Magnesium in PDB 6nk8: C-Terminal Region of the Burkholderia Pseudomallei Old Protein

Protein crystallography data

The structure of C-Terminal Region of the Burkholderia Pseudomallei Old Protein, PDB code: 6nk8 was solved by C.J.Schiltz, A.Lee, E.A.Partlow, C.J.Hosford, J.S.Chappie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.88 / 2.24
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 83.256, 105.669, 123.764, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein (pdb code 6nk8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein, PDB code: 6nk8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6nk8

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Magnesium binding site 1 out of 6 in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C-Terminal Region of the Burkholderia Pseudomallei Old Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:22.9
occ:1.00
 O A:HOH807 2.0 17.6 1.0
OE1 A:GLU400 2.1 16.0 1.0
OD2 A:ASP455 2.2 22.9 1.0
O A:HOH804 2.2 20.7 1.0
O A:HOH824 2.3 25.3 1.0
O A:HOH833 2.7 20.3 1.0
CD A:GLU400 3.2 19.1 1.0
CG A:ASP455 3.4 23.4 1.0
OE2 A:GLU400 3.6 22.6 1.0
O A:HOH813 3.6 22.8 1.0
O A:HOH823 3.9 24.4 1.0
OG1 A:THR506 3.9 31.9 1.0
CB A:ASP455 3.9 19.8 1.0
O A:HOH806 4.2 25.1 1.0
OD1 A:ASP457 4.3 20.9 1.0
O A:HOH814 4.4 28.8 1.0
OD1 A:ASP455 4.4 23.4 1.0
OD2 A:ASP457 4.4 22.7 1.0
CG A:GLU400 4.5 17.9 1.0
O A:HOH821 4.6 24.4 1.0
MG A:MG702 4.6 38.1 1.0
CB A:GLU400 4.7 16.4 1.0
CG2 A:THR432 4.7 19.7 1.0
CG A:ASP457 4.8 22.6 1.0

Magnesium binding site 2 out of 6 in 6nk8

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Magnesium binding site 2 out of 6 in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C-Terminal Region of the Burkholderia Pseudomallei Old Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:38.1
occ:1.00
 O A:HOH806 2.2 25.1 1.0
O A:HOH821 2.2 24.4 1.0
O A:HOH813 2.3 22.8 1.0
OE2 A:GLU508 3.3 30.3 1.0
O A:HOH833 3.4 20.3 1.0
NZ A:LYS562 3.7 30.1 1.0
OE1 A:GLU508 3.8 30.8 1.0
CE A:LYS562 3.8 35.1 1.0
O A:HOH828 3.9 11.9 1.0
CD A:GLU508 3.9 29.9 1.0
OE1 A:GLU404 4.2 17.7 1.0
OE2 A:GLU404 4.3 22.2 1.0
CB A:LEU507 4.4 19.8 1.0
MG A:MG701 4.6 22.9 1.0
CD A:GLU404 4.6 19.6 1.0
CB A:ALA403 4.7 12.4 1.0
CD A:LYS562 4.7 32.8 1.0
OG1 A:THR506 4.8 31.9 1.0
CD2 A:LEU507 4.8 18.8 1.0
OD2 A:ASP455 4.8 22.9 1.0

Magnesium binding site 3 out of 6 in 6nk8

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Magnesium binding site 3 out of 6 in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of C-Terminal Region of the Burkholderia Pseudomallei Old Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:29.6
occ:1.00
 O A:HOH802 2.4 24.6 1.0
O B:HOH803 2.6 20.8 1.0
O B:HOH823 2.7 17.4 1.0
O B:HOH806 2.8 15.6 1.0
OE2 B:GLU413 2.9 21.0 1.0
OE2 A:GLU413 2.9 18.5 1.0
OD2 B:ASP420 3.0 22.3 1.0
O A:HOH819 3.0 20.4 1.0
OD2 A:ASP420 3.1 26.4 1.0
O B:HOH819 3.1 17.7 1.0
CG A:GLU413 3.6 16.0 1.0
CG B:GLU413 3.6 14.3 1.0
CD B:GLU413 3.7 19.6 1.0
CD A:GLU413 3.7 17.0 1.0
CG B:ASP420 4.1 15.6 1.0
CG A:ASP420 4.3 24.2 1.0
O B:HOH844 4.4 16.8 1.0
OD1 B:ASP420 4.8 18.0 1.0
OE1 B:GLU413 4.9 20.4 1.0
OE1 A:GLU413 4.9 16.8 1.0
O B:PRO409 4.9 14.2 1.0
CB B:ASP420 5.0 13.1 1.0

