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Magnesium in PDB 9du8: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg Bound)

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

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

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg Bound), PDB code: 9du8 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) 48.66 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.375, 79.335, 91.822, 90, 90, 90
R / Rfree (%) 14.3 / 16.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg Bound) (pdb code 9du8). 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/Mg Bound), PDB code: 9du8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9du8

Go back to Magnesium Binding Sites List in 9du8
Magnesium binding site 1 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg 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/Mg Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:18.4
occ:1.00
 O A:HOH543 2.0 28.3 1.0
O A:HOH406 2.1 19.4 1.0
OE1 A:GLU120 2.1 20.4 1.0
O A:HOH413 2.1 18.9 1.0
OE2 A:GLU124 2.2 18.0 1.0
OE2 A:GLU172 2.2 21.3 0.6
CD A:GLU120 3.1 20.6 1.0
CD A:GLU124 3.2 17.7 1.0
CD A:GLU172 3.2 21.8 0.6
OE2 A:GLU120 3.4 21.8 1.0
OE1 A:GLU172 3.5 20.4 0.6
CG A:GLU124 3.5 16.6 1.0
MG A:MG302 3.5 25.4 1.0
O A:HOH402 3.7 22.0 1.0
O A:ALA104 4.0 16.4 1.0
O1A A:ADP303 4.0 27.1 0.6
OE1 A:GLU172 4.0 27.7 0.4
OE2 A:GLU172 4.1 27.4 0.4
O A:HOH493 4.1 35.1 1.0
O3A A:ADP303 4.2 31.5 0.4
OE1 A:GLU123 4.2 23.8 1.0
OE1 A:GLU124 4.2 19.6 1.0
CD A:GLU172 4.2 27.9 0.4
CG A:GLU120 4.4 18.2 1.0
O3A A:ADP303 4.5 31.5 0.6
CG A:GLU172 4.6 23.5 0.6
CB A:GLU120 4.8 16.7 1.0
O1A A:ADP303 4.8 26.6 0.4
C5' A:ADP303 4.9 27.1 0.4
PA A:ADP303 4.9 26.7 0.6
O3B A:ADP303 4.9 36.0 0.4

Magnesium binding site 2 out of 4 in 9du8

Go back to Magnesium Binding Sites List in 9du8
Magnesium binding site 2 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg 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/Mg Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:25.4
occ:1.00
 O A:HOH402 2.2 22.0 1.0
OE2 A:GLU124 2.3 18.0 1.0
O A:ALA104 2.3 16.4 1.0
O1B A:ADP303 2.3 36.0 0.6
O A:HOH462 2.3 25.8 1.0
O1B A:ADP303 2.5 33.2 0.4
O A:HOH406 2.6 19.4 1.0
CD A:GLU124 3.0 17.7 1.0
OE1 A:GLU124 3.1 19.6 1.0
PB A:ADP303 3.3 35.2 0.4
C A:ALA104 3.4 14.4 1.0
O3B A:ADP303 3.4 36.0 0.4
O3A A:ADP303 3.5 31.5 0.4
MG A:MG301 3.5 18.4 1.0
PB A:ADP303 3.6 38.8 0.6
O3A A:ADP303 3.6 31.5 0.6
O1A A:ADP303 3.8 27.1 0.6
NH2 A:ARG87 3.9 21.7 1.0
OE2 A:GLU172 3.9 21.3 0.6
N A:ALA104 4.0 13.7 1.0
CA A:ALA104 4.1 14.0 1.0
PA A:ADP303 4.3 26.7 0.6
OE1 A:GLU120 4.3 20.4 1.0
NE2 A:GLN85 4.4 26.2 1.0
CB A:ALA104 4.4 14.8 1.0
O3B A:ADP303 4.4 42.0 0.6
N A:GLY105 4.4 14.5 1.0
OE1 A:GLN85 4.5 24.5 1.0
CG A:GLU124 4.5 16.6 1.0
CA A:GLY105 4.6 14.5 1.0
O2B A:ADP303 4.7 40.4 0.6
O2B A:ADP303 4.8 36.5 0.4
O2A A:ADP303 4.8 27.2 0.6
CD A:GLN85 4.9 23.8 1.0
CZ A:ARG87 4.9 20.2 1.0
CD A:GLU120 5.0 20.6 1.0

