Magnesium in PDB 6h2j: Crystal Structure of the Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain

Enzymatic activity of Crystal Structure of the Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain

All present enzymatic activity of Crystal Structure of the Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain:
3.1.21.3;

Protein crystallography data

The structure of Crystal Structure of the Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain, PDB code: 6h2j was solved by P.Grinkevich, J.R.Mesters, R.H.Ettrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.910, 129.922, 161.010, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain (pdb code 6h2j). 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 Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain, PDB code: 6h2j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6h2j

Go back to Magnesium Binding Sites List in 6h2j
Magnesium binding site 1 out of 2 in the Crystal Structure of the Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain


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 Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:33.0
occ:1.00
OG1 A:THR314 1.9 43.1 1.0
O1B A:ATP1101 2.0 32.1 1.0
O A:HOH1281 2.0 32.6 1.0
O1G A:ATP1101 2.1 27.7 1.0
O A:HOH1260 2.1 23.2 1.0
PB A:ATP1101 3.2 40.1 1.0
PG A:ATP1101 3.3 19.5 1.0
CB A:THR314 3.3 28.9 1.0
O3B A:ATP1101 3.4 28.0 1.0
O A:HOH1214 3.6 28.6 1.0
O A:HOH1258 3.9 20.3 1.0
N A:THR314 4.1 24.1 1.0
OD2 A:ASP408 4.1 40.6 1.0
CG2 A:THR314 4.1 31.1 1.0
CA A:THR314 4.2 24.2 1.0
NZ A:LYS313 4.2 27.1 1.0
O3G A:ATP1101 4.3 31.8 1.0
O2A A:ATP1101 4.3 33.5 1.0
OD1 A:ASP408 4.3 38.4 1.0
O3A A:ATP1101 4.3 42.3 1.0
O2B A:ATP1101 4.3 29.9 1.0
O2G A:ATP1101 4.4 32.4 1.0
O A:GLY662 4.4 28.9 1.0
CA A:GLY662 4.5 29.8 1.0
CG A:ASP408 4.6 35.9 1.0
PA A:ATP1101 4.6 35.7 1.0
O1A A:ATP1101 4.8 31.6 1.0
CB A:LYS313 4.9 24.9 1.0
C A:GLY662 5.0 31.8 1.0

Magnesium binding site 2 out of 2 in 6h2j

Go back to Magnesium Binding Sites List in 6h2j
Magnesium binding site 2 out of 2 in the Crystal Structure of the Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain


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 Hsdr Subunit of the ECOR124I Restriction Enzyme with the C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:13.5
occ:1.00
O1G B:ATP1101 1.9 30.9 1.0
O1B B:ATP1101 1.9 24.1 1.0
O B:HOH1261 2.0 24.9 1.0
O B:HOH1269 2.1 27.3 1.0
OG1 B:THR314 2.1 31.1 1.0
O B:HOH1284 2.2 31.4 1.0
PB B:ATP1101 3.1 39.9 1.0
PG B:ATP1101 3.2 23.7 1.0
O3B B:ATP1101 3.4 30.6 1.0
CB B:THR314 3.4 32.8 1.0
O B:HOH1205 3.9 42.3 1.0
NZ B:LYS313 3.9 0.8 1.0
N B:THR314 4.0 26.6 1.0
O2A B:ATP1101 4.0 35.0 1.0
OD2 B:ASP408 4.1 28.1 1.0
O3G B:ATP1101 4.1 30.9 1.0
O B:HOH1248 4.1 30.6 1.0
O2B B:ATP1101 4.2 30.2 1.0
O3A B:ATP1101 4.2 32.9 1.0
O2G B:ATP1101 4.3 30.2 1.0
CA B:THR314 4.3 31.2 1.0
CG2 B:THR314 4.4 27.5 1.0
O B:GLY662 4.4 32.1 1.0
OD1 B:ASP408 4.4 35.0 1.0
PA B:ATP1101 4.5 33.8 1.0
CA B:GLY662 4.5 28.0 1.0
O B:HOH1252 4.7 33.8 1.0
CG B:ASP408 4.7 31.0 1.0
O1A B:ATP1101 4.7 28.6 1.0
C B:GLY662 4.9 29.6 1.0
CB B:LYS313 4.9 29.3 1.0
CE B:LYS313 5.0 58.4 1.0

Reference:

P.Grinkevich, D.Sinha, I.Iermak, A.Guzanova, M.Weiserova, J.Ludwig, J.R.Mesters, R.H.Ettrich. Crystal Structure of A Novel Domain of the Motor Subunit of the Type I Restriction Enzyme ECOR124 Involved in Complex Assembly and Dna Binding. J. Biol. Chem. V. 293 15043 2018.
ISSN: ESSN 1083-351X
PubMed: 30054276
DOI: 10.1074/JBC.RA118.003978
Page generated: Mon Dec 14 22:47:15 2020

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