Magnesium in PDB 8w8o: Thermus Thermophilus Initiation Complex in the Half-Translocated State

Enzymatic activity of Thermus Thermophilus Initiation Complex in the Half-Translocated State

All present enzymatic activity of Thermus Thermophilus Initiation Complex in the Half-Translocated State:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initiation Complex in the Half-Translocated State, PDB code: 8w8o was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.88 / 2.51
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.397, 103.796, 295.035, 90, 99.19, 90
R / Rfree (%) 18.7 / 22.6

Other elements in 8w8o:

The structure of Thermus Thermophilus Initiation Complex in the Half-Translocated State also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Initiation Complex in the Half-Translocated State (pdb code 8w8o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Thermus Thermophilus Initiation Complex in the Half-Translocated State, PDB code: 8w8o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8w8o

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Magnesium binding site 1 out of 7 in the Thermus Thermophilus Initiation Complex in the Half-Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Initiation Complex in the Half-Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:73.2
occ:1.00
 OD1 B:ASP183 2.3 86.1 1.0
OD1 B:ASP191 2.3 82.4 1.0
OD1 B:ASP193 2.4 65.3 1.0
O B:ASP191 3.2 68.2 1.0
O B:LEU192 3.5 65.7 1.0
CG B:ASP183 3.5 85.5 1.0
CG B:ASP191 3.6 83.7 1.0
CG B:ASP193 3.7 60.2 1.0
C B:ASP191 3.7 74.1 1.0
C B:LEU192 3.9 65.3 1.0
CA B:ASP183 4.2 70.8 1.0
CA B:ASP191 4.2 74.8 1.0
CB B:ASP183 4.3 74.3 1.0
OD2 B:ASP183 4.3 89.2 1.0
N B:ASP193 4.3 59.7 1.0
N B:LEU192 4.3 73.4 1.0
OD2 B:ASP191 4.4 81.5 1.0
CB B:ASP191 4.4 76.4 1.0
CA B:ASP193 4.4 58.0 1.0
OD2 B:ASP193 4.4 55.6 1.0
CA B:LEU192 4.6 65.3 1.0
CG B:ARG30 4.6 54.6 1.0
CB B:ASP193 4.7 53.1 1.0
N B:ASP183 4.8 69.5 1.0
CA B:ARG30 4.9 55.7 1.0
O B:GLU182 5.0 65.8 1.0

Magnesium binding site 2 out of 7 in 8w8o

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Magnesium binding site 2 out of 7 in the Thermus Thermophilus Initiation Complex in the Half-Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Initiation Complex in the Half-Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1603

b:33.8
occ:1.00
 OD1 D:ASP741 2.0 39.3 1.0
O3' I:A7 2.1 41.0 1.0
OD1 D:ASP743 2.1 42.6 1.0
O D:HOH1711 2.1 34.2 1.0
OD1 D:ASP739 2.2 42.7 1.0
O D:HOH1780 2.3 42.3 1.0
CG D:ASP743 2.9 38.9 1.0
CG D:ASP741 2.9 41.7 1.0
OD2 D:ASP743 3.0 37.9 1.0
OD2 D:ASP741 3.1 45.5 1.0
CG D:ASP739 3.2 42.4 1.0
C3' I:A7 3.3 41.5 1.0
O2' I:A7 3.5 40.9 1.0
OD2 D:ASP739 3.6 48.7 1.0
C4' I:A7 3.7 41.3 1.0
C2' I:A7 3.9 41.2 1.0
C5' I:A7 4.3 34.6 1.0
CB D:ASP741 4.3 37.8 1.0
O D:ASP739 4.3 35.1 1.0
CB D:ASP743 4.3 35.0 1.0
O I:HOH216 4.4 51.5 1.0
N D:ASP741 4.4 36.2 1.0
N D:ASP739 4.4 41.8 1.0
C D:ASP739 4.4 36.3 1.0
O D:HOH1878 4.4 46.3 1.0
CB D:ASP739 4.5 32.4 1.0
N D:ASP743 4.5 34.0 1.0
O D:HOH1961 4.6 53.5 1.0
CA D:ASP739 4.7 37.8 1.0
CA D:ASP741 4.7 37.4 1.0
C D:ASP741 4.8 39.9 1.0
CA D:ASP743 4.8 32.9 1.0
N D:PHE740 4.9 33.7 1.0
O4' I:A7 4.9 47.9 1.0
N D:GLY742 5.0 39.0 1.0

