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Magnesium in PDB 6n9w: 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 (LAGS2)

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 (LAGS2)

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 (LAGS2):
2.7.7.7; 3.6.4.12;

Other elements in 6n9w:

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 (LAGS2) 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 (LAGS2) (pdb code 6n9w). 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 (LAGS2), PDB code: 6n9w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6n9w

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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 (LAGS2)


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 (LAGS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:0.6
occ:1.00
 OG B:SER319 2.1 0.5 1.0
O1G B:TTP700 2.1 0.4 1.0
O1B B:TTP700 2.3 0.4 1.0
OE1 B:GLN343 2.3 0.8 1.0
NE2 B:GLN343 2.9 0.8 1.0
CD B:GLN343 2.9 0.8 1.0
CB B:SER319 2.9 0.5 1.0
O2A B:TTP700 3.0 0.4 1.0
PG B:TTP700 3.1 0.4 1.0
PB B:TTP700 3.2 0.4 1.0
O3B B:TTP700 3.2 0.4 1.0
O3G B:TTP700 3.6 0.4 1.0
O3A B:TTP700 3.8 0.4 1.0
N B:SER319 3.9 0.5 1.0
PA B:TTP700 4.0 0.4 1.0
CA B:SER319 4.0 0.5 1.0
O2G B:TTP700 4.4 0.4 1.0
CG B:GLN343 4.4 0.8 1.0
O2B B:TTP700 4.5 0.4 1.0
OD2 B:ASP424 4.6 0.2 1.0
O1A B:TTP700 4.7 0.4 1.0
NE A:ARG522 4.8 0.4 1.0
CZ A:ARG522 4.8 0.4 1.0
NH2 A:ARG522 4.9 0.4 1.0

Magnesium binding site 2 out of 6 in 6n9w

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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 (LAGS2)


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 (LAGS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:0.2
occ:1.00
 O1B C:TTP700 2.1 0.5 1.0
O1G C:TTP700 2.2 0.5 1.0
OG C:SER319 2.2 0.1 1.0
OE1 C:GLN343 2.4 0.8 1.0
CB C:SER319 3.1 0.1 1.0
PB C:TTP700 3.1 0.5 1.0
O3B C:TTP700 3.1 0.5 1.0
PG C:TTP700 3.2 0.5 1.0
CD C:GLN343 3.2 0.8 1.0
O2A C:TTP700 3.6 0.5 1.0
NE2 C:GLN343 3.6 0.8 1.0
O3A C:TTP700 3.8 0.5 1.0
PA C:TTP700 4.0 0.5 1.0
O1A C:TTP700 4.1 0.5 1.0
O3G C:TTP700 4.1 0.5 1.0
CG C:GLN343 4.2 0.8 1.0
O2G C:TTP700 4.2 0.5 1.0
CA C:SER319 4.3 0.1 1.0
N C:SER319 4.3 0.1 1.0
O2B C:TTP700 4.4 0.5 1.0
CG C:LYS318 4.7 0.9 1.0
NE B:ARG522 4.8 0.1 1.0
CB C:GLN343 4.9 0.8 1.0

Magnesium binding site 3 out of 6 in 6n9w

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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 (LAGS2)


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 (LAGS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:0.2
occ:1.00
 O2G D:TTP700 2.2 0.4 1.0
OG D:SER319 2.3 0.6 1.0
O2B D:TTP700 2.5 0.4 1.0
OE1 D:GLN343 2.5 0.3 1.0
CD D:GLN343 3.3 0.3 1.0
NE2 D:GLN343 3.5 0.3 1.0
PG D:TTP700 3.5 0.4 1.0
CB D:SER319 3.6 0.6 1.0
PB D:TTP700 3.7 0.4 1.0
OD1 D:ASP424 3.8 0.1 1.0
O3B D:TTP700 3.8 0.4 1.0
O1A D:TTP700 4.3 0.4 1.0
N D:SER319 4.4 0.6 1.0
O3G D:TTP700 4.4 0.4 1.0
O1G D:TTP700 4.5 0.4 1.0
CA D:SER319 4.5 0.6 1.0
CG D:ASP424 4.6 0.1 1.0
O3A D:TTP700 4.7 0.4 1.0
OD2 D:ASP424 4.7 0.1 1.0
O1B D:TTP700 4.7 0.4 1.0
CG D:GLN343 4.8 0.3 1.0
NZ D:LYS318 4.9 0.2 1.0
PA D:TTP700 4.9 0.4 1.0
O2A D:TTP700 4.9 0.4 1.0