Magnesium binding site 4 out of 6 in 6nk8

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Magnesium binding site 4 out of 6 in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of C-Terminal Region of the Burkholderia Pseudomallei Old Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:17.9
occ:1.00
 O B:HOH818 2.1 11.8 1.0
O B:HOH827 2.1 16.4 1.0
O A:HOH816 2.2 14.6 1.0
OD1 B:ASP416 2.2 12.9 1.0
OD1 A:ASP416 2.3 20.0 1.0
CG B:ASP416 3.3 12.5 1.0
CG A:ASP416 3.3 22.1 1.0
NE2 B:HIS418 3.8 14.6 1.0
NE2 A:HIS418 3.9 16.1 1.0
CB A:ASP416 3.9 14.9 1.0
CB B:ASP416 4.0 10.2 1.0
O B:HOH844 4.1 16.8 1.0
CA A:ASP416 4.1 17.6 1.0
OD2 B:ASP416 4.1 9.7 1.0
OD2 A:ASP416 4.1 19.1 1.0
CA B:ASP416 4.2 9.4 1.0
O A:GLU413 4.3 15.6 1.0
O B:HOH809 4.3 18.1 1.0
CD2 B:HIS418 4.4 12.8 1.0
O B:GLU413 4.7 10.0 1.0
CD2 A:HIS418 4.7 14.3 1.0
CE1 B:HIS418 4.9 12.2 1.0
O A:HOH808 4.9 16.7 1.0
N A:ASP416 4.9 14.6 1.0
CE1 A:HIS418 4.9 16.4 1.0

Magnesium binding site 5 out of 6 in 6nk8

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Magnesium binding site 5 out of 6 in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of C-Terminal Region of the Burkholderia Pseudomallei Old Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:19.2
occ:1.00
 O B:HOH824 2.0 15.2 1.0
O B:HOH805 2.1 14.1 1.0
OD1 B:ASP576 2.2 14.8 1.0
CG B:ASP576 3.2 15.8 1.0
OD2 B:ASP576 3.5 13.5 1.0
O B:HOH839 4.3 6.8 1.0
CB B:ASP576 4.5 14.8 1.0
N B:ASP576 4.7 11.0 1.0
CB B:ALA575 5.0 9.0 1.0

Magnesium binding site 6 out of 6 in 6nk8

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Magnesium binding site 6 out of 6 in the C-Terminal Region of the Burkholderia Pseudomallei Old Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of C-Terminal Region of the Burkholderia Pseudomallei Old Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:27.4
occ:1.00
 OE1 B:GLU400 2.0 20.3 1.0
O B:HOH810 2.1 22.0 1.0
OD2 B:ASP455 2.2 25.9 1.0
O B:HOH830 2.2 32.9 1.0
O B:HOH802 2.2 29.5 1.0
O B:HOH837 3.1 30.8 1.0
CD B:GLU400 3.1 21.6 1.0
CG B:ASP455 3.3 27.2 1.0
OE2 B:GLU400 3.5 24.3 1.0
CB B:ASP455 3.8 24.4 1.0
OG1 B:THR506 4.2 29.8 1.0
OD1 B:ASP457 4.3 29.4 1.0
O B:HOH813 4.3 26.8 1.0
OD1 B:ASP455 4.3 22.6 1.0
OD2 B:ASP457 4.3 28.9 1.0
CG B:GLU400 4.4 22.2 1.0
O B:HOH829 4.5 21.8 1.0
CB B:GLU400 4.6 20.6 1.0
CG B:ASP457 4.7 31.0 1.0
O B:HOH835 4.7 26.8 1.0
N B:ASP455 5.0 23.1 1.0

Reference:

C.J.Schiltz, A.Lee, E.A.Partlow, C.J.Hosford, J.S.Chappie. Structural Characterization of Class 2 Old Family Nucleases Supports A Two-Metal Catalysis Mechanism For Cleavage. Nucleic Acids Res. V. 47 9448 2019.
ISSN: ESSN 1362-4962
PubMed: 31400118
DOI: 10.1093/NAR/GKZ703
Page generated: Mon Dec 14 23:40:25 2020

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