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Magnesium in PDB 6rnd: Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 15 Ms Timepoint

Enzymatic activity of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 15 Ms Timepoint

All present enzymatic activity of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 15 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 15 Ms Timepoint, PDB code: 6rnd 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) 68.53 / 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 (%) 16.4 / 21.1

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 15 Ms Timepoint (pdb code 6rnd). 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 15 Ms Timepoint, PDB code: 6rnd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6rnd

Go back to Magnesium Binding Sites List in 6rnd
Magnesium binding site 1 out of 2 in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 15 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 15 Ms Timepoint within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:20.4
occ:1.00
 OE1 A:GLU181 1.9 16.2 1.0
OD2 A:ASP245 2.1 17.4 1.0
OD2 A:ASP287 2.1 18.5 1.0
OE1 A:GLU217 2.1 14.4 1.0
O4 A:GLC403 2.2 21.9 0.6
O3 A:GLC403 2.3 20.0 0.6
CD A:GLU181 2.8 17.6 1.0
C4 A:GLC403 2.9 25.1 0.6
C3 A:GLC403 2.9 27.1 0.6
OE2 A:GLU181 3.2 19.9 1.0
CG A:ASP287 3.2 19.2 1.0
CG A:ASP245 3.3 18.2 1.0
CD A:GLU217 3.3 15.9 1.0
CB A:ASP287 3.8 15.7 1.0
O A:HOH627 3.8 19.8 1.0
O A:HOH513 3.9 28.1 1.0
CB A:ASP245 4.0 14.4 1.0
CE1 A:HIS220 4.1 13.8 1.0
CG A:GLU181 4.1 14.1 1.0
CG A:GLU217 4.2 12.1 1.0
CB A:GLU217 4.2 11.6 1.0
OD1 A:ASP245 4.2 16.6 1.0
OE2 A:GLU217 4.2 12.2 1.0
OD1 A:ASP287 4.3 19.6 1.0
C5 A:GLC403 4.3 29.0 0.6
C2 A:GLC403 4.3 32.8 0.6
NE2 A:HIS220 4.7 14.1 1.0
ND1 A:HIS220 4.8 10.8 1.0
MG A:MG402 4.9 15.0 1.0
ND2 A:ASN215 4.9 14.5 1.0
O2 A:GLC403 5.0 40.0 0.6
C6 A:GLC403 5.0 30.3 0.6

Magnesium binding site 2 out of 2 in 6rnd

Go back to Magnesium Binding Sites List in 6rnd
Magnesium binding site 2 out of 2 in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Xylose Isomerase 15 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 15 Ms Timepoint within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:15.0
occ:1.00
 OE2 A:GLU217 2.1 12.2 1.0
OD1 A:ASP257 2.2 15.7 1.0
O A:HOH627 2.2 19.8 1.0
OD2 A:ASP255 2.2 15.7 1.0
OD1 A:ASP255 2.3 14.6 1.0
NE2 A:HIS220 2.4 14.1 1.0
CG A:ASP255 2.6 14.0 1.0
CD A:GLU217 3.0 15.9 1.0
CD2 A:HIS220 3.1 12.1 1.0
CG A:ASP257 3.1 18.2 1.0
OE1 A:GLU217 3.3 14.4 1.0
OD2 A:ASP257 3.4 20.0 1.0
CE1 A:HIS220 3.4 13.8 1.0
O A:HOH522 3.8 25.9 1.0
ND2 A:ASN247 4.1 13.5 1.0
O A:HOH605 4.1 14.1 1.0
CB A:ASP255 4.1 13.1 1.0
CG A:HIS220 4.3 11.1 1.0
O3 A:GLC403 4.3 20.0 0.6
ND1 A:HIS220 4.4 10.8 1.0
CG A:GLU217 4.4 12.1 1.0
CB A:ASP257 4.5 14.3 1.0
O A:HOH648 4.7 33.8 1.0
OD2 A:ASP287 4.7 18.5 1.0
CE A:LYS183 4.8 15.5 1.0
MG A:MG401 4.9 20.4 1.0
CA A:ASP257 4.9 14.5 1.0
NZ A:LYS183 4.9 18.6 1.0
N A:ASP257 4.9 13.8 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 17:26:37 2024

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