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Magnesium in PDB 9g6n: Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds

Enzymatic activity of Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds

All present enzymatic activity of Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds:
5.3.1.5;

Protein crystallography data

The structure of Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds, PDB code: 9g6n was solved by E.C.Schulz, A.Prester, D.V.Stetten, G.Gore, C.E.Hatton, K.Bartels, J.P.Leimkohl, H.Schikora, H.M.Ginn, F.Tellkamp, P.Mehrabi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.49 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.2, 103.05, 99.25, 90, 90, 90
R / Rfree (%) 16 / 20

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds (pdb code 9g6n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds, PDB code: 9g6n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9g6n

Go back to Magnesium Binding Sites List in 9g6n
Magnesium binding site 1 out of 3 in the Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:13.9
occ:0.95
 O A:HOH527 1.9 15.6 0.3
OE2 A:GLU181 2.0 17.2 1.0
OE1 A:GLU217 2.0 17.4 1.0
OD2 A:ASP287 2.0 19.7 1.0
O4 A:GLO402 2.1 18.8 0.4
OD2 A:ASP245 2.1 16.9 1.0
O A:HOH511 2.1 18.4 0.3
O2 A:GLO402 2.2 17.5 0.4
O4 A:GLC401 2.3 18.7 0.3
O3 A:GLC401 2.4 18.7 0.3
CD A:GLU181 3.0 21.5 1.0
C3 A:GLC401 3.0 17.5 0.3
C4 A:GLC401 3.1 19.5 0.3
CG A:ASP287 3.2 14.9 1.0
CD A:GLU217 3.2 11.8 1.0
C4 A:GLO402 3.3 19.7 0.4
CG A:ASP245 3.3 14.4 1.0
OE1 A:GLU181 3.3 20.3 1.0
C2 A:GLO402 3.3 18.6 0.4
O3 A:GLO402 3.5 20.2 0.4
MG A:MG404 3.5 30.4 0.9
C3 A:GLO402 3.6 12.9 0.4
CB A:ASP287 3.7 12.8 1.0
O A:HOH707 3.8 16.5 0.3
CB A:ASP245 3.9 14.5 1.0
O A:HOH506 3.9 34.7 1.0
O A:HOH526 3.9 17.8 1.0
OE2 A:GLU217 4.0 16.3 1.0
CE1 A:HIS220 4.1 15.3 1.0
CG A:GLU217 4.2 9.9 1.0
CB A:GLU217 4.2 12.4 1.0
OD1 A:ASP287 4.2 16.3 1.0
CG A:GLU181 4.3 13.3 1.0
OD1 A:ASP245 4.3 14.2 1.0
C5 A:GLC401 4.4 19.8 0.3
C5 A:GLO402 4.5 15.1 0.4
C2 A:GLC401 4.5 18.2 0.3
NE2 A:HIS220 4.6 17.1 1.0
C1 A:GLO402 4.6 18.8 0.4
O1 A:GLO402 4.8 10.1 0.4
ND1 A:HIS220 4.8 14.3 1.0
O A:HOH692 4.9 19.0 0.3
ND2 A:ASN215 4.9 18.0 1.0
MG A:MG405 4.9 17.9 1.0
C6 A:GLO402 5.0 23.1 0.4

