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Magnesium in PDB 6rnf: Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint

Enzymatic activity of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint

All present enzymatic activity of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint:
5.3.1.5;

Protein crystallography data

The structure of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint, PDB code: 6rnf was solved by P.Mehrabi, E.C.Schulz, R.J.D.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.72 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.600, 99.400, 87.600, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint (pdb code 6rnf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint, PDB code: 6rnf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6rnf

Go back to Magnesium Binding Sites List in 6rnf
Magnesium binding site 1 out of 2 in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:18.0
occ:1.00
 OE1 A:GLU181 1.9 16.3 1.0
OD2 A:ASP245 2.1 16.9 1.0
OD2 A:ASP287 2.1 20.3 1.0
OE1 A:GLU217 2.1 16.2 1.0
O4 A:GLC403 2.1 20.7 0.6
O3 A:GLC403 2.3 15.8 0.6
CD A:GLU181 2.9 19.0 1.0
C4 A:GLC403 3.0 20.2 0.6
C3 A:GLC403 3.0 21.8 0.6
CG A:ASP287 3.2 16.9 1.0
OE2 A:GLU181 3.2 20.8 1.0
CG A:ASP245 3.3 17.5 1.0
CD A:GLU217 3.3 15.8 1.0
CB A:ASP287 3.7 15.4 1.0
O A:HOH549 3.8 19.1 1.0
O A:HOH529 3.9 25.4 1.0
CB A:ASP245 4.0 14.2 1.0
CE1 A:HIS220 4.1 15.8 1.0
CG A:GLU217 4.1 12.1 1.0
CB A:GLU217 4.2 12.3 1.0
CG A:GLU181 4.2 14.4 1.0
OE2 A:GLU217 4.3 14.7 1.0
OD1 A:ASP245 4.3 16.8 1.0
OD1 A:ASP287 4.3 17.4 1.0
C5 A:GLC403 4.3 23.9 0.6
C2 A:GLC403 4.4 24.4 0.6
NE2 A:HIS220 4.7 13.1 1.0
ND1 A:HIS220 4.8 11.7 1.0
MG A:MG402 4.8 14.8 1.0
ND2 A:ASN215 4.9 17.9 1.0
C6 A:GLC403 5.0 23.3 0.6

Magnesium binding site 2 out of 2 in 6rnf

Go back to Magnesium Binding Sites List in 6rnf
Magnesium binding site 2 out of 2 in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 30 Ms Timepoint within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:14.8
occ:1.00
 OE2 A:GLU217 2.1 14.7 1.0
O A:HOH549 2.1 19.1 1.0
OD2 A:ASP255 2.2 15.9 1.0
OD1 A:ASP257 2.2 14.7 1.0
OD1 A:ASP255 2.4 13.6 1.0
NE2 A:HIS220 2.4 13.1 1.0
CG A:ASP255 2.6 13.3 1.0
CD A:GLU217 3.0 15.8 1.0
CD2 A:HIS220 3.1 13.1 1.0
CG A:ASP257 3.1 18.7 1.0
OE1 A:GLU217 3.3 16.2 1.0
OD2 A:ASP257 3.3 18.8 1.0
CE1 A:HIS220 3.4 15.8 1.0
O A:HOH511 3.8 24.9 1.0
ND2 A:ASN247 4.0 12.8 1.0
O A:HOH599 4.1 14.5 1.0
CB A:ASP255 4.1 13.2 1.0
O3 A:GLC403 4.2 15.8 0.6
CG A:HIS220 4.2 12.2 1.0
CG A:GLU217 4.4 12.1 1.0
ND1 A:HIS220 4.4 11.7 1.0
O A:HOH604 4.5 33.0 1.0
CB A:ASP257 4.5 14.1 1.0
OD2 A:ASP287 4.6 20.3 1.0
MG A:MG401 4.8 18.0 1.0
CE A:LYS183 4.8 15.5 1.0
CA A:ASP257 4.9 13.7 1.0
NZ A:LYS183 5.0 16.2 1.0
N A:ASP257 5.0 14.2 1.0

Reference:

P.Mehrabi, E.C.Schulz, M.Agthe, S.Horrell, G.Bourenkov, D.Von Stetten, J.P.Leimkohl, H.Schikora, T.R.Schneider, A.R.Pearson, F.Tellkamp, R.J.D.Miller. Liquid Application Method For Time-Resolved Analyses By Serial Synchrotron Crystallography. Nat.Methods V. 16 979 2019.
ISSN: ESSN 1548-7105
PubMed: 31527838
DOI: 10.1038/S41592-019-0553-1
Page generated: Tue Oct 1 17:26:42 2024

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