Magnesium in PDB 6x7e: Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site

Protein crystallography data

The structure of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site, PDB code: 6x7e was solved by F.A.Tezcan, A.Kakkis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.70 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.090, 78.003, 50.189, 90.00, 106.48, 90.00
R / Rfree (%) 16.2 / 21.3

Other elements in 6x7e:

The structure of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site also contains other interesting chemical elements:

Cobalt (Co) 1 atom
Iron (Fe) 3 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site (pdb code 6x7e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site, PDB code: 6x7e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6x7e

Go back to Magnesium Binding Sites List in 6x7e
Magnesium binding site 1 out of 6 in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:57.1
occ:1.00
MG A:MG206 2.1 46.2 1.0
MG A:MG207 2.3 52.0 1.0
O A:HOH355 3.6 68.1 1.0
OD1 A:ASP12 4.4 23.8 1.0
OE1 A:GLU8 4.5 31.8 0.4
OD2 A:ASP12 4.7 24.5 1.0
O A:HOH301 4.7 28.4 1.0
CG A:ASP12 5.0 22.2 1.0

Magnesium binding site 2 out of 6 in 6x7e

Go back to Magnesium Binding Sites List in 6x7e
Magnesium binding site 2 out of 6 in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:46.2
occ:1.00
MG A:MG205 2.1 57.1 1.0
OD1 A:ASP12 3.9 23.8 1.0
NZ A:LYS15 4.2 52.4 1.0
MG A:MG207 4.3 52.0 1.0
O A:HOH301 4.6 28.4 1.0
CG A:ASP12 4.7 22.2 1.0
OD2 A:ASP12 4.9 24.5 1.0

Magnesium binding site 3 out of 6 in 6x7e

Go back to Magnesium Binding Sites List in 6x7e
Magnesium binding site 3 out of 6 in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:52.0
occ:1.00
O A:HOH355 1.9 68.1 1.0
MG A:MG205 2.3 57.1 1.0
OE1 A:GLU8 4.1 31.8 0.4
MG A:MG206 4.3 46.2 1.0

Magnesium binding site 4 out of 6 in 6x7e

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Magnesium binding site 4 out of 6 in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:36.3
occ:1.00
OD2 B:ASP2 1.9 46.1 1.0
O B:HOH352 2.6 43.0 1.0
CG B:ASP2 2.7 39.2 1.0
OD1 B:ASP2 3.0 52.2 1.0
MG B:MG204 3.9 39.8 1.0
CB B:ASP2 4.0 25.9 1.0
O B:HOH310 4.9 31.2 1.0

Magnesium binding site 5 out of 6 in 6x7e

Go back to Magnesium Binding Sites List in 6x7e
Magnesium binding site 5 out of 6 in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:32.6
occ:1.00
OD1 B:ASP5 2.0 30.8 1.0
MG B:MG204 2.3 39.8 1.0
CG B:ASP5 3.0 24.9 1.0
OD2 B:ASP5 3.2 32.3 1.0
O B:HOH352 4.1 43.0 1.0
CB B:ASP5 4.4 18.1 1.0
OE2 B:GLU8 4.7 54.0 1.0
CA B:ASP5 4.7 21.7 1.0
N B:ASP5 4.8 13.1 1.0
OD2 B:ASP2 5.0 46.1 1.0

Magnesium binding site 6 out of 6 in 6x7e

Go back to Magnesium Binding Sites List in 6x7e
Magnesium binding site 6 out of 6 in the Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Bound Structure of An Engineered Protein Trimer, TRICYT3, with Delta Isomerism at the Hexahistidine Coordination Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:39.8
occ:1.00
MG B:MG203 2.3 32.6 1.0
OD2 B:ASP5 2.4 32.3 1.0
O B:HOH352 2.6 43.0 1.0
OD2 B:ASP2 3.0 46.1 1.0
OD1 B:ASP5 3.1 30.8 1.0
CG B:ASP5 3.1 24.9 1.0
MG B:MG202 3.9 36.3 1.0
O B:HOH310 3.9 31.2 1.0
CG B:ASP2 4.0 39.2 1.0
CB B:ASP2 4.5 25.9 1.0
CB B:ASP5 4.5 18.1 1.0
OD1 B:ASP2 4.9 52.2 1.0

Reference:

F.A.Tezcan, A.Kakkis, D.Gagnon, J.Esselborn, R.D.Britt. Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32830423
DOI: 10.1002/ANIE.202009226
Page generated: Tue Dec 15 01:41:06 2020

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