Magnesium binding site 3 out of 7 in 8w8o

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Magnesium binding site 3 out of 7 in the Thermus Thermophilus Initiation Complex in the Half-Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Initiation Complex in the Half-Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:64.9
occ:1.00
 O D:HOH1800 2.1 56.7 1.0
O D:HOH1811 2.2 54.8 1.0
O B:HOH2114 2.2 58.7 1.0
O B:HOH2125 2.2 64.5 1.0
O D:LYS840 2.2 51.9 1.0
O B:HOH2109 2.3 55.1 1.0
C D:LYS840 3.3 53.1 1.0
CA D:LYS840 4.0 52.8 1.0
O D:LEU839 4.1 56.3 1.0
OE1 B:GLU64 4.2 90.1 1.0
OD2 B:ASP168 4.2 61.2 1.0
OE2 B:GLU64 4.3 82.0 1.0
N D:TYR841 4.3 54.3 1.0
OE2 B:GLU154 4.4 72.1 1.0
OE1 B:GLU154 4.4 82.7 1.0
O D:HOH1881 4.5 57.9 1.0
OD1 B:ASP168 4.5 60.0 1.0
CA D:TYR841 4.7 51.9 1.0
CD B:GLU64 4.7 86.6 1.0
O B:HOH2115 4.7 58.6 1.0
CG B:ASP168 4.8 58.4 1.0
CD B:GLU154 4.8 80.3 1.0
N D:VAL842 4.8 50.3 1.0
CG D:LYS840 4.9 47.2 1.0
N D:LYS840 5.0 50.4 1.0
C D:LEU839 5.0 56.2 1.0

Magnesium binding site 4 out of 7 in 8w8o

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Magnesium binding site 4 out of 7 in the Thermus Thermophilus Initiation Complex in the Half-Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Initiation Complex in the Half-Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1605

b:56.1
occ:1.00
 O D:HOH1949 2.4 63.0 1.0
O D:TRP897 2.7 50.1 1.0
O D:ILE900 2.7 55.2 1.0
O D:GLU898 3.0 56.0 1.0
C D:GLU898 3.4 53.8 1.0
CA D:GLU898 3.7 53.9 1.0
C D:TRP897 3.8 51.2 1.0
C D:ILE900 3.9 48.6 1.0
N D:LEU899 4.2 50.2 1.0
N D:ILE900 4.3 48.6 1.0
N D:GLU898 4.3 49.1 1.0
C D:LEU899 4.6 50.8 1.0
CA D:ILE900 4.7 51.3 1.0
CG1 D:ILE900 4.7 46.0 1.0
N D:GLN901 4.9 48.6 1.0
CA D:LEU899 5.0 50.2 1.0

Magnesium binding site 5 out of 7 in 8w8o

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Magnesium binding site 5 out of 7 in the Thermus Thermophilus Initiation Complex in the Half-Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Initiation Complex in the Half-Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:56.8
occ:1.00
 O F:TRP299 2.4 56.8 1.0
O F:GLY296 2.4 61.9 1.0
O F:ALA292 2.9 58.4 1.0
C F:ALA292 3.4 60.4 1.0
C F:GLY296 3.5 67.5 1.0
C F:TRP299 3.6 58.0 1.0
N F:GLU293 3.9 57.9 1.0
CA F:GLU293 3.9 60.7 1.0
CB F:ALA292 4.3 59.5 1.0
CA F:GLY296 4.3 66.4 1.0
N F:GLY296 4.3 67.2 1.0
CA F:ALA292 4.3 57.1 1.0
CA F:TRP299 4.3 55.6 1.0
O F:GLU293 4.3 66.6 1.0
N F:TRP299 4.4 61.8 1.0
CB F:TRP299 4.4 54.8 1.0
N F:PRO297 4.4 69.4 1.0
C F:GLU293 4.5 55.8 1.0
CA F:PRO297 4.6 66.7 1.0
N F:ASP300 4.6 51.9 1.0
CA F:ASP300 4.9 54.8 1.0

