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Magnesium in PDB 9dtc: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)

Enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)

All present enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2):
3.6.1.13;

Protein crystallography data

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2), PDB code: 9dtc 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) 48.71 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.426, 79.749, 91.982, 90, 90, 90
R / Rfree (%) 16.2 / 18.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2) (pdb code 9dtc). 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, Orthrhombic FORM2), PDB code: 9dtc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9dtc

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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, Orthrhombic FORM2)


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, Orthrhombic FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:24.3
occ:1.00
OE2 A:GLU116 2.1 19.3 1.0
O A:HOH505 2.2 35.0 1.0
O A:HOH406 2.2 22.6 1.0
O A:HOH476 2.2 32.4 1.0
OE1 A:GLU112 2.2 26.0 1.0
OE2 A:GLU164 2.3 30.4 1.0
CD A:GLU116 3.0 19.0 1.0
CD A:GLU112 3.2 24.9 1.0
CD A:GLU164 3.3 34.5 1.0
MG A:MG304 3.3 20.9 1.0
CG A:GLU116 3.4 17.9 1.0
O A:HOH411 3.4 30.8 1.0
OE2 A:GLU112 3.6 25.7 1.0
OE1 A:GLU164 3.6 29.4 1.0
O A:HOH401 3.7 20.3 1.0
O1A A:AR6301 3.7 80.9 0.8
O A:ALA96 4.0 17.9 1.0
OE1 A:GLU116 4.2 19.8 1.0
OE1 A:GLU115 4.3 33.6 1.0
CG A:GLU112 4.5 21.3 1.0
CG A:GLU164 4.6 27.3 1.0
O1P A:AMP302 4.8 34.9 0.2
O A:HOH432 4.8 29.1 0.8
CB A:GLU112 4.8 18.9 1.0
CB A:GLU116 4.9 18.1 1.0
O1B A:AR6301 4.9 32.4 0.8
O2P A:AMP302 4.9 36.6 0.2
O A:HOH428 5.0 26.2 1.0
CD1 A:ILE166 5.0 19.1 1.0

Magnesium binding site 2 out of 4 in 9dtc

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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, Orthrhombic FORM2)


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, Orthrhombic FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:20.9
occ:1.00
O2B A:AR6301 2.1 17.5 0.8
OE2 A:GLU116 2.2 19.3 1.0
O A:HOH401 2.2 20.3 1.0
O A:HOH406 2.2 22.6 1.0
O A:HOH428 2.2 26.2 1.0
O A:ALA96 2.3 17.9 1.0
O1A A:AR6301 3.1 80.9 0.8
CD A:GLU116 3.1 19.0 1.0
PB A:AR6301 3.3 24.7 0.8
O2P A:AMP302 3.3 36.6 0.2
MG A:MG303 3.3 24.3 1.0
OE1 A:GLU116 3.4 19.8 1.0
C A:ALA96 3.4 16.3 1.0
O1B A:AR6301 3.6 32.4 0.8
OE2 A:GLU164 3.8 30.4 1.0
NH2 A:ARG79 4.0 17.3 1.0
O3A A:AR6301 4.1 40.4 0.8
PA A:AR6301 4.2 103.8 0.8
N A:ALA96 4.2 15.5 1.0
CA A:ALA96 4.3 15.3 1.0
OE1 A:GLU112 4.3 26.0 1.0
N A:GLY97 4.4 15.8 1.0
O A:HOH410 4.4 24.3 1.0
CA A:GLY97 4.4 16.3 1.0
NE2 A:GLN77 4.5 22.3 1.0
CG A:GLU116 4.5 17.9 1.0
CB A:ALA96 4.6 15.1 1.0
OE1 A:GLN77 4.6 22.5 1.0
P A:AMP302 4.6 25.0 0.2
O5D A:AR6301 4.6 22.6 0.8
O1P A:AMP302 4.8 34.9 0.2
C5D A:AR6301 4.9 27.2 0.8
O A:HOH505 4.9 35.0 1.0
CD A:GLU112 4.9 24.9 1.0
CD A:GLN77 5.0 19.8 1.0

