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Magnesium in PDB 5xox: Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae

Enzymatic activity of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae

All present enzymatic activity of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae:
2.7.7.79;

Protein crystallography data

The structure of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae, PDB code: 5xox was solved by K.Lee, E.H.Lee, J.Son, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 3.00
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 164.703, 164.703, 275.891, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae (pdb code 5xox). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae, PDB code: 5xox:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5xox

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Magnesium binding site 1 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


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 Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:72.1
occ:1.00
 OD2 A:ASP29 3.0 99.9 1.0
OD1 A:ASP77 3.6 88.7 1.0
O5' A:GTP301 3.7 94.5 1.0
OE1 A:GLU78 3.8 75.5 1.0
C5' A:GTP301 3.9 95.8 1.0
O2A A:GTP301 4.0 0.6 1.0
CG A:ASP29 4.1 0.2 1.0
PA A:GTP301 4.2 100.0 1.0
O1A A:GTP301 4.2 96.8 1.0
CB A:GLU78 4.5 84.6 1.0
CG A:ASP77 4.6 85.1 1.0
OD1 A:ASP29 4.6 0.4 1.0
OD2 A:ASP77 4.8 96.6 1.0
CD A:GLU78 5.0 93.3 1.0
NH2 A:ARG150 5.0 88.9 1.0

Magnesium binding site 2 out of 10 in 5xox

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Magnesium binding site 2 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:73.5
occ:1.00
 O3B A:GTP301 1.9 99.6 1.0
O2G A:GTP301 2.0 0.4 1.0
OD1 A:ASP29 2.3 0.4 1.0
PG A:GTP301 2.4 96.8 1.0
O1A A:GTP301 2.5 96.8 1.0
O A:GLY30 2.9 72.2 1.0
O2A A:GTP301 3.1 0.6 1.0
O3G A:GTP301 3.2 0.5 1.0
PA A:GTP301 3.2 100.0 1.0
PB A:GTP301 3.3 0.2 1.0
OD2 A:ASP77 3.4 96.6 1.0
CG A:ASP29 3.4 0.2 1.0
O3A A:GTP301 3.7 0.3 1.0
O1G A:GTP301 3.7 94.7 1.0
C A:GLY30 3.8 65.6 1.0
OD2 A:ASP29 3.9 99.9 1.0
O2B A:GTP301 4.1 0.2 1.0
CA A:LYS31 4.2 73.6 1.0
O A:ASP29 4.3 63.8 1.0
N A:LYS32 4.4 68.4 1.0
N A:LYS31 4.4 67.1 1.0
C A:ASP29 4.5 65.4 1.0
CB A:ASP29 4.5 90.9 1.0
O1B A:GTP301 4.5 0.9 1.0
CG A:ASP77 4.5 85.1 1.0
N A:GLY30 4.6 62.7 1.0
C A:LYS31 4.6 73.5 1.0
O5' A:GTP301 4.7 94.5 1.0
CA A:GLY30 4.8 64.6 1.0
N A:PHE33 4.9 82.2 1.0

Magnesium binding site 3 out of 10 in 5xox

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Magnesium binding site 3 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:0.3
occ:1.00
 OE1 B:GLU75 3.7 0.8 1.0
OE1 B:GLU78 3.8 0.8 1.0
OD2 B:ASP153 3.9 0.4 1.0
CD B:GLU75 4.2 0.5 1.0
NH2 B:ARG150 4.3 92.3 1.0
OE2 B:GLU75 4.3 0.7 1.0
O5' B:GTP302 4.3 0.3 1.0
OD1 B:ASP77 4.5 0.1 1.0
OD2 B:ASP29 4.6 0.5 1.0
C5' B:GTP302 4.7 0.9 1.0
O1A B:GTP302 4.7 0.4 1.0
O2A B:GTP302 4.9 0.0 1.0
PA B:GTP302 4.9 0.6 1.0
CB B:GLU78 5.0 0.8 1.0
CG B:ASP153 5.0 0.9 1.0
CD B:GLU78 5.0 0.5 1.0

Magnesium binding site 4 out of 10 in 5xox

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Magnesium binding site 4 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:0.5
occ:1.00
 O3B B:GTP302 2.0 0.7 1.0
OD1 B:ASP29 2.0 0.8 1.0
O1G B:GTP302 2.2 0.8 1.0
O B:GLY30 2.4 88.3 1.0
PG B:GTP302 2.6 1.0 1.0
OD2 B:ASP77 2.8 0.3 1.0
O1A B:GTP302 2.8 0.4 1.0
CG B:ASP29 3.1 0.3 1.0
C B:GLY30 3.3 84.8 1.0
PB B:GTP302 3.4 0.0 1.0
O2G B:GTP302 3.6 0.9 1.0
PA B:GTP302 3.7 0.6 1.0
O3A B:GTP302 3.8 0.6 1.0
O3G B:GTP302 3.8 0.7 1.0
OD2 B:ASP29 3.8 0.5 1.0
O2A B:GTP302 3.9 0.0 1.0
N B:GLY30 4.0 79.1 1.0
O1B B:GTP302 4.0 0.4 1.0
C B:ASP29 4.0 84.7 1.0
CG B:ASP77 4.1 0.9 1.0
N B:LYS31 4.1 79.5 1.0
O B:ASP29 4.1 99.3 1.0
CB B:ASP29 4.2 97.4 1.0
CA B:LYS31 4.2 88.6 1.0
CA B:GLY30 4.2 80.1 1.0
O2B B:GTP302 4.6 0.8 1.0
OD1 B:ASP77 4.6 0.1 1.0
CA B:ASP29 4.7 85.4 1.0
N B:LYS32 4.7 83.1 1.0
C B:LYS31 4.7 93.0 1.0

