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

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

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

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound, P21 Form), PDB code: 9drf 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) 49.23 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.034, 80.131, 116.189, 90, 90.13, 90
R / Rfree (%) 17.9 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp Bound, P21 Form) (pdb code 9drf). 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 (Dtp Bound, P21 Form), PDB code: 9drf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 9drf

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Magnesium binding site 1 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp 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 (Dtp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:73.0
occ:1.00
 OE2 B:GLU116 2.7 90.5 1.0
O B:ALA96 3.0 41.4 1.0
OE2 B:GLU112 3.3 58.3 1.0
OE1 B:GLU112 3.4 58.5 1.0
O B:HOH469 3.5 48.9 1.0
CD B:GLU112 3.5 62.8 1.0
CA B:GLY97 3.9 44.2 1.0
CD B:GLU116 4.0 83.7 1.0
C B:ALA96 4.1 48.4 1.0
N B:GLY97 4.5 39.4 1.0
CG B:GLU112 4.7 54.9 1.0
OE1 B:GLU116 4.7 70.9 1.0
CG B:GLU116 4.9 85.2 1.0

Magnesium binding site 2 out of 7 in 9drf

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Magnesium binding site 2 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp 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 (Dtp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:56.8
occ:1.00
 O C:ALA96 2.3 35.9 1.0
OE2 C:GLU116 2.8 70.6 1.0
C C:ALA96 3.4 32.1 1.0
OE1 C:GLU112 3.7 49.7 1.0
CD C:GLU116 3.7 61.7 1.0
N C:ALA96 4.0 31.1 1.0
OE1 C:GLU116 4.1 57.1 1.0
CA C:ALA96 4.2 32.6 1.0
CD C:GLU112 4.3 46.3 1.0
N C:GLY97 4.4 31.2 1.0
CA C:GLY97 4.5 32.5 1.0
NH2 C:ARG79 4.6 48.3 1.0
OE2 C:GLU112 4.7 50.3 1.0
CB C:ALA96 4.7 33.4 1.0
NE2 C:GLN77 4.8 47.1 1.0
CG C:GLU116 5.0 58.7 1.0
OE2 C:GLU115 5.0 45.9 0.4

Magnesium binding site 3 out of 7 in 9drf

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Magnesium binding site 3 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp 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 (Dtp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:64.4
occ:1.00
 O E:ALA96 2.5 41.4 1.0
OE2 E:GLU116 3.0 90.6 1.0
C E:ALA96 3.5 44.4 1.0
NH2 E:ARG79 3.8 52.6 1.0
N E:ALA96 4.0 42.9 1.0
CD E:GLU116 4.0 81.8 1.0
OE1 E:GLU116 4.1 74.9 1.0
CA E:ALA96 4.2 49.0 1.0
NE2 E:GLN77 4.3 57.4 1.0
CB E:ALA96 4.4 38.0 1.0
OE1 E:GLU112 4.4 68.2 1.0
N E:GLY97 4.5 39.3 1.0
CA E:GLY97 4.7 41.6 1.0
CZ E:ARG79 5.0 53.0 1.0
CD E:GLU112 5.0 59.7 1.0

Magnesium binding site 4 out of 7 in 9drf

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Magnesium binding site 4 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp 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 (Dtp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:52.7
occ:1.00
 O F:HOH474 2.2 53.1 1.0
O F:HOH457 2.3 50.9 1.0
O E:HOH453 2.5 44.3 1.0
OD2 F:ASP186 2.7 37.1 1.0
O F:GLY183 2.7 34.1 1.0
O F:HOH470 3.3 52.1 1.0
CG F:ASP186 3.5 35.0 1.0
C F:GLY183 3.6 33.7 1.0
CA F:GLY183 3.9 36.5 1.0
CB F:ASP186 4.0 31.0 1.0
O F:HOH456 4.0 52.5 1.0
NH1 E:ARG140 4.2 33.4 1.0
O F:HOH480 4.4 62.7 1.0
OD1 F:ASP186 4.4 34.1 1.0
NH2 E:ARG140 4.5 33.1 1.0
O F:HOH428 4.5 35.2 1.0
CZ E:ARG140 4.8 32.6 1.0
O E:HOH465 4.8 32.6 1.0
N F:LYS184 4.8 28.9 1.0
O E:SER129 4.9 32.4 1.0

Magnesium binding site 5 out of 7 in 9drf

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Magnesium binding site 5 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp 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 (Dtp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:61.2
occ:1.00
 OE2 F:GLU116 2.5 80.2 1.0
O F:ALA96 2.6 41.2 1.0
CD F:GLU116 3.3 75.6 1.0
OE1 F:GLU116 3.4 62.8 1.0
O F:HOH414 3.6 50.1 1.0
C F:ALA96 3.7 40.7 1.0
NH2 F:ARG79 3.9 46.8 1.0
N F:ALA96 4.2 35.4 1.0
CA F:ALA96 4.3 32.9 1.0
OE1 F:GLU112 4.5 58.5 1.0
CB F:ALA96 4.6 32.3 1.0
NE2 F:GLN77 4.6 48.2 1.0
N F:GLY97 4.7 38.8 1.0
CG F:GLU116 4.7 68.0 1.0
CA F:GLY97 4.9 47.6 1.0

Magnesium binding site 6 out of 7 in 9drf

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Magnesium binding site 6 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp 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 (Dtp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg303

b:62.6
occ:1.00
 OE2 G:GLU116 2.4 69.5 1.0
O G:ALA96 2.6 40.2 1.0
CD G:GLU116 3.4 63.3 1.0
NH2 G:ARG79 3.4 57.0 1.0
C G:ALA96 3.6 37.5 1.0
OE1 G:GLU116 3.7 52.0 1.0
N G:ALA96 4.2 36.4 1.0
CA G:ALA96 4.3 35.6 1.0
NE2 G:GLN77 4.4 60.3 1.0
OE1 G:GLU112 4.4 56.9 1.0
CB G:ALA96 4.4 35.8 1.0
CZ G:ARG79 4.5 51.8 1.0
N G:GLY97 4.5 34.5 1.0
CA G:GLY97 4.7 36.8 1.0
NH1 G:ARG79 4.7 51.7 1.0
CG G:GLU116 4.8 54.1 1.0
OE1 G:GLN77 4.8 55.0 1.0
CD G:GLN77 4.9 52.0 1.0

Magnesium binding site 7 out of 7 in 9drf

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Magnesium binding site 7 out of 7 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Dtp 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 (Dtp Bound, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:60.0
occ:1.00
 O G:HOH473 2.2 47.8 1.0
OD2 H:ASP186 2.6 36.5 1.0
O H:GLY183 2.7 37.2 1.0
O H:HOH470 2.7 46.2 1.0
CG H:ASP186 3.5 38.4 1.0
C H:GLY183 3.6 39.6 1.0
CB H:ASP186 3.9 34.0 1.0
CA H:GLY183 3.9 39.6 1.0
NH1 G:ARG140 4.2 32.8 1.0
OD1 H:ASP186 4.4 38.2 1.0
NH2 G:ARG140 4.5 33.5 1.0
O G:HOH476 4.7 36.5 1.0
O H:HOH418 4.7 41.4 1.0
CZ G:ARG140 4.7 31.3 1.0
O G:SER129 4.8 33.1 1.0
N H:LYS184 4.8 32.5 1.0

Reference:

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

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