Magnesium binding site 6 out of 7 in 8w8o

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Magnesium binding site 6 out of 7 in the Thermus Thermophilus Initiation Complex in the Half-Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus Initiation Complex in the Half-Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg101

b:43.0
occ:1.00
 OP2 I:G6 1.8 43.4 1.0
O3G I:GTP5 2.1 38.5 1.0
O2A I:GTP5 2.1 42.7 1.0
O I:HOH212 2.2 38.8 1.0
O I:HOH205 2.2 36.9 1.0
O I:HOH208 2.3 39.0 1.0
PG I:GTP5 3.3 47.4 1.0
P I:G6 3.3 35.1 1.0
PA I:GTP5 3.6 40.8 1.0
O1G I:GTP5 3.7 40.8 1.0
O3B I:GTP5 4.0 41.7 1.0
O I:HOH215 4.1 40.8 1.0
N C:GLU445 4.1 41.9 1.0
OP1 I:G6 4.1 40.2 1.0
N C:GLY446 4.1 41.9 1.0
O3' I:GTP5 4.2 40.8 1.0
O I:HOH206 4.2 44.7 1.0
CB C:PRO444 4.2 40.3 1.0
O5' I:G6 4.3 36.0 1.0
C3' I:GTP5 4.3 40.8 1.0
O C:HOH1234 4.3 37.8 1.0
O3A I:GTP5 4.3 37.2 1.0
O1A I:GTP5 4.4 42.1 1.0
O5' I:GTP5 4.5 41.5 1.0
O2G I:GTP5 4.5 42.9 1.0
PB I:GTP5 4.6 42.5 1.0
N7 I:G6 4.6 44.3 1.0
O2B I:GTP5 4.6 46.5 1.0
O I:HOH211 4.6 41.9 1.0
CA C:PRO444 4.6 41.2 1.0
C8 I:G6 4.8 45.8 1.0
C C:PRO444 4.8 41.0 1.0
CA C:GLY446 4.9 42.2 1.0
CA C:GLU445 4.9 42.9 1.0
C8 I:GTP5 4.9 40.5 1.0
C C:GLU445 5.0 38.2 1.0

Magnesium binding site 7 out of 7 in 8w8o

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Magnesium binding site 7 out of 7 in the Thermus Thermophilus Initiation Complex in the Half-Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermus Thermophilus Initiation Complex in the Half-Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg102

b:44.8
occ:1.00
 O I:HOH217 2.0 41.9 1.0
O I:HOH201 2.0 41.1 1.0
O2B I:GTP5 2.2 46.5 1.0
O1G I:GTP5 2.2 40.8 1.0
O I:HOH213 2.2 40.6 1.0
N7 I:GTP5 2.4 43.1 1.0
C8 I:GTP5 3.3 40.5 1.0
PB I:GTP5 3.4 42.5 1.0
C5 I:GTP5 3.4 45.9 1.0
O6 I:GTP5 3.5 45.0 1.0
PG I:GTP5 3.5 47.4 1.0
O I:HOH209 3.7 43.4 1.0
O3B I:GTP5 3.8 41.7 1.0
O I:HOH208 3.9 39.0 1.0
C6 I:GTP5 3.9 44.8 1.0
O G:HOH102 4.0 48.0 1.0
O1B I:GTP5 4.1 45.2 1.0
O I:HOH204 4.1 41.9 1.0
O I:HOH211 4.3 41.9 1.0
O2G I:GTP5 4.3 42.9 1.0
N9 I:GTP5 4.5 41.7 1.0
O3G I:GTP5 4.5 38.5 1.0
C4 I:GTP5 4.6 40.4 1.0
O3A I:GTP5 4.7 37.2 1.0
ND2 C:ASN448 5.0 39.9 1.0

Reference:

I.C.Nova, J.M.Craig, A.Mazumder, A.H.Laszlo, I.M.Derrington, M.T.Noakes, H.Brinkerhoff, S.Yang, H.Vahedian-Movahed, L.Li, Y.Zhang, J.L.Bowman, J.R.Huang, J.W.Mount, R.H.Ebright, J.H.Gundlach. Nanopore Tweezers Show Fractional-Nucleotide Translocation in Sequence-Dependent Pausing By Rna Polymerase. Proc.Natl.Acad.Sci.Usa V. 121 17121 2024.
ISSN: ESSN 1091-6490
PubMed: 38990947
DOI: 10.1073/PNAS.2321017121
Page generated: Fri Oct 4 22:40:18 2024

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