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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy