Magnesium in PDB 9du9: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Gdp/Mg Bound)

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

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

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Gdp/Mg Bound), PDB code: 9du9 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) 48.69 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.437, 79.552, 91.796, 90, 90, 90
R / Rfree (%) 15.7 / 18.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Gdp/Mg Bound) (pdb code 9du9). 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 (Gdp/Mg Bound), PDB code: 9du9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9du9

Go back to Magnesium Binding Sites List in 9du9
Magnesium binding site 1 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Gdp/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 (Gdp/Mg Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:20.5
occ:1.00
 O A:HOH519 2.1 14.2 0.5
O3B A:GDP301 2.1 71.6 0.5
OE2 A:GLU124 2.2 15.6 1.0
O A:HOH406 2.2 22.1 1.0
O A:HOH402 2.2 21.2 1.0
O A:ALA104 2.2 12.7 1.0
O A:HOH449 2.3 9.1 0.5
O3B A:GDP301 2.5 64.7 0.5
CD A:GLU124 3.1 15.7 1.0
OE1 A:GLU124 3.3 16.4 1.0
C A:ALA104 3.4 11.1 1.0
MG A:MG303 3.4 16.1 1.0
PB A:GDP301 3.4 71.5 0.5
O2A A:GDP301 3.6 71.1 0.5
O1B A:GDP301 3.7 71.6 0.5
PB A:GDP301 3.9 64.9 0.5
OE2 A:GLU172 3.9 27.7 1.0
O2A A:GDP301 4.0 72.7 0.5
NH2 A:ARG87 4.0 21.9 1.0
N A:ALA104 4.1 9.9 1.0
OE1 A:GLU120 4.1 18.3 1.0
CA A:ALA104 4.2 11.1 1.0
O2B A:GDP301 4.2 65.5 0.5
O2B A:GDP301 4.2 71.7 0.5
O A:HOH401 4.3 21.0 1.0
N A:GLY105 4.4 11.8 1.0
NE2 A:GLN85 4.4 21.4 1.0
CB A:ALA104 4.5 11.2 1.0
CA A:GLY105 4.5 12.5 1.0
CG A:GLU124 4.5 15.1 1.0
O3A A:GDP301 4.5 71.8 0.5
OE1 A:GLN85 4.6 21.2 1.0
O3A A:GDP301 4.8 67.8 0.5
PA A:GDP301 4.8 70.3 0.5
CD A:GLU120 4.8 17.8 1.0
PA A:GDP301 4.8 72.2 0.5
O1B A:GDP301 4.9 63.3 0.5
CD A:GLN85 4.9 19.2 1.0
O A:HOH536 5.0 22.4 1.0
CZ A:ARG87 5.0 19.8 1.0

Magnesium binding site 2 out of 4 in 9du9

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

b:16.1
occ:1.00
 O A:HOH407 2.0 21.1 1.0
OE1 A:GLU120 2.1 18.3 1.0
O A:HOH536 2.1 22.4 1.0
O A:HOH449 2.1 9.1 0.5
OE2 A:GLU124 2.2 15.6 1.0
OE2 A:GLU172 2.2 27.7 1.0
O3B A:GDP301 2.7 64.7 0.5
CD A:GLU120 3.0 17.8 1.0
CD A:GLU124 3.1 15.7 1.0
CD A:GLU172 3.2 28.3 1.0
OE2 A:GLU120 3.3 18.7 1.0
MG A:MG302 3.4 20.5 1.0
CG A:GLU124 3.5 15.1 1.0
OE1 A:GLU172 3.6 26.5 1.0
O A:HOH402 3.7 21.2 1.0
PB A:GDP301 3.9 64.9 0.5
O A:ALA104 4.0 12.7 1.0
O1B A:GDP301 4.1 63.3 0.5
OE1 A:GLU123 4.2 24.7 1.0
OE1 A:GLU124 4.2 16.4 1.0
CG A:GLU120 4.4 16.6 1.0
O3A A:GDP301 4.4 67.8 0.5
O2A A:GDP301 4.5 71.1 0.5
CG A:GLU172 4.6 29.7 1.0
O A:HOH416 4.7 27.6 1.0
CB A:GLU120 4.7 15.3 1.0
C5' A:GDP301 4.8 69.7 0.5
O3B A:GDP301 4.8 71.6 0.5
O1B A:GDP301 4.9 71.6 0.5
O2A A:GDP301 4.9 72.7 0.5
CB A:GLU124 5.0 14.6 1.0
O A:HOH519 5.0 14.2 0.5

