Magnesium in PDB 8ucg: Thermophilic Rna Ligase From Palaeococcus Pacificus K92A

Enzymatic activity of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A

All present enzymatic activity of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A:
6.5.1.3;

Protein crystallography data

The structure of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A, PDB code: 8ucg was solved by M.D.Rousseau, J.L.Hicks, T.Oulavallickal, A.Williamson, V.L.Arcus, M.W.Patrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.88 / 1.86
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.793, 99.699, 142.477, 90, 90, 90
R / Rfree (%) 20.7 / 23.5

Other elements in 8ucg:

The structure of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A (pdb code 8ucg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A, PDB code: 8ucg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8ucg

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Magnesium binding site 1 out of 7 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:18.7
occ:0.47
 O A:HOH556 2.0 29.6 1.0
O A:HOH574 2.0 25.5 1.0
O A:HOH688 2.2 24.9 1.0
OD1 A:ASP248 2.3 17.8 1.0
MG A:MG402 2.3 14.5 1.0
O A:HOH667 2.3 35.4 1.0
OD1 A:ASP94 3.0 28.1 1.0
O A:HOH510 3.3 42.9 1.0
CG A:ASP248 3.3 23.4 1.0
CG A:ASP94 3.5 49.3 1.0
O A:HOH743 3.6 30.3 1.0
OD2 A:ASP94 3.6 35.6 1.0
OD2 A:ASP248 3.7 18.2 1.0
OE1 A:GLU224 3.7 24.2 1.0
O A:HOH511 4.0 13.1 1.0
O A:HOH757 4.1 35.8 1.0
O A:HOH626 4.3 31.9 1.0
O A:ALA244 4.4 17.9 1.0
O A:HOH736 4.5 31.6 1.0
CD A:GLU224 4.6 22.8 1.0
OE2 A:GLU224 4.6 23.0 1.0
CB A:ASP248 4.6 10.3 1.0
CB A:ASP94 4.6 18.4 1.0
O A:HOH526 4.7 24.2 1.0
O A:HOH594 4.8 32.8 1.0
CA A:ASP248 4.8 10.3 1.0
N A:ASP248 5.0 13.1 1.0

Magnesium binding site 2 out of 7 in 8ucg

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Magnesium binding site 2 out of 7 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:14.5
occ:1.00
 O A:HOH556 1.9 29.6 1.0
MG A:MG401 2.3 18.7 0.5
O A:HOH736 2.4 31.6 1.0
O A:HOH574 2.4 25.5 1.0
O A:HOH757 2.5 35.8 1.0
OD1 A:ASP248 2.7 17.8 1.0
O A:HOH526 2.7 24.2 1.0
OD2 A:ASP248 2.8 18.2 1.0
CG A:ASP248 3.1 23.4 1.0
OD1 A:ASP94 3.7 28.1 1.0
O A:HOH743 3.9 30.3 1.0
O A:HOH667 4.1 35.4 1.0
O A:HOH688 4.3 24.9 1.0
OH A:TYR263 4.4 19.4 1.0
OE2 A:GLU224 4.4 23.0 1.0
O A:HOH625 4.4 19.5 1.0
CB A:ASP248 4.5 10.3 1.0
O A:HOH600 4.6 35.1 1.0
NH2 A:ARG267 4.7 15.5 1.0
OE1 A:GLU224 4.7 24.2 1.0
CG A:ASP94 4.7 49.3 1.0
O A:HOH597 4.8 9.4 1.0
CD A:GLU224 5.0 22.8 1.0

Magnesium binding site 3 out of 7 in 8ucg

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Magnesium binding site 3 out of 7 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:20.5
occ:1.00
 O A:HOH518 1.8 31.5 1.0
O A:HOH672 2.3 32.9 1.0
O A:HOH593 2.3 30.0 1.0
O A:PRO148 2.4 23.0 1.0
O A:HOH565 2.6 24.9 1.0
O A:HOH727 2.8 41.8 1.0
O A:VAL154 2.9 34.6 1.0
C A:PRO148 3.4 18.9 1.0
C A:VAL154 3.7 33.8 1.0
O A:HOH709 3.8 47.2 1.0
O A:LEU153 4.0 25.0 1.0
CA A:VAL154 4.1 27.4 1.0
CA A:PRO148 4.2 16.7 1.0
N A:GLU149 4.3 18.9 1.0
N A:SER150 4.4 16.4 1.0
CB A:PHE318 4.5 25.2 1.0
CA A:GLU149 4.5 20.3 1.0
N A:GLU155 4.6 23.6 1.0
CA A:PHE318 4.8 27.7 1.0
N A:THR319 4.8 20.2 1.0
O A:HOH756 4.9 47.7 1.0
C A:LEU153 4.9 22.9 1.0
CA A:GLU155 4.9 24.2 1.0
O A:SER150 5.0 17.2 1.0
O A:GLY147 5.0 15.3 1.0

