Atomistry » Magnesium » PDB 6or7-6p1p » 6oy6
Atomistry »
  Magnesium »
    PDB 6or7-6p1p »
      6oy6 »

Magnesium in PDB 6oy6: X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min

Enzymatic activity of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min

All present enzymatic activity of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min, PDB code: 6oy6 was solved by Y.Shin, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.67 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 186.882, 102.138, 297.364, 90.00, 98.81, 90.00
R / Rfree (%) 21.2 / 26.5

Other elements in 6oy6:

The structure of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min (pdb code 6oy6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min, PDB code: 6oy6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6oy6

Go back to Magnesium Binding Sites List in 6oy6
Magnesium binding site 1 out of 3 in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:64.8
occ:1.00
O D:LYS840 2.0 76.2 1.0
OE2 B:GLU154 2.7 88.6 1.0
C D:LYS840 3.2 83.7 1.0
OD2 B:ASP168 3.5 80.6 1.0
CD B:GLU154 3.7 91.4 1.0
OE1 B:GLU154 3.9 90.7 1.0
OD1 B:ASP168 4.0 80.4 1.0
O D:LEU839 4.0 78.1 1.0
OE2 B:GLU64 4.0 0.2 1.0
N D:TYR841 4.1 83.5 1.0
CA D:LYS840 4.2 80.6 1.0
CG B:ASP168 4.2 83.2 1.0
CA D:TYR841 4.3 74.9 1.0
N D:VAL842 4.4 68.3 1.0
OE1 B:GLU64 4.5 99.2 1.0
CD B:GLU64 4.7 0.1 1.0
C D:TYR841 4.8 73.2 1.0
C D:LEU839 5.0 77.3 1.0

Magnesium binding site 2 out of 3 in 6oy6

Go back to Magnesium Binding Sites List in 6oy6
Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1601

b:59.5
occ:1.00
O3' I:G8 2.3 81.6 1.0
OD1 D:ASP739 2.4 79.2 1.0
OD1 D:ASP743 2.5 56.9 1.0
OD1 D:ASP741 2.7 60.7 1.0
CB D:ASP739 3.0 57.4 1.0
OD2 D:ASP743 3.0 58.3 1.0
OD2 D:ASP741 3.0 68.9 1.0
CG D:ASP739 3.0 70.8 1.0
CG D:ASP743 3.1 59.2 1.0
CG D:ASP741 3.2 65.1 1.0
C3' I:G8 3.5 80.0 1.0
O2' I:G8 3.6 78.6 1.0
N D:ASP739 3.6 63.1 1.0
CA D:ASP739 3.8 55.5 1.0
C2' I:G8 4.1 79.3 1.0
C4' I:G8 4.1 73.7 1.0
OD2 D:ASP739 4.2 72.0 1.0
NH2 D:ARG704 4.3 70.6 1.0
C4' D:GTP1604 4.3 86.3 0.8
O5' D:GTP1604 4.4 97.0 0.8
C D:ASP739 4.5 58.4 1.0
O4' D:GTP1604 4.5 83.2 0.8
C D:ALA738 4.6 60.3 1.0
O D:ASN737 4.7 64.1 1.0
CB D:ASP741 4.7 60.8 1.0
CB D:ASP743 4.7 55.9 1.0
O D:ASP739 4.8 64.5 1.0
C5' D:GTP1604 4.8 87.6 0.8
C5' I:G8 4.9 81.6 1.0
O1A D:GTP1604 4.9 88.5 0.8
N D:ASP741 4.9 59.2 1.0

Magnesium binding site 3 out of 3 in 6oy6

Go back to Magnesium Binding Sites List in 6oy6
Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1605

b:76.5
occ:1.00
O2G D:GTP1604 2.4 81.9 0.8
OD2 D:ASP739 2.4 72.0 1.0
O1A D:GTP1604 2.5 88.5 0.8
O1B D:GTP1604 2.9 89.8 0.8
O3A D:GTP1604 3.0 99.3 0.8
OD1 D:ASP739 3.0 79.2 1.0
CG D:ASP739 3.1 70.8 1.0
PA D:GTP1604 3.3 0.4 0.8
PB D:GTP1604 3.5 0.9 0.8
PG D:GTP1604 3.6 80.6 0.8
NH2 D:ARG1029 3.7 82.7 1.0
O3B D:GTP1604 3.8 99.1 0.8
NH2 C:ARG879 3.9 71.4 1.0
O5' D:GTP1604 4.1 97.0 0.8
OE1 C:GLU685 4.2 69.7 1.0
O1G D:GTP1604 4.3 84.9 0.8
CB D:ASP739 4.5 57.4 1.0
O2A D:GTP1604 4.6 98.5 0.8
OD2 C:ASP686 4.6 75.1 1.0
CZ D:ARG1029 4.7 78.4 1.0
NH1 D:ARG1029 4.7 87.7 1.0
O3G D:GTP1604 4.7 79.0 0.8
CD C:GLU685 4.9 66.7 1.0
O2B D:GTP1604 4.9 0.1 0.8
OE2 C:GLU685 5.0 54.7 1.0

Reference:

Y.Shin, K.S.Murakami. Structural Basis of Reiterative Transcription From the Pyrg Promoter To Be Published.
Page generated: Tue Oct 1 13:42:35 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy