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Magnesium in PDB 6n9x: Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)

Enzymatic activity of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)

All present enzymatic activity of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3):
2.7.7.7; 3.6.4.12;

Other elements in 6n9x:

The structure of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) (pdb code 6n9x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3), PDB code: 6n9x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6n9x

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Magnesium binding site 1 out of 6 in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:54.4
occ:1.00
 O1G B:TTP602 2.2 59.9 1.0
OG B:SER319 2.3 49.6 1.0
O1B B:TTP602 2.3 59.9 1.0
OE1 B:GLN343 2.3 65.3 1.0
CD B:GLN343 3.1 65.3 1.0
NE2 B:GLN343 3.3 65.3 1.0
CB B:SER319 3.4 49.6 1.0
PB B:TTP602 3.5 59.9 1.0
O2A B:TTP602 3.5 59.9 1.0
PG B:TTP602 3.5 59.9 1.0
O3B B:TTP602 3.8 59.9 1.0
O3A B:TTP602 4.0 59.9 1.0
OD2 B:ASP424 4.1 47.0 1.0
PA B:TTP602 4.4 59.9 1.0
N B:SER319 4.4 49.6 1.0
O3G B:TTP602 4.5 59.9 1.0
O2G B:TTP602 4.5 59.9 1.0
CA B:SER319 4.5 49.6 1.0
CG B:GLN343 4.5 65.3 1.0
OD1 B:ASP424 4.6 47.0 1.0
O2B B:TTP602 4.7 59.9 1.0
CG B:ASP424 4.8 47.0 1.0
O1A B:TTP602 4.9 59.9 1.0

Magnesium binding site 2 out of 6 in 6n9x

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Magnesium binding site 2 out of 6 in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:28.5
occ:1.00
 O1G C:TTP700 2.1 34.5 1.0
OG C:SER319 2.2 32.3 1.0
O1B C:TTP700 2.3 34.5 1.0
OE1 C:GLN343 2.4 47.8 1.0
CB C:SER319 2.9 32.3 1.0
PG C:TTP700 3.4 34.5 1.0
PB C:TTP700 3.4 34.5 1.0
CD C:GLN343 3.4 47.8 1.0
O3B C:TTP700 3.6 34.5 1.0
O2A C:TTP700 3.8 34.5 1.0
NE2 C:GLN343 3.8 47.8 1.0
O1A C:TTP700 3.9 34.5 1.0
O3A C:TTP700 3.9 34.5 1.0
PA C:TTP700 4.1 34.5 1.0
CA C:SER319 4.2 32.3 1.0
N C:SER319 4.2 32.3 1.0
O2G C:TTP700 4.3 34.5 1.0
CG C:LYS318 4.4 30.4 1.0
O3G C:TTP700 4.5 34.5 1.0
O2B C:TTP700 4.7 34.5 1.0
CG C:GLN343 4.8 47.8 1.0
OD1 C:ASP424 4.8 34.6 1.0
CB C:GLN343 5.0 47.8 1.0

Magnesium binding site 3 out of 6 in 6n9x

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Magnesium binding site 3 out of 6 in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:31.8
occ:1.00
 O2G D:TTP700 2.3 36.0 1.0
OG D:SER319 2.4 42.4 1.0
O2B D:TTP700 2.5 36.0 1.0
OE1 D:GLN343 2.6 44.9 1.0
CB D:SER319 3.5 42.4 1.0
CD D:GLN343 3.6 44.9 1.0
PG D:TTP700 3.7 36.0 1.0
PB D:TTP700 3.9 36.0 1.0
NE2 D:GLN343 3.9 44.9 1.0
O3B D:TTP700 4.2 36.0 1.0
O1G D:TTP700 4.2 36.0 1.0
OD1 D:ASP424 4.3 37.2 1.0
N D:SER319 4.6 42.4 1.0
O2A D:TTP700 4.6 36.0 1.0
CA D:SER319 4.6 42.4 1.0
O1B D:TTP700 4.7 36.0 1.0
O3G D:TTP700 4.7 36.0 1.0
OD2 D:ASP424 4.9 37.2 1.0
O3A D:TTP700 4.9 36.0 1.0
CG D:ASP424 4.9 37.2 1.0
O1A D:TTP700 4.9 36.0 1.0
CG D:GLN343 4.9 44.9 1.0
CD2 D:HIS425 5.0 33.7 1.0
O D:ASP424 5.0 37.2 1.0

