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Magnesium in PDB 9g6l: Xylose Isomerase Collected at 20C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds

Enzymatic activity of Xylose Isomerase Collected at 20C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds

All present enzymatic activity of Xylose Isomerase Collected at 20C 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 20C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds, PDB code: 9g6l 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 (%) 16.6 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Xylose Isomerase Collected at 20C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds (pdb code 9g6l). 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 20C Using Time-Resolved Serial Synchrotron Crystallography with Glucose at 60 Seconds, PDB code: 9g6l:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9g6l

Go back to Magnesium Binding Sites List in 9g6l
Magnesium binding site 1 out of 3 in the Xylose Isomerase Collected at 20C 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 20C 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:10.4
occ:0.93
 O A:HOH517 1.9 11.2 0.3
OE2 A:GLU181 2.0 14.8 1.0
OE1 A:GLU217 2.1 13.9 1.0
OD2 A:ASP287 2.1 17.5 1.0
O A:HOH516 2.1 17.4 0.3
OD2 A:ASP245 2.1 12.7 1.0
O4 A:GLO402 2.1 17.6 0.3
O4 A:GLC401 2.2 17.6 0.4
O2 A:GLO402 2.2 12.8 0.3
O3 A:GLC401 2.4 13.2 0.4
CD A:GLU181 3.0 16.6 1.0
C3 A:GLC401 3.0 14.8 0.4
C4 A:GLC401 3.0 13.4 0.4
CG A:ASP287 3.2 12.8 1.0
CG A:ASP245 3.3 13.1 1.0
OE1 A:GLU181 3.3 15.9 1.0
CD A:GLU217 3.3 11.4 1.0
C4 A:GLO402 3.3 14.7 0.3
C2 A:GLO402 3.4 13.0 0.3
O A:HOH744 3.4 16.4 0.3
MG A:MG404 3.4 27.6 0.9
O3 A:GLO402 3.6 16.8 0.3
C3 A:GLO402 3.6 13.6 0.3
CB A:ASP287 3.7 9.0 1.0
O A:HOH536 3.9 13.1 1.0
CB A:ASP245 3.9 10.6 1.0
O A:HOH510 3.9 22.9 1.0
CE1 A:HIS220 4.1 11.2 1.0
OE2 A:GLU217 4.1 13.1 1.0
CG A:GLU217 4.2 7.7 1.0
CB A:GLU217 4.2 7.1 1.0
OD1 A:ASP287 4.2 11.6 1.0
CG A:GLU181 4.3 11.8 1.0
OD1 A:ASP245 4.3 12.3 1.0
C5 A:GLC401 4.3 12.7 0.4
C5 A:GLO402 4.5 12.7 0.3
C2 A:GLC401 4.5 11.5 0.4
NE2 A:HIS220 4.6 12.9 1.0
C1 A:GLO402 4.7 16.4 0.3
ND1 A:HIS220 4.8 11.0 1.0
C6 A:GLC401 4.9 14.3 0.4
MG A:MG405 4.9 11.7 1.0
O1 A:GLO402 4.9 7.4 0.3
C6 A:GLO402 4.9 15.8 0.3