Magnesium binding site 5 out of 10 in 5xox

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Magnesium binding site 5 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:95.6
occ:1.00
 O5' C:GTP301 3.5 0.2 1.0
OD2 C:ASP29 3.5 93.5 1.0
O1A C:GTP301 3.6 0.4 1.0
O2A C:GTP301 3.7 0.9 1.0
PA C:GTP301 3.8 0.1 1.0
C5' C:GTP301 4.0 0.3 1.0
OD1 C:ASP77 4.2 0.5 1.0
OD1 C:ASP29 4.3 0.6 1.0
CG C:ASP29 4.3 92.5 1.0
OE1 C:GLU78 4.5 72.8 1.0
OE1 C:GLU75 4.8 0.3 1.0

Magnesium binding site 6 out of 10 in 5xox

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Magnesium binding site 6 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:0.1
occ:1.00
 O3B C:GTP301 2.0 0.1 1.0
O2A C:GTP301 2.1 0.9 1.0
O C:GLY30 2.4 60.6 1.0
OD1 C:ASP29 2.5 0.6 1.0
PA C:GTP301 2.9 0.1 1.0
PB C:GTP301 3.0 0.6 1.0
OD2 C:ASP77 3.0 0.7 1.0
PG C:GTP301 3.2 0.2 1.0
O3A C:GTP301 3.2 0.9 1.0
O1A C:GTP301 3.3 0.4 1.0
O2G C:GTP301 3.3 0.1 1.0
O2B C:GTP301 3.4 0.9 1.0
CG C:ASP29 3.5 92.5 1.0
C C:GLY30 3.7 61.0 1.0
O1G C:GTP301 3.9 0.4 1.0
CG C:ASP77 4.2 92.7 1.0
OD2 C:ASP29 4.2 93.5 1.0
O1B C:GTP301 4.4 1.0 1.0
N C:GLY30 4.4 56.2 1.0
O5' C:GTP301 4.4 0.2 1.0
C C:ASP29 4.4 80.5 1.0
O3G C:GTP301 4.4 0.0 1.0
CB C:ASP29 4.5 81.8 1.0
O C:ASP29 4.5 97.4 1.0
CA C:GLY30 4.5 65.6 1.0
N C:LYS31 4.6 63.7 1.0
CA C:LYS31 4.6 63.6 1.0
OD1 C:ASP77 4.7 0.5 1.0
N C:LYS32 4.8 64.6 1.0
C5' C:GTP301 5.0 0.3 1.0
C C:LYS31 5.0 63.8 1.0
CA C:ASP29 5.0 72.4 1.0

Magnesium binding site 7 out of 10 in 5xox

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Magnesium binding site 7 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:91.6
occ:1.00
 OD2 D:ASP29 3.5 0.7 1.0
OE1 D:GLU78 3.5 95.6 1.0
O2A D:GTP302 3.5 0.2 1.0
OD1 D:ASP77 3.6 1.0 1.0
OD1 D:ASP29 3.7 0.5 1.0
O5' D:GTP302 3.7 93.2 1.0
OE1 D:GLU75 3.9 0.6 1.0
CG D:ASP29 4.0 0.2 1.0
PA D:GTP302 4.0 90.1 1.0
O1A D:GTP302 4.1 98.0 1.0
C5' D:GTP302 4.2 94.2 1.0
CD D:GLU75 4.3 0.2 1.0
CB D:GLU78 4.3 66.1 1.0
OE2 D:GLU75 4.4 0.5 1.0
CD D:GLU78 4.6 83.8 1.0
CG D:ASP77 4.6 96.6 1.0
NH2 D:ARG150 4.6 98.9 1.0
MG D:MG304 4.7 99.1 1.0
OD2 D:ASP77 4.9 0.4 1.0
CB D:SER76 4.9 79.5 1.0
OD2 D:ASP153 4.9 0.2 1.0

