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Magnesium in PDB 6ybo: Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.

Enzymatic activity of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.

All present enzymatic activity of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.:
5.3.1.5;

Protein crystallography data

The structure of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip., PDB code: 6ybo was solved by J.A.Gavira, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.12 / 1.06
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.940, 99.370, 103.040, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 13.1

Other elements in 6ybo:

The structure of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip. also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip. (pdb code 6ybo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip., PDB code: 6ybo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ybo

Go back to Magnesium Binding Sites List in 6ybo
Magnesium binding site 1 out of 2 in the Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.0
occ:1.00
OE2 A:GLU181 2.0 18.0 0.6
OE2 A:GLU181 2.0 15.0 0.4
OD2 A:ASP245 2.1 15.4 1.0
OE1 A:GLU217 2.1 13.1 1.0
OD2 A:ASP287 2.1 16.4 1.0
O A:HOH513 2.3 28.0 1.0
O A:HOH509 2.3 32.2 1.0
CD A:GLU181 2.9 15.7 0.6
CD A:GLU181 2.9 14.7 0.4
OE1 A:GLU181 3.2 16.3 0.4
OE1 A:GLU181 3.2 18.6 0.6
CG A:ASP287 3.2 13.2 1.0
CG A:ASP245 3.3 12.9 1.0
CD A:GLU217 3.3 11.1 1.0
CB A:ASP287 3.7 12.5 1.0
O A:HOH627 3.9 14.6 1.0
CB A:ASP245 3.9 12.2 1.0
O A:HOH718 3.9 27.7 1.0
CG A:GLU217 4.1 10.8 1.0
CE1 A:HIS220 4.2 11.2 1.0
CB A:GLU217 4.2 10.0 1.0
CG A:GLU181 4.2 13.9 0.6
OD1 A:ASP245 4.2 13.9 1.0
OE2 A:GLU217 4.2 11.6 1.0
OD1 A:ASP287 4.3 13.2 1.0
CG A:GLU181 4.3 13.3 0.4
NE2 A:HIS220 4.8 11.5 1.0
ND2 A:ASN215 4.8 14.9 1.0
ND1 A:HIS220 4.8 11.2 1.0
MG A:MG402 4.9 7.0 1.0

Magnesium binding site 2 out of 2 in 6ybo

Go back to Magnesium Binding Sites List in 6ybo
Magnesium binding site 2 out of 2 in the Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:7.0
occ:1.00
OE2 A:GLU217 2.0 11.6 1.0
O A:HOH627 2.2 14.6 1.0
OD1 A:ASP257 2.2 12.4 1.0
OD2 A:ASP255 2.2 13.7 1.0
OD1 A:ASP255 2.3 11.7 1.0
NE2 A:HIS220 2.4 11.5 1.0
CG A:ASP255 2.6 12.1 1.0
CD A:GLU217 3.0 11.1 1.0
CD2 A:HIS220 3.1 10.9 1.0
CG A:ASP257 3.1 12.7 1.0
OE1 A:GLU217 3.3 13.1 1.0
OD2 A:ASP257 3.3 15.9 1.0
CE1 A:HIS220 3.4 11.2 1.0
O A:HOH693 3.8 25.8 1.0
ND2 A:ASN247 4.0 11.6 1.0
O A:HOH597 4.1 12.2 1.0
CB A:ASP255 4.1 11.3 1.0
CG A:HIS220 4.3 10.1 1.0
CG A:GLU217 4.3 10.8 1.0
ND1 A:HIS220 4.4 11.2 1.0
CB A:ASP257 4.5 12.2 1.0
O A:HOH513 4.6 28.0 1.0
O A:HOH577 4.6 41.3 1.0
OD2 A:ASP287 4.6 16.4 1.0
CE A:LYS183 4.8 12.8 1.0
NZ A:LYS183 4.8 16.6 1.0
MG A:MG401 4.9 13.0 1.0
CA A:ASP257 4.9 10.9 1.0
N A:ASP257 5.0 10.3 1.0

Reference:

J.A.Gavira, I.Rodriguez-Ruiz, S.Martinez-Rodriguez, S.Basu, S.Teychene, A.A.Mccarthy, C.Mueller-Dieckman. Attaining Atomic Resolution From in Situ Data Collection at Room Temperature Using Counter-Diffusion-Based Low-Cost Microchips. Acta Crystallogr D Struct V. 76 751 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32744257
DOI: 10.1107/S2059798320008475
Page generated: Wed Oct 2 00:16:17 2024

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