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Magnesium in PDB 9duf: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn Bound)

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

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

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn Bound), PDB code: 9duf 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) 48.67 / 1.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.374, 79.575, 91.903, 90, 90, 90
R / Rfree (%) 14.2 / 16.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn Bound) (pdb code 9duf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn Bound), PDB code: 9duf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 9duf

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Magnesium binding site 1 out of 5 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn 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 (Fmn Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:28.3
occ:1.00
 O A:HOH470 2.0 25.7 1.0
O A:HOH573 2.1 41.8 1.0
OE2 A:GLU116 2.1 26.1 1.0
O A:HOH426 2.1 29.7 1.0
OE2 A:GLU164 2.2 39.0 1.0
OE1 A:GLU112 2.3 26.6 1.0
CD A:GLU116 3.1 25.3 1.0
CD A:GLU164 3.1 40.1 1.0
CD A:GLU112 3.2 25.6 1.0
OE1 A:GLU164 3.4 39.9 1.0
O A:HOH401 3.4 20.3 1.0
CG A:GLU116 3.4 23.6 1.0
OE2 A:GLU112 3.6 26.8 1.0
O A:HOH420 3.6 26.4 1.0
O A:ALA96 3.9 20.6 1.0
OE1 A:GLU116 4.2 25.6 1.0
OE1 A:GLU115 4.5 36.6 1.0
CG A:GLU164 4.5 40.7 1.0
CG A:GLU112 4.6 23.8 1.0
O A:HOH544 4.6 34.2 1.0
CB A:GLU112 4.9 22.4 1.0
CB A:GLU116 4.9 23.8 1.0
CD1 A:ILE166 5.0 24.8 1.0

Magnesium binding site 2 out of 5 in 9duf

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Magnesium binding site 2 out of 5 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn 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 (Fmn Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:36.7
occ:1.00
 O A:HOH406 2.1 34.3 1.0
O A:HOH401 2.5 20.3 1.0
OE1 A:GLU116 2.8 25.6 1.0
NE2 A:GLN77 3.0 26.2 1.0
O A:MET94 3.3 18.3 1.0
CD A:GLU116 3.4 25.3 1.0
OE2 A:GLU116 3.4 26.1 1.0
N A:ALA96 3.5 17.6 1.0
O A:HOH521 3.5 31.4 1.0
NH2 A:ARG79 3.6 25.1 1.0
O A:HOH420 3.6 26.4 1.0
O A:ALA96 3.7 20.6 1.0
CG2 A:VAL75 4.0 18.2 1.0
CD A:GLN77 4.1 22.6 1.0
C A:VAL95 4.2 16.7 1.0
CA A:VAL95 4.2 18.1 1.0
CB A:ALA96 4.2 18.3 1.0
CA A:ALA96 4.3 18.6 1.0
C A:MET94 4.3 16.8 1.0
O A:HOH542 4.4 43.8 1.0
C A:ALA96 4.4 19.6 1.0
OE1 A:GLN77 4.5 23.6 1.0
OE1 A:GLU93 4.5 26.8 1.0
N A:VAL95 4.7 16.8 1.0
CG A:GLU116 4.8 23.6 1.0
O A:HOH470 4.8 25.7 1.0
CZ A:ARG79 4.9 20.9 1.0

Magnesium binding site 3 out of 5 in 9duf

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Magnesium binding site 3 out of 5 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn 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 (Fmn Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:19.8
occ:1.00
 O B:HOH568 2.0 26.1 1.0
OE1 B:GLU112 2.1 18.5 1.0
O B:HOH419 2.1 20.8 1.0
O B:HOH472 2.1 19.5 1.0
OE2 B:GLU116 2.1 20.8 1.0
OE2 B:GLU164 2.1 27.4 1.0
CD B:GLU112 3.1 18.3 1.0
CD B:GLU116 3.1 19.4 1.0
CD B:GLU164 3.2 27.6 1.0
OE2 B:GLU112 3.4 19.7 1.0
MG B:MG303 3.5 25.2 1.0
OE1 B:GLU164 3.5 26.0 1.0
CG B:GLU116 3.5 17.8 1.0
O B:HOH483 3.7 21.1 1.0
O B:ALA96 3.9 15.5 1.0
OE1 B:GLU116 4.2 21.1 1.0
OE1 B:GLU115 4.3 24.6 1.0
CG B:GLU112 4.4 17.4 1.0
CG B:GLU164 4.5 29.5 1.0
O B:HOH544 4.6 25.8 1.0
CB B:GLU112 4.7 16.5 1.0
O B:HOH468 4.7 25.9 1.0
CB B:GLU116 5.0 17.0 1.0

Magnesium binding site 4 out of 5 in 9duf

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Magnesium binding site 4 out of 5 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn 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 (Fmn Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:25.2
occ:1.00
 O B:HOH562 2.2 24.9 1.0
OE2 B:GLU116 2.3 20.8 1.0
O B:HOH483 2.3 21.1 1.0
O B:ALA96 2.3 15.5 1.0
O B:HOH472 2.3 19.5 1.0
O B:HOH437 2.4 24.6 1.0
CD B:GLU116 3.1 19.4 1.0
OE1 B:GLU116 3.3 21.1 1.0
C B:ALA96 3.4 13.7 1.0
MG B:MG302 3.5 19.8 1.0
NH2 B:ARG79 3.8 25.3 1.0
O B:HOH557 3.8 41.7 1.0
OE2 B:GLU164 3.9 27.4 1.0
N B:ALA96 4.0 13.0 1.0
O B:HOH412 4.1 28.0 1.0
OE1 B:GLU112 4.2 18.5 1.0
CA B:ALA96 4.2 13.7 1.0
NE2 B:GLN77 4.4 25.0 1.0
N B:GLY97 4.4 14.2 1.0
CB B:ALA96 4.5 14.6 1.0
CA B:GLY97 4.5 15.3 1.0
OE1 B:GLN77 4.5 22.9 1.0
CG B:GLU116 4.5 17.8 1.0
CD B:GLU112 4.8 18.3 1.0
CZ B:ARG79 4.9 21.4 1.0
CD B:GLN77 4.9 22.4 1.0
O B:HOH568 4.9 26.1 1.0
O B:HOH544 4.9 25.8 1.0

Magnesium binding site 5 out of 5 in 9duf

Go back to Magnesium Binding Sites List in 9duf
Magnesium binding site 5 out of 5 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn Bound)


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 (Fmn Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:74.0
occ:1.00
 O A:HOH613 2.1 36.3 1.0
O B:HOH407 2.2 27.0 1.0
O B:HOH524 2.3 29.9 1.0
OE2 B:GLU17 4.1 23.6 1.0
O A:HOH427 4.2 24.0 1.0
O B:LYS13 4.3 20.3 1.0
OD1 B:ASN14 4.4 32.8 1.0
OE1 B:GLU17 4.6 21.2 1.0
CD B:GLU17 4.8 20.6 1.0
CA B:ASN14 4.9 21.4 1.0

Reference:

P.Enayati, L.Liu, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fmn Bound) To Be Published.
Page generated: Thu Oct 31 22:27:25 2024

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