Magnesium binding site 8 out of 10 in 5xox

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Magnesium binding site 8 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:99.1
occ:1.00
 O2A D:GTP302 1.9 0.2 1.0
O3B D:GTP302 2.0 1.0 1.0
OD1 D:ASP29 2.2 0.5 1.0
OD2 D:ASP77 2.2 0.4 1.0
O D:GLY30 2.8 73.0 1.0
O2G D:GTP302 2.8 1.0 1.0
PG D:GTP302 3.0 0.8 1.0
PA D:GTP302 3.0 90.1 1.0
PB D:GTP302 3.2 0.0 1.0
CG D:ASP77 3.3 96.6 1.0
CG D:ASP29 3.3 0.2 1.0
O1A D:GTP302 3.4 98.0 1.0
O3A D:GTP302 3.5 86.2 1.0
O2B D:GTP302 3.6 96.0 1.0
OD1 D:ASP77 3.7 1.0 1.0
O3G D:GTP302 3.8 0.1 1.0
C D:GLY30 3.9 71.6 1.0
C D:ASP29 4.1 70.9 1.0
OD2 D:ASP29 4.1 0.7 1.0
CB D:ASP29 4.2 79.8 1.0
N D:GLY30 4.2 73.6 1.0
O D:ASP29 4.2 0.4 1.0
O1G D:GTP302 4.3 0.9 1.0
O5' D:GTP302 4.4 93.2 1.0
CA D:GLY30 4.5 69.9 1.0
O1B D:GTP302 4.5 0.7 1.0
CB D:ASP77 4.6 78.4 1.0
CA D:ASP29 4.6 60.6 1.0
MG D:MG303 4.7 91.6 1.0
C5' D:GTP302 4.8 94.2 1.0
N D:LYS31 4.9 67.4 1.0

Magnesium binding site 9 out of 10 in 5xox

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Magnesium binding site 9 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:0.4
occ:1.00
 O2A E:GTP301 2.4 0.7 1.0
OD2 E:ASP29 3.0 0.8 1.0
OD1 E:ASP77 3.5 0.1 1.0
PA E:GTP301 3.5 0.7 1.0
OE1 E:GLU78 3.6 98.6 1.0
OE2 E:GLU75 3.7 0.3 1.0
O1A E:GTP301 3.8 0.1 1.0
O5' E:GTP301 3.9 0.5 1.0
CG E:ASP29 3.9 0.1 1.0
C5' E:GTP301 4.0 0.7 1.0
OD1 E:ASP29 4.0 0.5 1.0
CB E:GLU78 4.1 0.1 1.0
OE1 E:GLU75 4.5 0.1 1.0
CD E:GLU75 4.5 0.6 1.0
CG E:ASP77 4.5 1.0 1.0
CD E:GLU78 4.7 0.3 1.0
OD2 E:ASP77 4.8 0.9 1.0
NH2 E:ARG150 4.8 0.9 1.0
O3A E:GTP301 4.9 0.8 1.0
CG E:GLU78 5.0 0.7 1.0

Magnesium binding site 10 out of 10 in 5xox

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Magnesium binding site 10 out of 10 in the Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Trna(His) Guanylyltranserase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:0.4
occ:1.00
 O E:GLY30 2.2 0.5 1.0
O3B E:GTP301 2.4 0.9 1.0
OD1 E:ASP29 2.5 0.5 1.0
OD2 E:ASP77 2.6 0.9 1.0
O3A E:GTP301 2.7 0.8 1.0
PB E:GTP301 3.0 0.7 1.0
O2A E:GTP301 3.3 0.7 1.0
C E:GLY30 3.4 0.1 1.0
O2B E:GTP301 3.4 0.2 1.0
PA E:GTP301 3.4 0.7 1.0
PG E:GTP301 3.6 0.2 1.0
CG E:ASP29 3.7 0.1 1.0
O2G E:GTP301 3.8 0.7 1.0
CG E:ASP77 3.8 1.0 1.0
O1A E:GTP301 4.0 0.1 1.0
N E:GLY30 4.2 0.2 1.0
N E:LYS31 4.2 1.0 1.0
CA E:LYS31 4.2 0.3 1.0
C E:ASP29 4.3 0.2 1.0
CA E:GLY30 4.3 0.2 1.0
OD1 E:ASP77 4.3 0.1 1.0
O E:ASP29 4.3 0.8 1.0
O1B E:GTP301 4.4 0.5 1.0
N E:LYS32 4.4 0.1 1.0
CB E:PHE33 4.5 1.0 1.0
N E:PHE33 4.5 0.6 1.0
OD2 E:ASP29 4.5 0.8 1.0
O3G E:GTP301 4.5 0.4 1.0
CB E:ASP29 4.6 0.2 1.0
C E:LYS31 4.7 0.3 1.0
O1G E:GTP301 4.7 0.6 1.0
O5' E:GTP301 4.9 0.5 1.0
CA E:ASP29 4.9 0.7 1.0
CB E:ASP77 4.9 0.2 1.0

Reference:

K.Lee, E.H.Lee, J.Son, K.Y.Hwang. Crystal Structure of Trna(His) Guanylyltransferase From Saccharomyces Cerevisiae Biochem. Biophys. Res. V. 490 400 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28623126
DOI: 10.1016/J.BBRC.2017.06.054
Page generated: Mon Sep 30 09:37:23 2024

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