Magnesium in PDB 6irk: Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography

All present enzymatic activity of Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography:
5.3.1.5;

The structure of Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography, PDB code: 6irk was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.01 / 1.75
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.050, 99.000, 101.920, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography (pdb code 6irk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography, PDB code: 6irk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:34.6 occ:1.00 OE2 A:GLU217 1.9 34.8 1.0 OE2 A:GLU181 1.9 56.0 1.0 OD2 A:ASP287 2.1 36.6 1.0 OD2 A:ASP245 2.3 33.6 1.0 CD A:GLU181 2.9 42.4 1.0 CG A:ASP287 3.1 33.7 1.0 CD A:GLU217 3.1 29.9 1.0 OE1 A:GLU181 3.3 37.0 1.0 HB3 A:ASP287 3.3 33.3 1.0 CG A:ASP245 3.4 34.7 1.0 HB2 A:ASP287 3.4 33.3 1.0 O A:HOH525 3.4 43.9 1.0 HB2 A:GLU217 3.4 37.2 1.0 CB A:ASP287 3.5 27.8 1.0 HB3 A:ASP245 3.6 32.6 1.0 HE1 A:HIS220 3.7 34.2 1.0 CB A:ASP245 3.8 27.1 1.0 HB2 A:ASP245 3.8 32.6 1.0 OE1 A:GLU217 3.9 35.0 1.0 O A:HOH671 4.0 36.1 1.0 CG A:GLU217 4.1 29.3 1.0 CE1 A:HIS220 4.1 28.5 1.0 OD1 A:ASP287 4.2 29.8 1.0 CB A:GLU217 4.2 31.0 1.0 CG A:GLU181 4.3 29.3 1.0 HG3 A:GLU217 4.3 35.2 1.0 HG3 A:GLU181 4.4 35.2 1.0 OD1 A:ASP245 4.4 32.5 1.0 HD21 A:ASN215 4.5 38.5 1.0 HG2 A:GLU181 4.5 35.2 1.0 NE2 A:HIS220 4.5 31.5 1.0 HB3 A:GLU217 4.6 37.2 1.0 HZ2 A:TRP16 4.7 37.3 1.0 HD22 A:ASN215 4.8 38.5 1.0 ND1 A:HIS220 4.9 30.3 1.0 ND2 A:ASN215 4.9 32.1 1.0 MG A:MG402 4.9 27.3 1.0 HG2 A:GLU217 4.9 35.2 1.0 CA A:ASP287 5.0 26.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glucose Isomerase By Fixed-Target Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:27.3 occ:1.00 O A:HOH671 2.1 36.1 1.0 OE1 A:GLU217 2.1 35.0 1.0 OD2 A:ASP255 2.2 40.7 1.0 OD1 A:ASP257 2.2 34.4 1.0 OD1 A:ASP255 2.4 36.2 1.0 NE2 A:HIS220 2.6 31.5 1.0 CG A:ASP255 2.6 38.0 1.0 HD2 A:HIS220 3.0 34.2 1.0 CD2 A:HIS220 3.1 28.5 1.0 CD A:GLU217 3.2 29.9 1.0 CG A:ASP257 3.2 34.7 1.0 HD21 A:ASN247 3.3 39.0 1.0 OD2 A:ASP257 3.4 40.8 1.0 O A:HOH677 3.6 41.6 1.0 OE2 A:GLU217 3.7 34.8 1.0 CE1 A:HIS220 3.7 28.5 1.0 HD22 A:ASN247 3.8 39.0 1.0 ND2 A:ASN247 3.9 32.5 1.0 HE3 A:LYS183 4.0 37.6 1.0 CB A:ASP255 4.1 30.7 1.0 HE1 A:HIS220 4.1 34.2 1.0 O A:HOH530 4.2 33.1 1.0 HZ2 A:LYS183 4.2 40.3 1.0 HG2 A:GLU217 4.2 35.2 1.0 CG A:GLU217 4.4 29.3 1.0 CG A:HIS220 4.4 27.6 1.0 HB2 A:ASP255 4.4 36.9 1.0 OD2 A:ASP287 4.5 36.6 1.0 HB3 A:ASP255 4.5 36.9 1.0 HA A:ASP257 4.5 32.6 1.0 CB A:ASP257 4.6 31.6 1.0 O A:HOH533 4.6 60.2 1.0 H A:ASP257 4.6 32.0 1.0 HZ1 A:LYS183 4.6 40.3 1.0 ND1 A:HIS220 4.6 30.3 1.0 NZ A:LYS183 4.7 33.5 1.0 CE A:LYS183 4.7 31.3 1.0 HD2 A:LYS183 4.9 35.2 1.0 MG A:MG401 4.9 34.6 1.0 CA A:ASP257 4.9 27.1 1.0 HA A:ASP255 5.0 31.8 1.0 HG3 A:GLU217 5.0 35.2 1.0 HA3 A:GLY219 5.0 32.8 1.0

D.Lee, S.Baek, J.Park, K.Lee, J.Kim, S.J.Lee, W.K.Chung, J.L.Lee, Y.Cho, K.H.Nam. Nylon Mesh-Based Sample Holder For Fixed-Target Serial Femtosecond Crystallography. Sci Rep V. 9 6971 2019.
ISSN: ESSN 2045-2322
PubMed: 31061502
DOI: 10.1038/S41598-019-43485-Z