Magnesium binding site 2 out of 3 in 9g6l

Go back to Magnesium Binding Sites List in 9g6l
Magnesium binding site 2 out of 3 in the Xylose Isomerase Collected at 20C 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 20C 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:27.6
occ:0.93
 O A:HOH536 1.6 13.1 1.0
MG A:MG405 1.8 11.7 1.0
O2 A:GLO402 2.1 12.8 0.3
O A:HOH517 2.2 11.2 0.3
NE2 A:HIS220 2.2 12.9 1.0
O3 A:GLC401 2.5 13.2 0.4
O1 A:GLO402 2.5 7.4 0.3
OE2 A:GLU217 2.5 13.1 1.0
OE1 A:GLU217 2.6 13.9 1.0
CE1 A:HIS220 2.7 11.2 1.0
CD A:GLU217 2.8 11.4 1.0
OD2 A:ASP255 3.0 16.3 1.0
C2 A:GLO402 3.0 13.0 0.3
O A:HOH567 3.1 5.7 0.3
C1 A:GLO402 3.1 16.4 0.3
MG A:MG403 3.4 10.4 0.9
CD2 A:HIS220 3.4 8.4 1.0
C3 A:GLC401 3.5 14.8 0.4
OD2 A:ASP287 3.6 17.5 1.0
OD1 A:ASP257 3.6 12.2 1.0
CG A:ASP255 3.9 13.5 1.0
ND1 A:HIS220 3.9 11.0 1.0
OD1 A:ASP255 3.9 13.6 1.0
O A:HOH744 4.0 16.4 0.3
O2 A:GLC401 4.0 10.6 0.4
OD2 A:ASP257 4.0 15.5 1.0
O3 A:GLO402 4.1 16.8 0.3
OE2 A:GLU181 4.2 14.8 1.0
C3 A:GLO402 4.2 13.6 0.3
CG A:ASP257 4.2 13.1 1.0
C2 A:GLC401 4.2 11.5 0.4
CG A:HIS220 4.3 6.4 1.0
CG A:GLU217 4.3 7.7 1.0
CG A:ASP287 4.4 12.8 1.0
O4 A:GLO402 4.6 17.6 0.3
C4 A:GLC401 4.7 13.4 0.4
O A:HOH516 4.8 17.4 0.3
O4 A:GLC401 4.8 17.6 0.4
OD1 A:ASP287 4.9 11.6 1.0
ND2 A:ASN247 4.9 11.5 1.0
CB A:GLU217 4.9 7.1 1.0
CE A:LYS183 5.0 11.7 1.0

Magnesium binding site 3 out of 3 in 9g6l

Go back to Magnesium Binding Sites List in 9g6l
Magnesium binding site 3 out of 3 in the Xylose Isomerase Collected at 20C 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 20C 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:11.7
occ:1.00
 MG A:MG404 1.8 27.6 0.9
OE2 A:GLU217 2.0 13.1 1.0
OD2 A:ASP255 2.0 16.3 1.0
OD1 A:ASP255 2.2 13.6 1.0
OD1 A:ASP257 2.2 12.2 1.0
O A:HOH536 2.3 13.1 1.0
CG A:ASP255 2.4 13.5 1.0
NE2 A:HIS220 2.5 12.9 1.0
CD A:GLU217 3.0 11.4 1.0
CD2 A:HIS220 3.1 8.4 1.0
CG A:ASP257 3.1 13.1 1.0
OD2 A:ASP257 3.3 15.5 1.0
OE1 A:GLU217 3.5 13.9 1.0
CE1 A:HIS220 3.6 11.2 1.0
O1 A:GLO402 3.6 7.4 0.3
O A:HOH567 3.8 5.7 0.3
O2 A:GLO402 3.9 12.8 0.3
ND2 A:ASN247 4.0 11.5 1.0
CB A:ASP255 4.0 10.8 1.0
O A:HOH517 4.0 11.2 0.3
O A:HOH570 4.1 10.5 1.0
O3 A:GLC401 4.3 13.2 0.4
CG A:HIS220 4.3 6.4 1.0
CG A:GLU217 4.3 7.7 1.0
ND1 A:HIS220 4.5 11.0 1.0
O A:HOH712 4.5 27.8 1.0
CB A:ASP257 4.5 7.8 1.0
C1 A:GLO402 4.6 16.4 0.3
OD2 A:ASP287 4.8 17.5 1.0
C2 A:GLO402 4.8 13.0 0.3
CE A:LYS183 4.8 11.7 1.0
CA A:ASP257 4.9 9.9 1.0
MG A:MG403 4.9 10.4 0.9
CA A:ASP255 4.9 8.5 1.0
N A:ASP257 5.0 9.3 1.0
NZ A:LYS183 5.0 14.6 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 02:52:23 2025

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