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Magnesium in PDB 8awv: Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS

Enzymatic activity of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS

All present enzymatic activity of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS:
5.3.1.5;

Protein crystallography data

The structure of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS, PDB code: 8awv was solved by P.Mehrabi, S.Sung, D.Von Stetten, A.Prester, C.E.Hatton, S.Kleine-Doepke, A.Berkes, G.Gore, J.P.Leimkohl, H.Schikora, M.Kollewe, H.Rohde, M.Wilmanns, F.Tellkamp, E.C.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.19 / 2.08
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.656, 98.675, 102.376, 90, 90, 90
R / Rfree (%) 14.8 / 18.7

Other elements in 8awv:

The structure of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS (pdb code 8awv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS, PDB code: 8awv:

Magnesium binding site 1 out of 1 in 8awv

Go back to Magnesium Binding Sites List in 8awv
Magnesium binding site 1 out of 1 in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Xylose Isomerase with Glucose at 500MS within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:26.1
occ:1.00
 OE2 A:GLU181 1.9 25.7 1.0
OD2 A:ASP287 2.0 26.3 1.0
OE1 A:GLU217 2.2 18.4 1.0
OD2 A:ASP245 2.2 27.0 1.0
O3 A:GLC401 2.4 33.2 0.7
O4 A:GLC401 2.5 26.0 0.7
CD A:GLU181 2.8 25.7 1.0
C3 A:GLC401 3.0 27.3 0.7
CG A:ASP287 3.1 22.5 1.0
OE1 A:GLU181 3.1 23.0 1.0
C4 A:GLC401 3.2 30.1 0.7
CG A:ASP245 3.4 22.8 1.0
CD A:GLU217 3.4 16.9 1.0
O A:HOH567 3.6 23.7 1.0
CB A:ASP287 3.7 17.6 1.0
O A:HOH632 4.0 33.7 1.0
CB A:ASP245 4.0 12.7 1.0
CE1 A:HIS220 4.1 18.3 1.0
CG A:GLU181 4.1 21.9 1.0
OD1 A:ASP287 4.2 25.1 1.0
CG A:GLU217 4.2 14.2 1.0
CB A:GLU217 4.2 15.1 1.0
OE2 A:GLU217 4.3 17.9 1.0
OD1 A:ASP245 4.4 28.3 1.0
C2 A:GLC401 4.5 31.7 0.7
C5 A:GLC401 4.6 28.2 0.7
NE2 A:HIS220 4.6 16.2 1.0
ND1 A:HIS220 4.8 15.9 1.0
MN A:MN402 4.8 22.4 1.0
ND2 A:ASN215 4.9 19.1 1.0

Reference:

P.Mehrabi, S.Sung, D.Von Stetten, A.Prester, C.E.Hatton, S.Kleine-Dopke, A.Berkes, G.Gore, J.P.Leimkohl, H.Schikora, M.Kollewe, H.Rohde, M.Wilmanns, F.Tellkamp, E.C.Schulz. Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger Simplifies Time-Resolved Crystallography. Nat Commun V. 14 2365 2023.
ISSN: ESSN 2041-1723
PubMed: 37185266
DOI: 10.1038/S41467-023-37834-W
Page generated: Thu Oct 3 19:05:12 2024

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