Magnesium in PDB 9b21: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P Form)

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

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

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P Form), PDB code: 9b21 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) 48.61 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.365, 78.788, 91.564, 90, 90, 90
R / Rfree (%) 16.4 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P Form) (pdb code 9b21). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P Form), PDB code: 9b21:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9b21

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Magnesium binding site 1 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P 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 Ribose Bound, Orthorhombic P Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:27.8
occ:1.00
 O A:HOH402 2.1 27.1 1.0
O A:HOH415 2.1 28.7 1.0
OE2 A:GLU116 2.2 26.9 1.0
O A:ALA96 2.2 23.6 1.0
O A:HOH435 2.3 25.0 1.0
O1B A:AR6301 2.5 28.4 1.0
CD A:GLU116 3.1 27.5 1.0
OE1 A:GLU116 3.3 27.7 1.0
O2A A:AR6301 3.4 53.0 1.0
C A:ALA96 3.4 22.9 1.0
MG A:MG303 3.4 30.2 1.0
OE2 A:GLU164 3.8 34.8 1.0
PB A:AR6301 3.9 41.2 1.0
NH2 A:ARG79 4.0 24.0 1.0
N A:ALA96 4.1 20.6 1.0
O A:HOH424 4.2 41.9 1.0
O A:HOH409 4.2 30.4 1.0
CA A:ALA96 4.2 18.8 1.0
OE1 A:GLN77 4.3 33.1 1.0
N A:GLY97 4.4 20.9 1.0
OE1 A:GLU112 4.4 35.7 1.0
O3A A:AR6301 4.4 42.7 1.0
NE2 A:GLN77 4.5 27.3 1.0
CA A:GLY97 4.5 21.7 1.0
PA A:AR6301 4.5 77.6 1.0
CG A:GLU116 4.5 23.6 1.0
CB A:ALA96 4.5 21.6 1.0
O2B A:AR6301 4.6 35.6 1.0
CD A:GLN77 4.8 27.9 1.0
CD A:GLU112 4.9 30.2 1.0
O5D A:AR6301 5.0 44.6 1.0
C5D A:AR6301 5.0 40.2 1.0
CZ A:ARG79 5.0 26.4 1.0

Magnesium binding site 2 out of 4 in 9b21

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Magnesium binding site 2 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P 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 Ribose Bound, Orthorhombic P Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:30.2
occ:1.00
 O A:HOH432 2.1 35.5 1.0
OE2 A:GLU116 2.1 26.9 1.0
O A:HOH402 2.1 27.1 1.0
OE1 A:GLU112 2.2 35.7 1.0
OE2 A:GLU164 2.3 34.8 1.0
O A:HOH505 2.3 44.1 1.0
CD A:GLU116 3.0 27.5 1.0
CD A:GLU112 3.1 30.2 1.0
CD A:GLU164 3.2 43.6 1.0
CG A:GLU116 3.3 23.6 1.0
O A:HOH408 3.4 37.2 1.0
OE2 A:GLU112 3.4 33.0 1.0
MG A:MG302 3.4 27.8 1.0
OE1 A:GLU164 3.5 45.9 1.0
O2A A:AR6301 3.7 53.0 1.0
O A:HOH435 3.7 25.0 1.0
O A:ALA96 4.0 23.6 1.0
OE1 A:GLU116 4.2 27.7 1.0
OE1 A:GLU115 4.4 48.4 1.0
CG A:GLU112 4.5 24.3 1.0
CG A:GLU164 4.6 34.2 1.0
PA A:AR6301 4.7 77.6 1.0
O1A A:AR6301 4.8 44.3 1.0
CB A:GLU116 4.8 23.0 1.0
CB A:GLU112 4.9 25.2 1.0
O A:HOH415 4.9 28.7 1.0

Magnesium binding site 3 out of 4 in 9b21

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Magnesium binding site 3 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P 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 Ribose Bound, Orthorhombic P Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:27.7
occ:1.00
 O B:HOH452 2.1 30.5 1.0
O1B B:AR6301 2.2 25.1 1.0
O B:ALA96 2.2 19.1 1.0
OE2 B:GLU116 2.2 20.4 1.0
O B:HOH457 2.4 27.1 1.0
O B:HOH418 2.5 25.3 1.0
CD B:GLU116 3.1 22.9 1.0
OE1 B:GLU116 3.2 26.2 1.0
C B:ALA96 3.4 21.3 1.0
PB B:AR6301 3.4 57.1 1.0
MG B:MG303 3.5 28.8 1.0
O3A B:AR6301 3.6 38.9 1.0
N B:ALA96 4.0 18.5 1.0
OE2 B:GLU164 4.0 40.3 1.0
NH2 B:ARG79 4.0 26.9 1.0
CA B:ALA96 4.1 17.2 1.0
O2B B:AR6301 4.3 41.9 1.0
OE1 B:GLU112 4.3 27.3 1.0
N B:GLY97 4.4 18.8 1.0
OE1 B:GLN77 4.4 34.8 1.0
O B:HOH402 4.4 46.9 1.0
CB B:ALA96 4.5 21.0 1.0
NE2 B:GLN77 4.5 22.2 1.0
CA B:GLY97 4.5 21.1 1.0
CG B:GLU116 4.5 20.5 1.0
O5D B:AR6301 4.6 50.2 1.0
C5D B:AR6301 4.7 39.6 1.0
CD B:GLU112 4.8 24.9 1.0
CD B:GLN77 4.9 25.1 1.0

Magnesium binding site 4 out of 4 in 9b21

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Magnesium binding site 4 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P 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 Ribose Bound, Orthorhombic P Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:28.8
occ:1.00
 O B:HOH414 2.1 26.5 1.0
OE2 B:GLU116 2.1 20.4 1.0
OE1 B:GLU112 2.1 27.3 1.0
O B:HOH418 2.2 25.3 1.0
O B:HOH526 2.2 33.4 1.0
OE2 B:GLU164 2.2 40.3 1.0
CD B:GLU112 3.1 24.9 1.0
CD B:GLU116 3.1 22.9 1.0
CD B:GLU164 3.2 42.3 1.0
OE2 B:GLU112 3.4 29.8 1.0
CG B:GLU116 3.4 20.5 1.0
MG B:MG302 3.5 27.7 1.0
OE1 B:GLU164 3.5 39.3 1.0
O B:HOH457 3.7 27.1 1.0
O B:ALA96 4.1 19.1 1.0
O B:HOH509 4.1 45.4 1.0
OE1 B:GLU116 4.3 26.2 1.0
OE1 B:GLU115 4.3 32.8 1.0
CG B:GLU112 4.5 21.5 1.0
CG B:GLU164 4.6 33.8 1.0
O3A B:AR6301 4.7 38.9 1.0
CB B:GLU112 4.8 24.1 1.0
CB B:GLU116 4.9 19.9 1.0

Reference:

S.Lovell, L.Liu, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthorhombic P Form) To Be Published.
Page generated: Sat Oct 5 08:47:08 2024

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