Magnesium binding site 4 out of 7 in 8ucg

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Magnesium binding site 4 out of 7 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:22.6
occ:1.00
 O A:SER309 1.9 42.5 1.0
O A:HOH543 2.0 37.5 1.0
O A:HOH527 2.1 48.4 1.0
O A:HOH774 2.2 48.9 1.0
O A:ASP306 2.4 27.5 1.0
C A:SER309 3.2 35.8 1.0
C A:ASP306 3.5 30.1 1.0
OG A:SER309 3.9 52.1 1.0
CA A:SER309 4.0 54.2 1.0
CB A:SER309 4.1 60.7 1.0
CA A:ASP306 4.1 23.2 1.0
N A:GLY310 4.1 56.5 1.0
CA A:GLY310 4.2 51.7 1.0
N A:SER309 4.3 32.0 1.0
O A:HOH791 4.3 32.7 1.0
N A:ILE307 4.5 23.5 1.0
C A:GLY310 4.5 54.2 1.0
CB A:ASP306 4.6 22.4 1.0
CA A:ILE307 4.7 22.2 1.0
CB A:ASP312 4.7 45.9 1.0
N A:ASP312 4.8 31.9 1.0

Magnesium binding site 5 out of 7 in 8ucg

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Magnesium binding site 5 out of 7 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:25.2
occ:0.50
 O B:HOH604 2.0 23.7 1.0
O B:HOH756 2.0 35.7 1.0
O B:HOH675 2.1 29.5 1.0
O B:HOH741 2.2 34.6 1.0
OD1 B:ASP248 2.7 16.7 1.0
MG B:MG405 2.8 11.2 1.0
OD1 B:ASP94 3.1 30.6 1.0
CG B:ASP94 3.4 39.8 1.0
OE1 B:GLU224 3.5 22.3 1.0
OD2 B:ASP94 3.5 31.2 1.0
CG B:ASP248 3.7 17.4 1.0
O B:HOH639 3.8 35.4 1.0
O B:HOH546 3.8 19.0 1.0
O B:HOH759 3.9 30.6 1.0
OD2 B:ASP248 4.0 14.0 1.0
O B:HOH683 4.3 29.2 1.0
CB B:ASP94 4.3 16.4 1.0
CD B:GLU224 4.4 20.2 1.0
O B:HOH791 4.4 33.2 1.0
O B:ALA244 4.5 17.9 1.0
OE2 B:GLU224 4.5 26.1 1.0
O B:HOH520 4.6 23.4 1.0
O B:HOH735 4.7 30.9 1.0
CB B:ASP248 4.9 9.4 1.0

Magnesium binding site 6 out of 7 in 8ucg

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Magnesium binding site 6 out of 7 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:11.2
occ:1.00
 O B:HOH675 1.8 29.5 1.0
O B:HOH735 2.2 30.9 1.0
O B:HOH791 2.4 33.2 1.0
O B:HOH604 2.5 23.7 1.0
O B:HOH574 2.6 26.2 1.0
OD1 B:ASP248 2.7 16.7 1.0
MG B:MG404 2.8 25.2 0.5
O B:HOH639 2.8 35.4 1.0
OD2 B:ASP248 2.9 14.0 1.0
CG B:ASP248 3.1 17.4 1.0
O B:HOH759 3.9 30.6 1.0
OD1 B:ASP94 4.1 30.6 1.0
O B:HOH741 4.1 34.6 1.0
OE2 B:GLU224 4.4 26.1 1.0
O B:HOH602 4.4 21.0 1.0
O B:HOH580 4.5 26.0 1.0
OH B:TYR263 4.5 14.6 1.0
O B:HOH756 4.6 35.7 1.0
NH2 B:ARG267 4.6 13.6 1.0
CB B:ASP248 4.6 9.4 1.0
OE1 B:GLU224 4.7 22.3 1.0
O B:HOH635 4.8 9.3 1.0
CD B:GLU224 5.0 20.2 1.0

Magnesium binding site 7 out of 7 in 8ucg

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Magnesium binding site 7 out of 7 in the Thermophilic Rna Ligase From Palaeococcus Pacificus K92A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermophilic Rna Ligase From Palaeococcus Pacificus K92A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:14.1
occ:1.00
 O B:HOH731 2.1 27.5 1.0
O B:PRO148 2.3 18.5 1.0
O B:HOH703 2.4 28.2 1.0
O B:HOH663 2.5 39.7 1.0
O B:HOH693 2.7 35.0 1.0
O B:HOH607 2.7 20.0 1.0
O B:VAL154 2.7 25.4 1.0
O B:HOH542 3.3 44.7 1.0
C B:PRO148 3.4 16.3 1.0
C B:VAL154 3.6 23.0 1.0
CA B:PRO148 4.0 13.4 1.0
CA B:VAL154 4.2 23.6 1.0
O B:LEU153 4.2 22.1 1.0
N B:GLU149 4.3 18.7 1.0
N B:GLU155 4.5 17.8 1.0
CA B:GLU149 4.6 19.6 1.0
N B:SER150 4.6 12.7 1.0
CA B:GLU155 4.7 23.1 1.0
O B:HOH782 4.8 51.4 1.0
CB B:PRO148 4.8 14.5 1.0
CB B:PHE318 4.8 19.9 1.0
O B:GLY147 5.0 12.2 1.0
N B:THR319 5.0 16.8 1.0

Reference:

M.D.Rousseau, J.L.Hicks, T.Oulavallickal, A.Williamson, V.L.Arcus, M.W.Patrick. Characterisation and Engineering of A Thermophilic Rna Ligase From Palaeococcus Pacificus To Be Published.
Page generated: Fri Oct 4 21:14:22 2024

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