Magnesium binding site 3 out of 4 in 9du9

Go back to Magnesium Binding Sites List in 9du9
Magnesium binding site 3 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Gdp/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 (Gdp/Mg Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:20.9
occ:1.00
 O B:HOH411 2.0 13.9 0.5
O B:HOH446 2.0 25.0 1.0
OE1 B:GLU120 2.1 24.3 1.0
OE2 B:GLU124 2.1 19.5 1.0
O B:HOH514 2.2 34.4 1.0
OE2 B:GLU172 2.3 50.2 1.0
O3B B:GDP301 2.8 63.5 0.5
CD B:GLU124 3.1 18.5 1.0
CD B:GLU120 3.1 23.0 1.0
CD B:GLU172 3.3 50.7 1.0
MG B:MG303 3.4 25.9 1.0
CG B:GLU124 3.4 17.9 1.0
OE2 B:GLU120 3.4 23.7 1.0
OE1 B:GLU172 3.6 51.4 1.0
O B:HOH402 3.8 23.5 1.0
O B:ALA104 3.9 16.4 1.0
PB B:GDP301 4.0 62.8 0.5
O1B B:GDP301 4.0 62.5 0.5
OE1 B:GLU124 4.2 18.3 1.0
OE1 B:GLU123 4.3 28.1 1.0
CG B:GLU120 4.5 21.0 1.0
O5' B:GDP301 4.6 63.8 0.5
O2A B:GDP301 4.6 65.5 0.5
CG B:GLU172 4.7 49.4 1.0
O1B B:GDP301 4.7 65.8 0.5
O3B B:GDP301 4.7 65.4 0.5
O3A B:GDP301 4.8 63.9 0.5
O2A B:GDP301 4.8 65.8 0.5
CB B:GLU120 4.8 19.7 1.0
CB B:GLU124 4.9 17.9 1.0
C B:ALA104 5.0 15.4 1.0

Magnesium binding site 4 out of 4 in 9du9

Go back to Magnesium Binding Sites List in 9du9
Magnesium binding site 4 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Gdp/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 (Gdp/Mg Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:25.9
occ:1.00
 O3B B:GDP301 1.9 65.4 0.5
O B:HOH433 2.1 17.0 0.5
O B:HOH415 2.1 21.1 1.0
OE2 B:GLU124 2.2 19.5 1.0
O B:HOH402 2.2 23.5 1.0
O B:HOH411 2.3 13.9 0.5
O B:ALA104 2.3 16.4 1.0
O3B B:GDP301 2.5 63.5 0.5
CD B:GLU124 3.1 18.5 1.0
PB B:GDP301 3.2 65.5 0.5
O2A B:GDP301 3.3 65.8 0.5
OE1 B:GLU124 3.3 18.3 1.0
MG B:MG302 3.4 20.9 1.0
C B:ALA104 3.4 15.4 1.0
O1B B:GDP301 3.5 65.8 0.5
O2A B:GDP301 3.8 65.5 0.5
OE2 B:GLU172 3.9 50.2 1.0
PB B:GDP301 3.9 62.8 0.5
NH2 B:ARG87 4.0 17.7 1.0
O2B B:GDP301 4.1 65.5 0.5
N B:ALA104 4.1 14.2 1.0
CA B:ALA104 4.2 14.5 1.0
O2B B:GDP301 4.2 63.8 0.5
OE1 B:GLU120 4.3 24.3 1.0
O B:HOH418 4.3 41.1 1.0
NE2 B:GLN85 4.3 22.1 1.0
O3A B:GDP301 4.3 65.4 0.5
PA B:GDP301 4.4 65.0 0.5
N B:GLY105 4.4 16.3 1.0
CB B:ALA104 4.5 14.7 1.0
CG B:GLU124 4.5 17.9 1.0
OE1 B:GLN85 4.6 22.7 1.0
CA B:GLY105 4.6 16.9 1.0
O3A B:GDP301 4.7 63.9 0.5
PA B:GDP301 4.7 65.3 0.5
O5' B:GDP301 4.9 63.8 0.5
O B:HOH514 4.9 34.4 1.0
CD B:GLN85 4.9 20.3 1.0
O1B B:GDP301 4.9 62.5 0.5

Reference:

M.R.Mian, L.Liu, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Gdp/Mg Bound) To Be Published.
Page generated: Thu Oct 31 22:27:20 2024

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