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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

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