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Magnesium in PDB 9g6p: Xylose Isomerase Collected at 50C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds

Enzymatic activity of Xylose Isomerase Collected at 50C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds

All present enzymatic activity of Xylose Isomerase Collected at 50C 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 50C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds, PDB code: 9g6p 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 (%) 17.4 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Xylose Isomerase Collected at 50C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds (pdb code 9g6p). 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 50C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds, PDB code: 9g6p:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9g6p

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Magnesium binding site 1 out of 3 in the Xylose Isomerase Collected at 50C 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 50C 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:16.4
occ:0.96
 OE1 A:GLU217 2.0 21.0 1.0
OE2 A:GLU181 2.0 22.5 1.0
OD2 A:ASP287 2.0 22.7 1.0
O A:HOH515 2.0 22.4 0.3
O A:HOH532 2.0 20.4 0.3
O4 A:GLO402 2.0 23.0 0.4
OD2 A:ASP245 2.1 20.6 1.0
O2 A:GLO402 2.3 20.3 0.4
O4 A:GLC401 2.4 22.2 0.2
O3 A:GLC401 2.6 20.9 0.2
CD A:GLU181 3.0 22.5 1.0
C3 A:GLC401 3.0 20.8 0.2
CG A:ASP287 3.1 19.5 1.0
C4 A:GLO402 3.2 23.1 0.4
CD A:GLU217 3.2 15.1 1.0
C4 A:GLC401 3.2 22.9 0.2
CG A:ASP245 3.2 17.6 1.0
OE1 A:GLU181 3.3 22.0 1.0
C2 A:GLO402 3.4 22.3 0.4
MG A:MG404 3.5 32.2 1.0
O3 A:GLO402 3.5 22.2 0.4
C3 A:GLO402 3.6 19.3 0.4
CB A:ASP287 3.6 16.1 1.0
O A:HOH518 3.7 37.1 1.0
O A:HOH549 3.8 24.8 0.3
CB A:ASP245 3.8 14.6 1.0
O A:HOH512 4.0 19.9 1.0
OE2 A:GLU217 4.0 19.1 1.0
CE1 A:HIS220 4.1 16.4 1.0
CG A:GLU217 4.2 14.8 1.0
OD1 A:ASP287 4.2 18.2 1.0
CB A:GLU217 4.2 15.1 1.0
OD1 A:ASP245 4.3 18.3 1.0
CG A:GLU181 4.3 15.0 1.0
C5 A:GLO402 4.4 19.1 0.4
C5 A:GLC401 4.5 22.2 0.2
C2 A:GLC401 4.6 22.2 0.2
NE2 A:HIS220 4.6 19.7 1.0
C1 A:GLO402 4.7 18.0 0.4
O1 A:GLO402 4.8 17.8 0.4
C6 A:GLO402 4.9 22.1 0.4
ND1 A:HIS220 4.9 17.7 1.0
ND2 A:ASN215 4.9 16.1 1.0
MG A:MG405 5.0 20.5 1.0

Magnesium binding site 2 out of 3 in 9g6p

Go back to Magnesium Binding Sites List in 9g6p
Magnesium binding site 2 out of 3 in the Xylose Isomerase Collected at 50C 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 50C 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:32.2
occ:0.96
 MG A:MG405 1.7 20.5 1.0
O A:HOH512 1.8 19.9 1.0
O2 A:GLO402 2.2 20.3 0.4
NE2 A:HIS220 2.2 19.7 1.0
O1 A:GLO402 2.3 17.8 0.4
OE2 A:GLU217 2.3 19.1 1.0
O A:HOH532 2.4 20.4 0.3
O3 A:GLC401 2.6 20.9 0.2
OE1 A:GLU217 2.7 21.0 1.0
CE1 A:HIS220 2.8 16.4 1.0
CD A:GLU217 2.8 15.1 1.0
O A:HOH637 2.8 21.0 0.3
OD2 A:ASP255 3.0 26.8 1.0
C1 A:GLO402 3.1 18.0 0.4
C2 A:GLO402 3.1 22.3 0.4
CD2 A:HIS220 3.4 16.0 1.0
MG A:MG403 3.5 16.4 1.0
OD1 A:ASP257 3.6 20.4 1.0
OD2 A:ASP287 3.6 22.7 1.0
C3 A:GLC401 3.6 20.8 0.2
O2 A:GLC401 3.8 19.0 0.2
OD2 A:ASP257 3.9 20.9 1.0
CG A:ASP255 3.9 23.9 1.0
ND1 A:HIS220 4.0 17.7 1.0
O3 A:GLO402 4.1 22.2 0.4
OD1 A:ASP255 4.1 23.5 1.0
CG A:ASP257 4.2 19.5 1.0
C3 A:GLO402 4.2 19.3 0.4
C2 A:GLC401 4.3 22.2 0.2
OE2 A:GLU181 4.3 22.5 1.0
CG A:GLU217 4.3 14.8 1.0
CG A:HIS220 4.3 12.7 1.0
CG A:ASP287 4.4 19.5 1.0
O A:HOH549 4.4 24.8 0.3
O4 A:GLO402 4.6 23.0 0.4
ND2 A:ASN247 4.8 16.4 1.0
OD1 A:ASP287 4.8 18.2 1.0
C4 A:GLC401 4.9 22.9 0.2
CE A:LYS183 4.9 18.8 1.0
CB A:GLU217 4.9 15.1 1.0
NZ A:LYS183 5.0 21.5 1.0

Magnesium binding site 3 out of 3 in 9g6p

Go back to Magnesium Binding Sites List in 9g6p
Magnesium binding site 3 out of 3 in the Xylose Isomerase Collected at 50C 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 50C 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:20.5
occ:0.96
 MG A:MG404 1.7 32.2 1.0
OD2 A:ASP255 1.9 26.8 1.0
OE2 A:GLU217 2.0 19.1 1.0
OD1 A:ASP257 2.3 20.4 1.0
O A:HOH512 2.3 19.9 1.0
OD1 A:ASP255 2.4 23.5 1.0
CG A:ASP255 2.5 23.9 1.0
NE2 A:HIS220 2.5 19.7 1.0
CD2 A:HIS220 3.1 16.0 1.0
CD A:GLU217 3.1 15.1 1.0
CG A:ASP257 3.1 19.5 1.0
O1 A:GLO402 3.3 17.8 0.4
OD2 A:ASP257 3.3 20.9 1.0
O A:HOH637 3.5 21.0 0.3
CE1 A:HIS220 3.6 16.4 1.0
OE1 A:GLU217 3.6 21.0 1.0
O2 A:GLO402 3.9 20.3 0.4
CB A:ASP255 4.0 20.7 1.0
ND2 A:ASN247 4.0 16.4 1.0
O A:HOH589 4.2 19.4 1.0
O A:HOH532 4.2 20.4 0.3
CG A:HIS220 4.3 12.7 1.0
O3 A:GLC401 4.4 20.9 0.2
CG A:GLU217 4.4 14.8 1.0
C1 A:GLO402 4.4 18.0 0.4
ND1 A:HIS220 4.6 17.7 1.0
O A:HOH644 4.6 33.8 1.0
CB A:ASP257 4.6 14.9 1.0
CE A:LYS183 4.7 18.8 1.0
C2 A:GLO402 4.8 22.3 0.4
NZ A:LYS183 4.8 21.5 1.0
OD2 A:ASP287 4.9 22.7 1.0
MG A:MG403 5.0 16.4 1.0
CA A:ASP255 5.0 14.3 1.0
CA A:ASP257 5.0 15.8 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 02:55:36 2025

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