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Magnesium in PDB 8awy: Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS

Enzymatic activity of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS

All present enzymatic activity of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS:
5.3.1.5;

Protein crystallography data

The structure of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS, PDB code: 8awy 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) 71.27 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.7, 102.35, 99.3, 90, 90, 90
R / Rfree (%) 17.4 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS (pdb code 8awy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS, PDB code: 8awy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8awy

Go back to Magnesium Binding Sites List in 8awy
Magnesium binding site 1 out of 3 in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS


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, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.4
occ:1.00
 OE2 A:GLU181 1.9 11.6 1.0
OD2 A:ASP287 1.9 12.7 1.0
OE1 A:GLU217 2.1 10.4 1.0
OD2 A:ASP245 2.1 11.5 1.0
O6 A:BU9403 2.3 19.8 1.0
CD A:GLU181 2.8 12.9 1.0
CG A:ASP287 3.0 10.9 1.0
OE1 A:GLU181 3.2 13.8 1.0
CG A:ASP245 3.3 10.1 1.0
CD A:GLU217 3.3 9.4 1.0
CB A:ASP287 3.5 10.2 1.0
C05 A:BU9403 3.5 25.7 1.0
C01 A:BU9403 3.7 21.5 1.0
O A:HOH808 3.7 13.0 1.0
O A:HOH557 3.8 15.1 1.0
CB A:ASP245 3.9 9.1 1.0
OD1 A:ASP287 4.1 11.2 1.0
CG A:GLU217 4.1 8.4 1.0
CE1 A:HIS220 4.1 8.2 1.0
CB A:GLU217 4.1 8.6 1.0
CG A:GLU181 4.2 10.5 1.0
OE2 A:GLU217 4.2 10.7 1.0
OD1 A:ASP245 4.3 10.3 1.0
C04 A:BU9403 4.5 22.0 1.0
NE2 A:HIS220 4.7 10.7 1.0
ND1 A:HIS220 4.8 7.8 1.0
O A:HOH503 4.8 2.9 1.0
CA A:ASP287 5.0 8.9 1.0

Magnesium binding site 2 out of 3 in 8awy

Go back to Magnesium Binding Sites List in 8awy
Magnesium binding site 2 out of 3 in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:80.3
occ:1.00
 CG A:HIS54 2.2 11.5 1.0
ND1 A:HIS54 2.3 13.0 1.0
CD2 A:HIS54 2.5 11.4 1.0
CE1 A:HIS54 2.7 12.8 1.0
NE2 A:HIS54 2.7 12.9 1.0
O A:HOH640 2.9 16.8 1.0
CB A:HIS54 3.0 10.7 1.0
CZ A:PHE94 3.1 13.0 1.0
ND2 A:ASN92 3.1 12.9 1.0
CG A:ASN92 3.7 11.6 1.0
CB A:ASN92 3.7 10.1 1.0
CE1 A:PHE94 3.9 13.7 1.0
OD1 A:ASP57 3.9 13.9 1.0
CE2 A:PHE94 3.9 11.7 1.0
OD2 A:ASP57 4.1 11.1 1.0
CG A:ASP57 4.3 12.1 1.0
CA A:ASN92 4.3 9.8 1.0
CA A:HIS54 4.4 10.0 1.0
O A:HOH921 4.5 44.3 1.0
OD1 A:ASN92 4.6 11.5 1.0
N A:ASN92 4.8 9.9 1.0
N A:HIS54 4.9 10.1 1.0

Magnesium binding site 3 out of 3 in 8awy

Go back to Magnesium Binding Sites List in 8awy
Magnesium binding site 3 out of 3 in the Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger, Serial Measurement Xylose Isomerase with 2,3-Butanediol at 50MS within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:41.6
occ:1.00
 O A:HOH912 1.9 32.5 1.0
O A:HOH625 2.7 29.4 1.0
OE1 A:GLU210 2.8 18.8 1.0
O A:HOH948 2.8 46.0 1.0
O A:HOH933 3.0 36.9 1.0
O A:HOH955 3.0 38.5 1.0
O A:HOH560 3.0 24.4 1.0
O A:HOH582 3.4 31.1 1.0
CD A:GLU210 3.5 20.4 1.0
OE2 A:GLU210 3.5 25.2 1.0
O A:GLU207 3.7 16.6 1.0
CA A:ARG208 3.8 13.6 1.0
CD A:PRO209 3.9 15.8 1.0
O A:HOH976 4.2 35.0 1.0
N A:PRO209 4.4 13.8 1.0
C A:ARG208 4.4 13.0 1.0
CB A:ARG208 4.4 15.5 1.0
C A:GLU207 4.6 16.1 1.0
N A:ARG208 4.7 13.3 1.0
CG A:ARG208 4.7 17.9 1.0
O A:HOH565 4.9 33.6 1.0
CG A:GLU210 4.9 20.9 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 19:05:45 2024

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