1 37.3 1.0
O G:HOH401 2.2 39.6 1.0
O G:HOH484 2.2 33.7 1.0
OE2 G:GLU116 2.2 32.5 1.0
OE2 G:GLU164 2.3 49.8 1.0
CD G:GLU116 3.1 36.9 1.0
CD G:GLU112 3.1 35.1 1.0
CD G:GLU164 3.2 62.1 1.0
OE1 G:GLU164 3.4 51.9 1.0
CG G:GLU116 3.5 32.7 1.0
OE2 G:GLU112 3.5 42.4 1.0
MG G:MG301 3.5 37.5 1.0
OE2 G:GLU115 3.6 51.4 1.0
O G:HOH415 3.8 38.4 1.0
O G:ALA96 4.0 24.7 1.0
O G:HOH493 4.1 35.5 1.0
OE1 G:GLU116 4.2 34.3 1.0
CG G:GLU112 4.4 28.3 1.0
O G:HOH403 4.5 39.2 1.0
CD G:GLU115 4.6 46.7 1.0
CG G:GLU164 4.6 63.3 1.0
CG G:GLU115 4.7 48.8 1.0
CB G:GLU112 4.8 30.2 1.0
CB G:GLU116 5.0 33.2 1.0

Magnesium binding site 10 out of 10 in 9dsz

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Magnesium binding site 10 out of 10 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg303

b:79.8
occ:1.00
 O2B H:DTP302 2.2 91.1 1.0
O3B H:DTP302 2.3 97.2 1.0
OE2 H:GLU116 2.7 72.8 1.0
PB H:DTP302 2.8 107.1 1.0
CB H:GLU164 3.3 77.8 1.0
CD H:GLU116 3.6 71.5 1.0
CG H:GLU116 3.6 65.8 1.0
O3A H:DTP302 3.7 97.0 1.0
CD1 H:ILE166 3.8 73.2 1.0
O1B H:DTP302 4.0 87.0 1.0
OE2 H:GLU115 4.6 68.5 1.0
OE1 H:GLU112 4.7 55.7 1.0
OE1 H:GLU116 4.8 59.5 1.0
OE1 H:GLN77 4.8 46.2 1.0
CA H:GLU164 4.9 82.2 1.0
CB H:GLU116 5.0 66.4 1.0

Reference:

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

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