Magnesium in PDB 5thk: Crystal Structure of A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp

Protein crystallography data

The structure of Crystal Structure of A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp, PDB code: 5thk was solved by Seattle Structural 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) 45.19 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.540, 102.440, 122.250, 90.00, 97.28, 90.00
R / Rfree (%) 14 / 16.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp (pdb code 5thk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp, PDB code: 5thk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5thk

Go back to Magnesium Binding Sites List in 5thk
Magnesium binding site 1 out of 2 in the Crystal Structure of A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp


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 A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:14.1
occ:1.00
O C:GLY30 2.2 12.0 1.0
OH2 C:1PE303 2.3 12.2 0.4
OH2 C:1PE303 2.4 10.8 0.6
OH5 C:1PE303 2.5 7.5 0.6
OH4 C:1PE303 2.6 13.9 0.6
OH3 C:1PE303 2.6 13.9 0.6
OH3 C:1PE303 2.6 13.1 0.4
OH5 C:1PE303 2.7 21.9 0.4
OH7 C:1PE303 2.9 26.1 0.6
OH4 C:1PE303 2.9 14.7 0.4
OH6 C:1PE303 3.2 24.6 0.6
C13 C:1PE303 3.2 13.7 0.4
C14 C:1PE303 3.3 9.2 0.6
C12 C:1PE303 3.3 12.9 0.4
C23 C:1PE303 3.3 15.1 0.4
C12 C:1PE303 3.3 13.6 0.6
C24 C:1PE303 3.4 11.4 0.6
C14 C:1PE303 3.4 21.1 0.4
C22 C:1PE303 3.4 12.8 0.4
C25 C:1PE303 3.5 15.1 0.6
C C:GLY30 3.5 11.0 1.0
C24 C:1PE303 3.5 15.9 0.4
C22 C:1PE303 3.5 13.9 0.6
C13 C:1PE303 3.5 12.5 0.6
C23 C:1PE303 3.5 13.4 0.6
C15 C:1PE303 3.6 18.8 0.6
C26 C:1PE303 3.6 25.3 0.6
C25 C:1PE303 3.6 23.1 0.4
C16 C:1PE303 3.8 24.3 0.6
C15 C:1PE303 4.0 23.6 0.4
CA C:HIS31 4.1 11.1 1.0
N C:HIS31 4.2 11.6 1.0
C C:HIS31 4.5 10.9 1.0
CA C:GLY30 4.5 11.2 1.0
OH6 C:1PE303 4.7 21.5 0.4
N C:GLY32 4.7 11.1 1.0

Magnesium binding site 2 out of 2 in 5thk

Go back to Magnesium Binding Sites List in 5thk
Magnesium binding site 2 out of 2 in the Crystal Structure of A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp


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 A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:13.4
occ:1.00
O G:HOH470 3.0 17.4 1.0
O G:HOH641 3.2 50.3 1.0
NZ G:LYS18 3.2 13.4 1.0
ND2 G:ASN19 3.3 9.3 1.0
CE G:LYS18 3.8 11.3 1.0
CD G:LYS18 3.8 11.3 1.0
CB G:PRO195 3.9 9.8 1.0
CG G:PRO195 4.2 11.0 1.0
CG G:ASN19 4.4 8.5 1.0
O G:HOH437 4.4 23.7 1.0
OD1 G:ASN19 4.6 11.7 1.0
O G:HOH404 4.7 36.8 1.0
O2A G:NAP301 4.7 9.9 1.0
CD G:PRO195 4.8 10.9 1.0
O1A G:NAP301 4.9 10.2 1.0
CG G:LYS18 5.0 11.2 1.0

Reference:

D.M.Dranow, S.J.Mayclin, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Putative Dehydrogenase From Burkholderia Cenocepacia with Bound Nadp To Be Published.
Page generated: Mon Dec 14 21:12:05 2020

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