Magnesium binding site 4 out of 6 in 6n9x

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Magnesium binding site 4 out of 6 in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:65.5
occ:1.00
 O2B E:TTP700 2.2 73.6 1.0
OG E:SER319 2.3 76.5 1.0
OE1 E:GLN343 2.4 95.1 1.0
O2G E:TTP700 2.4 73.6 1.0
CD E:GLN343 3.2 95.1 1.0
PB E:TTP700 3.5 73.6 1.0
CB E:SER319 3.5 76.5 1.0
NE2 E:GLN343 3.7 95.1 1.0
PG E:TTP700 3.7 73.6 1.0
O3B E:TTP700 3.9 73.6 1.0
O2A E:TTP700 3.9 73.6 1.0
CG E:GLN343 4.3 95.1 1.0
O3A E:TTP700 4.4 73.6 1.0
O1G E:TTP700 4.4 73.6 1.0
PA E:TTP700 4.5 73.6 1.0
O1A E:TTP700 4.5 73.6 1.0
OD1 E:ASP424 4.5 0.4 1.0
O1B E:TTP700 4.6 73.6 1.0
CA E:SER319 4.6 76.5 1.0
N E:SER319 4.7 76.5 1.0
O3G E:TTP700 4.8 73.6 1.0
CB E:GLN343 4.9 95.1 1.0

Magnesium binding site 5 out of 6 in 6n9x

Go back to Magnesium Binding Sites List in 6n9x
Magnesium binding site 5 out of 6 in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg802

b:52.2
occ:1.00
 OD2 H:ASP654 2.2 49.2 1.0
O H:ALA476 2.3 53.5 1.0
O2B H:TTP801 2.4 53.4 1.0
O1G H:TTP801 2.4 53.4 1.0
OD1 H:ASP475 2.5 56.2 1.0
O2A H:TTP801 2.7 53.4 1.0
OD2 H:ASP475 3.0 56.2 1.0
CG H:ASP475 3.0 56.2 1.0
CG H:ASP654 3.4 49.2 1.0
C H:ALA476 3.5 53.5 1.0
PB H:TTP801 3.6 53.4 1.0
PG H:TTP801 3.8 53.4 1.0
PA H:TTP801 3.9 53.4 1.0
O3B H:TTP801 4.0 53.4 1.0
O3A H:TTP801 4.1 53.4 1.0
OD1 H:ASP654 4.1 49.2 1.0
N H:ALA476 4.3 53.5 1.0
CB H:ASP654 4.3 49.2 1.0
N H:SER477 4.4 57.7 1.0
CA H:SER477 4.4 57.7 1.0
CB H:ASP475 4.4 56.2 1.0
CA H:ALA476 4.5 53.5 1.0
O3G H:TTP801 4.5 53.4 1.0
C5' H:TTP801 4.8 53.4 1.0
O2G H:TTP801 4.8 53.4 1.0
C H:ASP475 4.8 56.2 1.0
O1B H:TTP801 4.8 53.4 1.0
O5' H:TTP801 4.9 53.4 1.0
O1A H:TTP801 5.0 53.4 1.0
N H:GLY478 5.0 53.7 1.0

Magnesium binding site 6 out of 6 in 6n9x

Go back to Magnesium Binding Sites List in 6n9x
Magnesium binding site 6 out of 6 in the Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Bacteriophage T7 Lagging-Strand Dna Polymerase (D5A/E7A) and GP4 (Helicase/Primase) Bound to Dna Including Rna/Dna Hybrid, and An Incoming Dttp (LAGS3) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg803

b:9.2
occ:1.00
 O H:HIS59 3.6 38.0 1.0
OD2 H:ASP65 4.4 35.6 1.0
OD2 H:ASP174 4.4 53.3 1.0
C H:HIS59 4.7 38.0 1.0
O H:ILE6 4.8 34.7 1.0
CG2 H:ILE6 4.9 34.7 1.0

Reference:

Y.Gao, Y.Cui, T.Fox, S.Lin, H.Wang, N.De Val, Z.H.Zhou, W.Yang. Structures and Operating Principles of the Replisome. Science V. 363 2019.
ISSN: ESSN 1095-9203
PubMed: 30679383
DOI: 10.1126/SCIENCE.AAV7003
Page generated: Tue Oct 1 12:37:00 2024

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