Magnesium binding site 3 out of 4 in 9dtc

Go back to Magnesium Binding Sites List in 9dtc
Magnesium binding site 3 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)


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, Orthrhombic FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:21.1
occ:1.00
O1B B:AR6301 2.2 11.6 0.6
OE2 B:GLU116 2.2 16.1 1.0
O B:HOH437 2.2 20.7 1.0
O B:ALA96 2.3 15.7 1.0
O B:HOH463 2.4 25.6 1.0
O B:HOH401 2.4 17.7 1.0
O3P B:AMP302 3.0 108.8 0.4
CD B:GLU116 3.1 16.2 1.0
OE1 B:GLU116 3.3 18.3 1.0
PB B:AR6301 3.4 23.1 0.6
MG B:MG304 3.4 20.6 1.0
C B:ALA96 3.5 14.0 1.0
O3A B:AR6301 3.5 17.8 0.6
OE2 B:GLU164 4.0 30.4 1.0
NH2 B:ARG79 4.0 18.3 1.0
P B:AMP302 4.0 31.0 0.4
O B:HOH414 4.1 29.8 1.0
N B:ALA96 4.1 13.4 1.0
O2P B:AMP302 4.2 36.7 0.4
CA B:ALA96 4.3 13.5 1.0
OE1 B:GLU112 4.3 20.2 1.0
NE2 B:GLN77 4.4 21.6 1.0
C5D B:AR6301 4.4 23.0 0.6
O2B B:AR6301 4.4 27.3 0.6
N B:GLY97 4.4 14.2 1.0
O5D B:AR6301 4.5 33.1 0.6
OE1 B:GLN77 4.5 23.4 1.0
CG B:GLU116 4.5 16.2 1.0
CB B:ALA96 4.6 15.1 1.0
CA B:GLY97 4.6 14.7 1.0
O1P B:AMP302 4.7 26.6 0.4
O4D B:AR6301 4.8 131.6 0.6
CD B:GLU112 4.9 19.5 1.0
CD B:GLN77 4.9 19.8 1.0
O B:HOH560 4.9 27.7 1.0
CZ B:ARG79 5.0 19.4 1.0

Magnesium binding site 4 out of 4 in 9dtc

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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, Orthrhombic FORM2)


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, Orthrhombic FORM2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:20.6
occ:1.00
O B:HOH421 2.1 23.6 1.0
O B:HOH560 2.1 27.7 1.0
OE1 B:GLU112 2.1 20.2 1.0
OE2 B:GLU116 2.1 16.1 1.0
O B:HOH401 2.2 17.7 1.0
OE2 B:GLU164 2.3 30.4 1.0
CD B:GLU116 3.1 16.2 1.0
CD B:GLU112 3.1 19.5 1.0
CD B:GLU164 3.3 27.9 1.0
MG B:MG303 3.4 21.1 1.0
OE2 B:GLU112 3.4 22.6 1.0
CG B:GLU116 3.4 16.2 1.0
OE1 B:GLU164 3.6 25.8 1.0
O B:HOH412 3.7 32.6 1.0
O B:HOH437 3.7 20.7 1.0
O3P B:AMP302 4.0 108.8 0.4
O B:ALA96 4.0 15.7 1.0
O B:HOH477 4.2 43.3 1.0
OE1 B:GLU116 4.2 18.3 1.0
OE1 B:GLU115 4.3 26.7 1.0
CG B:GLU112 4.4 17.0 1.0
O3A B:AR6301 4.5 17.8 0.6
CG B:GLU164 4.7 28.5 1.0
O2P B:AMP302 4.7 36.7 0.4
O B:HOH482 4.7 27.3 1.0
CB B:GLU112 4.8 16.4 1.0
P B:AMP302 4.9 31.0 0.4
CB B:GLU116 4.9 14.6 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 Ribose Bound, Orthrhombic FORM2) To Be Published.
Page generated: Thu Oct 31 22:27:19 2024

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