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Magnesium in PDB 6v9k: Crystal Structure of the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme

Enzymatic activity of Crystal Structure of the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme

All present enzymatic activity of Crystal Structure of the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme:
2.7.3.9;

Protein crystallography data

The structure of Crystal Structure of the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme, PDB code: 6v9k was solved by C.E.Stewart Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.82 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.380, 69.530, 84.657, 90.00, 108.73, 90.00
R / Rfree (%) 16.1 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme (pdb code 6v9k). 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 the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme, PDB code: 6v9k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6v9k

Go back to Magnesium Binding Sites List in 6v9k
Magnesium binding site 1 out of 2 in the Crystal Structure of the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme


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 the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:36.5
occ:1.00
 O A:HOH709 2.0 24.3 1.0
O A:HOH710 2.0 27.0 1.0
OD2 A:ASP455 2.0 21.9 1.0
OE1 A:GLU431 2.1 28.1 1.0
O A:HOH838 2.2 20.7 1.0
O A:HOH767 2.2 30.5 1.0
CD A:GLU431 3.0 29.7 1.0
HH22 A:ARG358 3.0 43.3 0.6
CG A:ASP455 3.1 20.9 1.0
OE2 A:GLU431 3.3 30.2 1.0
HB3 A:ASP455 3.6 18.1 1.0
NH2 A:ARG358 3.6 36.1 0.6
CB A:ASP455 3.8 15.1 1.0
HH21 A:ARG358 3.8 48.6 0.4
HH21 A:ARG358 3.8 43.3 0.6
HB2 A:ASP455 3.8 18.1 1.0
OD1 A:ASP335 3.8 34.2 1.0
HE A:ARG358 3.9 41.3 0.4
HE1 A:MET429 4.0 68.5 1.0
OD2 A:ASP335 4.0 32.9 1.0
OD1 A:ASP455 4.1 21.3 1.0
HE2 A:TYR459 4.2 19.8 1.0
HE1 A:PHE354 4.2 22.9 0.5
HE3 A:MET429 4.2 68.5 1.0
HH12 A:ARG358 4.3 47.4 0.6
CG A:ASP335 4.4 29.4 1.0
CG A:GLU431 4.4 23.4 1.0
HZ A:PHE354 4.4 19.9 0.5
CZ A:ARG358 4.4 37.6 0.6
CE A:MET429 4.5 57.0 1.0
NH2 A:ARG358 4.6 40.5 0.4
HB2 A:GLU431 4.6 21.9 1.0
CE1 A:PHE354 4.6 19.1 0.5
HG3 A:GLU431 4.6 28.1 1.0
OH A:TYR459 4.6 17.1 1.0
NH1 A:ARG358 4.7 39.5 0.6
NE A:ARG358 4.7 34.4 0.4
SD A:MET392 4.7 34.8 1.0
CZ A:PHE354 4.7 16.6 0.5
HB2 A:PRO391 4.8 18.1 1.0
HE2 A:MET429 4.9 68.5 1.0
CE2 A:TYR459 4.9 16.5 1.0
CB A:GLU431 5.0 18.2 1.0

Magnesium binding site 2 out of 2 in 6v9k

Go back to Magnesium Binding Sites List in 6v9k
Magnesium binding site 2 out of 2 in the Crystal Structure of the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme


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 the Hybrid C-Terminal Domain of Enzyme I of the Bacterial Phosphotransferase System Formed By Hybridizing the Scaffold of the Escherichia Coli Enzyme with the Active Site Loops From the Thermoanaerobacter Tengcongensis Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:33.2
occ:1.00
 O B:HOH702 2.0 13.2 1.0
OD2 B:ASP455 2.0 25.9 1.0
OE1 B:GLU431 2.0 21.0 1.0
O B:HOH799 2.0 13.8 1.0
O B:HOH725 2.2 20.6 1.0
O B:HOH811 2.2 33.2 1.0
HH12 B:ARG358 2.9 57.6 1.0
CD B:GLU431 3.0 23.9 1.0
CG B:ASP455 3.1 28.0 1.0
OE2 B:GLU431 3.2 22.4 1.0
HB3 B:ASP455 3.5 25.0 1.0
NH1 B:ARG358 3.6 48.0 1.0
HE1 B:MET429 3.7 49.8 1.0
CB B:ASP455 3.7 20.8 1.0
HB2 B:ASP455 3.7 25.0 1.0
OD1 B:ASP335 3.7 33.0 1.0
HH22 B:ARG358 3.9 68.6 1.0
OD2 B:ASP335 4.0 30.5 1.0
HH11 B:ARG358 4.0 57.6 1.0
HG2 B:MET392 4.1 34.6 1.0
OD1 B:ASP455 4.1 29.1 1.0
HE2 B:TYR459 4.2 14.4 1.0
CG B:ASP335 4.3 31.5 1.0
HE3 B:MET429 4.3 49.8 1.0
CG B:GLU431 4.4 24.5 1.0
O B:HOH916 4.4 55.0 1.0
CE B:MET429 4.4 41.5 1.0
O B:HOH900 4.4 40.2 1.0
HB2 B:GLU431 4.4 26.7 1.0
HE1 B:PHE354 4.4 42.3 1.0
CZ B:ARG358 4.5 48.3 1.0
NH2 B:ARG358 4.5 57.1 1.0
O B:HOH894 4.5 59.7 1.0
HG3 B:GLU431 4.7 29.4 1.0
HE2 B:MET429 4.7 49.8 1.0
HB3 B:GLU431 4.7 26.7 1.0
HB2 B:PRO391 4.7 16.4 1.0
OH B:TYR459 4.7 15.8 1.0
CB B:GLU431 4.8 22.2 1.0
HZ B:PHE354 4.8 40.5 1.0
SD B:MET392 4.8 29.0 1.0
CG B:MET392 4.9 28.8 1.0
CE1 B:PHE354 4.9 35.2 1.0
CE2 B:TYR459 5.0 12.0 1.0

Reference:

R.R.Dotas, T.T.Nguyen, C.E.Stewart Jr., R.Ghirlando, D.A.Potoyan, V.Venditti. Hybrid Thermophilic/Mesophilic Enzymes Reveal A Role For Conformational Disorder in Regulation of Bacterial Enzyme I. J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638
PubMed: 32504625
DOI: 10.1016/J.JMB.2020.05.024
Page generated: Tue Oct 1 21:25:51 2024

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