Magnesium binding site 4 out of 6 in 6n9w

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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 (LAGS2)


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 (LAGS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:0.3
occ:1.00
 OG E:SER319 2.2 0.3 1.0
O2G E:TTP700 2.3 0.9 1.0
O2B E:TTP700 2.3 0.9 1.0
OE1 E:GLN343 2.4 0.2 1.0
CD E:GLN343 3.1 0.2 1.0
NE2 E:GLN343 3.2 0.2 1.0
PG E:TTP700 3.2 0.9 1.0
O3B E:TTP700 3.2 0.9 1.0
CB E:SER319 3.2 0.3 1.0
PB E:TTP700 3.3 0.9 1.0
O2A E:TTP700 3.3 0.9 1.0
O1G E:TTP700 3.8 0.9 1.0
O3A E:TTP700 4.0 0.9 1.0
N E:SER319 4.1 0.3 1.0
PA E:TTP700 4.2 0.9 1.0
CA E:SER319 4.3 0.3 1.0
O3G E:TTP700 4.5 0.9 1.0
O1A E:TTP700 4.5 0.9 1.0
CG E:GLN343 4.5 0.2 1.0
O1B E:TTP700 4.5 0.9 1.0
NZ E:LYS318 4.6 0.1 1.0
OD1 E:ASP424 4.8 0.4 1.0

Magnesium binding site 5 out of 6 in 6n9w

Go back to Magnesium Binding Sites List in 6n9w
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 (LAGS2)


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 (LAGS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg802

b:0.8
occ:1.00
 OD2 H:ASP654 2.1 0.6 1.0
O H:ALA476 2.2 0.8 1.0
O1G H:TTP801 2.2 1.0 1.0
O2B H:TTP801 2.3 1.0 1.0
OD1 H:ASP475 2.4 0.2 1.0
OD2 H:ASP475 2.5 0.2 1.0
O2A H:TTP801 2.6 1.0 1.0
CG H:ASP475 2.7 0.2 1.0
CG H:ASP654 3.2 0.6 1.0
C H:ALA476 3.3 0.8 1.0
PB H:TTP801 3.4 1.0 1.0
PG H:TTP801 3.4 1.0 1.0
O3B H:TTP801 3.7 1.0 1.0
OD1 H:ASP654 3.8 0.6 1.0
PA H:TTP801 3.8 1.0 1.0
O3A H:TTP801 3.8 1.0 1.0
CB H:ASP475 4.0 0.2 1.0
O3G H:TTP801 4.0 1.0 1.0
N H:ALA476 4.1 0.8 1.0
N H:SER477 4.2 0.3 1.0
CA H:SER477 4.2 0.3 1.0
CB H:ASP654 4.2 0.6 1.0
CA H:ALA476 4.3 0.8 1.0
C H:ASP475 4.5 0.2 1.0
OG H:SER477 4.6 0.3 1.0
O2G H:TTP801 4.7 1.0 1.0
O1B H:TTP801 4.7 1.0 1.0
CA H:ASP475 4.8 0.2 1.0
O1A H:TTP801 4.8 1.0 1.0
O5' H:TTP801 4.8 1.0 1.0
C5' H:TTP801 4.9 1.0 1.0

Magnesium binding site 6 out of 6 in 6n9w

Go back to Magnesium Binding Sites List in 6n9w
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 (LAGS2)


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 (LAGS2) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg803

b:79.3
occ:1.00
 O H:HIS59 3.9 1.0 1.0
OD2 H:ASP174 4.4 0.7 1.0
CD2 H:HIS59 4.9 1.0 1.0
O H:ILE6 5.0 0.5 1.0
CB H:HIS59 5.0 1.0 1.0
C H:HIS59 5.0 1.0 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 12:36:40 2024

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