Magnesium binding site 2 out of 3 in 9g6n

Go back to Magnesium Binding Sites List in 9g6n
Magnesium binding site 2 out of 3 in the Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:30.4
occ:0.95
 O A:HOH526 1.7 17.8 1.0
MG A:MG405 1.8 17.9 1.0
O2 A:GLO402 2.1 17.5 0.4
NE2 A:HIS220 2.2 17.1 1.0
O1 A:GLO402 2.3 10.1 0.4
O A:HOH527 2.4 15.6 0.3
OE2 A:GLU217 2.4 16.3 1.0
O3 A:GLC401 2.5 18.7 0.3
CE1 A:HIS220 2.7 15.3 1.0
OE1 A:GLU217 2.7 17.4 1.0
CD A:GLU217 2.9 11.8 1.0
O A:HOH568 2.9 13.2 0.3
C2 A:GLO402 3.0 18.6 0.4
OD2 A:ASP255 3.0 22.8 1.0
C1 A:GLO402 3.1 18.8 0.4
CD2 A:HIS220 3.4 13.2 1.0
MG A:MG403 3.5 13.9 0.9
C3 A:GLC401 3.6 17.5 0.3
OD1 A:ASP257 3.7 18.2 1.0
OD2 A:ASP287 3.7 19.7 1.0
O2 A:GLC401 3.9 14.0 0.3
ND1 A:HIS220 3.9 14.3 1.0
CG A:ASP255 3.9 24.2 1.0
OD2 A:ASP257 4.0 18.8 1.0
OD1 A:ASP255 4.0 20.6 1.0
O A:HOH707 4.1 16.5 0.3
O3 A:GLO402 4.1 20.2 0.4
C3 A:GLO402 4.2 12.9 0.4
OE2 A:GLU181 4.2 17.2 1.0
C2 A:GLC401 4.2 18.2 0.3
CG A:ASP257 4.2 15.9 1.0
CG A:HIS220 4.3 11.2 1.0
CG A:GLU217 4.3 9.9 1.0
CG A:ASP287 4.5 14.9 1.0
O4 A:GLO402 4.7 18.8 0.4
C4 A:GLC401 4.8 19.5 0.3
CE A:LYS183 4.8 14.2 1.0
NZ A:LYS183 4.8 18.7 1.0
ND2 A:ASN247 4.9 14.1 1.0
OD1 A:ASP287 4.9 16.3 1.0
O4 A:GLC401 5.0 18.7 0.3
CB A:GLU217 5.0 12.4 1.0
O A:HOH509 5.0 39.9 1.0
O A:HOH511 5.0 18.4 0.3

Magnesium binding site 3 out of 3 in 9g6n

Go back to Magnesium Binding Sites List in 9g6n
Magnesium binding site 3 out of 3 in the Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Xylose Isomerase Collected at 40C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:17.9
occ:1.00
 MG A:MG404 1.8 30.4 0.9
OE2 A:GLU217 2.0 16.3 1.0
OD2 A:ASP255 2.0 22.8 1.0
OD1 A:ASP257 2.3 18.2 1.0
O A:HOH526 2.3 17.8 1.0
OD1 A:ASP255 2.4 20.6 1.0
NE2 A:HIS220 2.4 17.1 1.0
CG A:ASP255 2.5 24.2 1.0
CD2 A:HIS220 3.1 13.2 1.0
CD A:GLU217 3.1 11.8 1.0
CG A:ASP257 3.2 15.9 1.0
OD2 A:ASP257 3.3 18.8 1.0
O1 A:GLO402 3.4 10.1 0.4
CE1 A:HIS220 3.6 15.3 1.0
OE1 A:GLU217 3.6 17.4 1.0
O A:HOH568 3.7 13.2 0.3
O2 A:GLO402 3.9 17.5 0.4
CB A:ASP255 4.0 14.4 1.0
ND2 A:ASN247 4.0 14.1 1.0
O A:HOH575 4.1 15.7 1.0
O A:HOH527 4.1 15.6 0.3
CG A:HIS220 4.3 11.2 1.0
O3 A:GLC401 4.3 18.7 0.3
CG A:GLU217 4.3 9.9 1.0
ND1 A:HIS220 4.5 14.3 1.0
C1 A:GLO402 4.5 18.8 0.4
CB A:ASP257 4.6 10.5 1.0
O A:HOH545 4.6 31.4 1.0
CE A:LYS183 4.8 14.2 1.0
C2 A:GLO402 4.8 18.6 0.4
NZ A:LYS183 4.8 18.7 1.0
OD2 A:ASP287 4.9 19.7 1.0
MG A:MG403 4.9 13.9 0.9
CA A:ASP255 5.0 11.9 1.0
CA A:ASP257 5.0 12.1 1.0

Reference:

E.C.Schulz, A.Prester, D.Von Stetten, G.Gore, C.E.Hatton, K.Bartels, J.P.Leimkohl, H.Schikora, H.M.Ginn, F.Tellkamp, P.Mehrabi. Probing the Modulation of Enzyme Kinetics By Multi-Temperature, Time-Resolved Serial Crystallography. Nat Commun V. 16 6553 2025.
ISSN: ESSN 2041-1723
PubMed: 40670369
DOI: 10.1038/S41467-025-61631-2
Page generated: Sat Aug 16 02:53:56 2025

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