Magnesium in PDB 9b22: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp Bound)

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

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

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp Bound), PDB code: 9b22 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) 36.58 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.826, 92.659, 57.716, 90, 91.68, 90
R / Rfree (%) 13.7 / 16.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp Bound) (pdb code 9b22). 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 and Amp Bound), PDB code: 9b22:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9b22

Go back to Magnesium Binding Sites List in 9b22
Magnesium binding site 1 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp Bound)


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 and Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:23.4
occ:1.00
 O2B A:AR6303 2.2 19.1 1.0
OE2 A:GLU116 2.3 21.1 1.0
O A:HOH455 2.3 25.3 1.0
O A:ALA96 2.4 16.4 1.0
O A:HOH412 2.5 30.2 1.0
O2A A:AR6303 2.5 26.7 1.0
CD A:GLU116 3.2 20.9 1.0
MG A:MG302 3.4 26.1 1.0
OE1 A:GLU116 3.4 22.3 1.0
PB A:AR6303 3.5 20.0 1.0
C A:ALA96 3.5 14.7 1.0
PA A:AR6303 3.7 28.5 1.0
O3A A:AR6303 3.9 25.4 1.0
OE2 A:GLU164 3.9 37.3 1.0
NH2 A:ARG79 4.1 18.9 1.0
N A:ALA96 4.3 14.4 1.0
CA A:ALA96 4.3 14.6 1.0
O1B A:AR6303 4.4 21.0 1.0
N A:GLY97 4.4 14.5 1.0
CA A:GLY97 4.4 15.2 1.0
OE1 A:GLU112 4.5 27.5 0.5
O A:HOH464 4.5 54.3 1.0
O A:HOH403 4.5 31.7 1.0
OE1 A:GLU112 4.6 21.8 0.5
CB A:ALA96 4.6 15.5 1.0
CG A:GLU116 4.6 19.9 1.0
O5D A:AR6303 4.7 20.6 1.0
NE2 A:GLN77 4.7 23.4 1.0
O A:HOH468 4.7 50.4 1.0
OE1 A:GLN77 4.7 22.7 1.0
O1A A:AR6303 4.8 25.0 1.0
C5D A:AR6303 4.8 22.1 1.0
CD A:GLU112 4.8 20.1 0.5
O5' A:AR6303 5.0 30.4 1.0

Magnesium binding site 2 out of 4 in 9b22

Go back to Magnesium Binding Sites List in 9b22
Magnesium binding site 2 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp Bound)


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

b:26.1
occ:1.00
 O A:HOH468 2.0 50.4 1.0
O A:HOH436 2.1 46.6 1.0
OE2 A:GLU116 2.1 21.1 1.0
OE1 A:GLU112 2.2 27.5 0.5
OE2 A:GLU164 2.4 37.3 1.0
OE1 A:GLU112 2.4 21.8 0.5
O2A A:AR6303 2.7 26.7 1.0
CD A:GLU116 3.1 20.9 1.0
CD A:GLU112 3.2 20.1 0.5
CD A:GLU164 3.3 37.7 1.0
MG A:MG301 3.4 23.4 1.0
CD A:GLU112 3.4 26.0 0.5
OE2 A:GLU112 3.4 21.8 0.5
CG A:GLU116 3.5 19.9 1.0
OE1 A:GLU164 3.6 38.1 1.0
O A:HOH455 3.7 25.3 1.0
PA A:AR6303 4.1 28.5 1.0
OE2 A:GLU112 4.1 26.7 0.5
O A:ALA96 4.1 16.4 1.0
OE1 A:GLU116 4.3 22.3 1.0
CG A:GLU112 4.4 22.5 0.5
CG A:GLU112 4.5 18.0 0.5
OE1 A:GLU115 4.6 40.0 1.0
O1A A:AR6303 4.7 25.0 1.0
CG A:GLU164 4.7 37.1 1.0
CB A:GLU112 4.8 20.3 0.5
O5' A:AR6303 4.8 30.4 1.0
CB A:GLU112 4.9 17.1 0.5
C5' A:AR6303 5.0 29.8 1.0
CB A:GLU116 5.0 18.9 1.0