Magnesium binding site 3 out of 4 in 9du8

Go back to Magnesium Binding Sites List in 9du8
Magnesium binding site 3 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg 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/Mg Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:19.9
occ:1.00
 O B:HOH405 1.9 23.7 0.5
O B:HOH448 2.1 22.4 1.0
O B:HOH534 2.1 27.4 1.0
OE1 B:GLU120 2.1 25.0 1.0
OE2 B:GLU124 2.2 20.9 1.0
OE2 B:GLU172 2.2 25.0 1.0
O1A B:ADP303 2.3 13.5 0.6
CD B:GLU124 3.2 19.7 1.0
CD B:GLU120 3.2 24.6 1.0
CD B:GLU172 3.2 25.1 1.0
O1A B:ADP303 3.3 41.8 0.5
MG B:MG302 3.3 21.8 1.0
PA B:ADP303 3.4 14.5 0.6
CG B:GLU124 3.5 19.8 1.0
OE2 B:GLU120 3.5 25.7 1.0
OE1 B:GLU172 3.5 25.1 1.0
O B:HOH406 3.6 23.6 1.0
O B:HOH401 3.8 18.0 1.0
O5' B:ADP303 3.9 17.6 0.6
O B:ALA104 4.0 18.0 1.0
O2A B:ADP303 4.0 13.8 0.6
O B:HOH403 4.1 35.9 1.0
O B:HOH512 4.1 32.9 1.0
OE1 B:GLU123 4.2 28.9 1.0
OE1 B:GLU124 4.3 19.2 1.0
CG B:GLU120 4.5 22.4 1.0
O1B B:ADP303 4.6 47.4 0.5
CG B:GLU172 4.6 24.5 1.0
PA B:ADP303 4.7 40.3 0.5
C5' B:ADP303 4.8 32.0 0.5
O3A B:ADP303 4.8 15.4 0.6
O2B B:ADP303 4.9 14.2 0.6
CB B:GLU120 4.9 20.7 1.0
O B:HOH441 4.9 21.9 1.0
CA B:GLY105 4.9 17.1 1.0
CB B:GLU124 5.0 19.3 1.0

Magnesium binding site 4 out of 4 in 9du8

Go back to Magnesium Binding Sites List in 9du8
Magnesium binding site 4 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg 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/Mg Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:21.8
occ:1.00
 O2B B:ADP303 2.0 14.2 0.6
O B:HOH405 2.0 23.7 0.5
O B:HOH441 2.1 21.9 1.0
OE2 B:GLU124 2.1 20.9 1.0
O B:ALA104 2.2 18.0 1.0
O1A B:ADP303 2.2 13.5 0.6
O B:HOH401 2.2 18.0 1.0
O3B B:ADP303 2.3 46.9 0.5
O1A B:ADP303 2.6 41.8 0.5
CD B:GLU124 3.1 19.7 1.0
PB B:ADP303 3.2 46.9 0.5
O1B B:ADP303 3.3 47.4 0.5
MG B:MG301 3.3 19.9 1.0
OE1 B:GLU124 3.3 19.2 1.0
C B:ALA104 3.3 16.8 1.0
PB B:ADP303 3.3 16.1 0.6
PA B:ADP303 3.4 14.5 0.6
O3A B:ADP303 3.6 44.2 0.5
O3A B:ADP303 3.6 15.4 0.6
PA B:ADP303 3.7 40.3 0.5
OE2 B:GLU172 3.8 25.0 1.0
NH2 B:ARG87 4.0 19.5 1.0
OE1 B:GLU120 4.2 25.0 1.0
N B:ALA104 4.2 16.4 1.0
CA B:ALA104 4.2 16.9 1.0
O1B B:ADP303 4.2 18.5 0.6
N B:GLY105 4.3 16.1 1.0
CA B:GLY105 4.4 17.1 1.0
O B:HOH422 4.4 22.9 1.0
O5' B:ADP303 4.4 17.6 0.6
CB B:ALA104 4.5 18.0 1.0
CG B:GLU124 4.5 19.8 1.0
O3B B:ADP303 4.5 19.0 0.6
O2A B:ADP303 4.5 13.8 0.6
OE1 B:GLN85 4.5 27.4 1.0
NE2 B:GLN85 4.6 24.9 1.0
O2B B:ADP303 4.6 47.7 0.5
O2A B:ADP303 4.7 40.5 0.5
O5' B:ADP303 4.9 36.2 0.5
O B:HOH534 4.9 27.4 1.0
CD B:GLU120 4.9 24.6 1.0
CD B:GLU172 4.9 25.1 1.0

Reference:

M.R.Mian, L.Liu, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp/Mg Bound) To Be Published.
Page generated: Thu Oct 31 22:27:24 2024

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