Magnesium binding site 3 out of 4 in 9b22

Go back to Magnesium Binding Sites List in 9b22
Magnesium binding site 3 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp Bound)


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 and Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:23.1
occ:1.00
 O B:HOH454 2.1 20.5 0.4
O B:HOH481 2.1 15.3 0.4
OE2 B:GLU116 2.1 25.6 1.0
O B:ALA96 2.2 17.7 1.0
O B:HOH404 2.3 23.3 1.0
O B:HOH444 2.3 26.1 1.0
O2B B:AR6303 2.4 21.6 0.6
O2A B:AR6303 3.0 27.9 0.6
CD B:GLU116 3.1 23.8 1.0
C B:ALA96 3.4 15.7 1.0
OE1 B:GLU116 3.4 22.7 1.0
O3P B:AMP304 3.6 15.1 0.4
PB B:AR6303 3.8 21.6 0.6
O2P B:AMP304 4.0 16.4 0.4
PA B:AR6303 4.1 26.9 0.6
MG B:MG302 4.1 67.4 1.0
NH2 B:ARG79 4.1 19.6 1.0
O B:HOH443 4.2 40.2 0.6
O3A B:AR6303 4.2 22.9 0.6
N B:ALA96 4.2 14.9 1.0
N B:GLY97 4.2 15.4 1.0
CA B:ALA96 4.2 14.9 1.0
CA B:GLY97 4.3 15.0 1.0
P B:AMP304 4.3 14.6 0.4
OE2 B:GLU164 4.3 34.0 0.4
NE2 B:GLN77 4.4 22.9 1.0
CG B:GLU116 4.5 21.9 1.0
O B:HOH418 4.5 29.4 1.0
CB B:ALA96 4.6 15.8 1.0
OE1 B:GLN77 4.6 26.1 1.0
OE1 B:GLU112 4.6 27.3 1.0
O B:HOH431 4.7 17.4 0.4
CD B:GLU112 4.7 26.0 1.0
OE2 B:GLU112 4.7 28.1 1.0
O1B B:AR6303 4.7 21.8 0.6
C5D B:AR6303 4.9 18.9 0.6
O5D B:AR6303 4.9 18.8 0.6
O1A B:AR6303 4.9 27.5 0.6
CD B:GLN77 4.9 21.7 1.0
O1P B:AMP304 5.0 16.9 0.4

Magnesium binding site 4 out of 4 in 9b22

Go back to Magnesium Binding Sites List in 9b22
Magnesium binding site 4 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp 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 (Adp Ribose and Amp Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:67.4
occ:1.00
 O B:HOH443 2.6 40.2 0.6
OE1 B:GLU112 2.6 27.3 1.0
OE2 B:GLU164 2.7 34.0 0.4
O B:HOH481 2.7 15.3 0.4
OE2 B:GLU116 3.1 25.6 1.0
OE2 B:GLU112 3.2 28.1 1.0
CD B:GLU112 3.3 26.0 1.0
O2A B:AR6303 3.5 27.9 0.6
CD B:GLU164 3.5 33.6 0.4
OE1 B:GLU164 3.7 34.7 0.4
CG B:GLU116 3.9 21.9 1.0
CD B:GLU116 3.9 23.8 1.0
OE1 B:GLU162 4.0 66.2 1.0
OE1 B:GLU115 4.0 43.3 1.0
MG B:MG301 4.1 23.1 1.0
O B:HOH404 4.3 23.3 1.0
O B:HOH421 4.3 48.2 1.0
CD B:GLU162 4.6 64.6 1.0
OE2 B:GLU162 4.7 66.1 1.0
CG B:GLU112 4.7 21.3 1.0
PA B:AR6303 4.8 26.9 0.6
O B:ALA96 4.8 17.7 1.0
CB B:GLU115 4.9 29.6 1.0
O B:HOH431 5.0 17.4 0.4
CG B:GLU164 5.0 32.0 0.4

Reference:

L.Liu, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose and Amp Bound) To Be Published.
Page generated: Sat Oct 5 08:47:29 2024

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