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Magnesium in PDB 6n9v: 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 (LAGS1)

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 (LAGS1)

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 (LAGS1):
2.7.7.7; 3.6.4.12;

Other elements in 6n9v:

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 (LAGS1) 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 (LAGS1) (pdb code 6n9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 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 (LAGS1), PDB code: 6n9v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6n9v

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Magnesium binding site 1 out of 7 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 (LAGS1)


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 (LAGS1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:50.3
occ:1.00
 O1G B:TTP700 2.2 51.6 1.0
O1B B:TTP700 2.2 51.6 1.0
OG B:SER319 2.2 49.3 1.0
OE1 B:GLN343 2.2 70.9 1.0
CD B:GLN343 2.9 70.9 1.0
NE2 B:GLN343 3.1 70.9 1.0
CB B:SER319 3.4 49.3 1.0
PB B:TTP700 3.4 51.6 1.0
PG B:TTP700 3.5 51.6 1.0
O3B B:TTP700 3.7 51.6 1.0
O2A B:TTP700 4.2 51.6 1.0
OD2 B:ASP424 4.3 52.4 1.0
CG B:GLN343 4.3 70.9 1.0
O3A B:TTP700 4.4 51.6 1.0
N B:SER319 4.4 49.3 1.0
O3G B:TTP700 4.4 51.6 1.0
CA B:SER319 4.4 49.3 1.0
O2G B:TTP700 4.4 51.6 1.0
O2B B:TTP700 4.5 51.6 1.0
OD1 B:ASP424 4.5 52.4 1.0
PA B:TTP700 4.7 51.6 1.0
O1A B:TTP700 4.8 51.6 1.0
CG B:ASP424 4.9 52.4 1.0
CB B:GLN343 4.9 70.9 1.0

Magnesium binding site 2 out of 7 in 6n9v

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Magnesium binding site 2 out of 7 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 (LAGS1)


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 (LAGS1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:56.7
occ:1.00
 O1B C:TTP700 2.3 40.2 1.0
O1G C:TTP700 2.3 40.2 1.0
OG C:SER319 2.3 47.9 1.0
OE1 C:GLN343 2.3 67.8 1.0
NE2 C:GLN343 2.4 67.8 1.0
CD C:GLN343 2.7 67.8 1.0
O3B C:TTP700 3.1 40.2 1.0
PB C:TTP700 3.2 40.2 1.0
PG C:TTP700 3.2 40.2 1.0
CB C:SER319 3.2 47.9 1.0
O2A C:TTP700 3.9 40.2 1.0
O3A C:TTP700 4.2 40.2 1.0
CG C:GLN343 4.2 67.8 1.0
O2G C:TTP700 4.2 40.2 1.0
O3G C:TTP700 4.3 40.2 1.0
O2B C:TTP700 4.4 40.2 1.0
CG C:LYS318 4.4 43.9 1.0
CA C:SER319 4.4 47.9 1.0
N C:SER319 4.5 47.9 1.0
NE B:ARG522 4.6 47.8 1.0
PA C:TTP700 4.6 40.2 1.0
CZ B:ARG522 5.0 47.8 1.0
CB C:GLN343 5.0 67.8 1.0

Magnesium binding site 3 out of 7 in 6n9v

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Magnesium binding site 3 out of 7 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 (LAGS1)


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 (LAGS1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:47.8
occ:1.00
 O2G D:TTP700 2.1 49.6 1.0
OG D:SER319 2.2 42.5 1.0
O2B D:TTP700 2.4 49.6 1.0
OE1 D:GLN343 2.5 63.8 1.0
CD D:GLN343 3.3 63.8 1.0
CB D:SER319 3.3 42.5 1.0
NE2 D:GLN343 3.4 63.8 1.0
PG D:TTP700 3.5 49.6 1.0
PB D:TTP700 3.7 49.6 1.0
O3B D:TTP700 4.0 49.6 1.0
O2A D:TTP700 4.0 49.6 1.0
N D:SER319 4.1 42.5 1.0
OD1 D:ASP424 4.2 52.2 1.0
O1G D:TTP700 4.3 49.6 1.0
CA D:SER319 4.3 42.5 1.0
NZ D:LYS318 4.3 43.2 1.0
O3G D:TTP700 4.6 49.6 1.0
O3A D:TTP700 4.6 49.6 1.0
CG D:GLN343 4.7 63.8 1.0
OD2 D:ASP424 4.8 52.2 1.0
O1B D:TTP700 4.8 49.6 1.0
PA D:TTP700 4.9 49.6 1.0
CG D:ASP424 4.9 52.2 1.0
CB D:LYS318 4.9 43.2 1.0

Magnesium binding site 4 out of 7 in 6n9v

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Magnesium binding site 4 out of 7 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 (LAGS1)


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 (LAGS1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:59.3
occ:1.00
 O2B E:TTP602 2.2 57.6 1.0
O2G E:TTP602 2.2 57.6 1.0
OG E:SER319 2.2 42.2 1.0
OE1 E:GLN343 2.3 68.4 1.0
CD E:GLN343 3.0 68.4 1.0
NE2 E:GLN343 3.1 68.4 1.0
CB E:SER319 3.4 42.2 1.0
PB E:TTP602 3.6 57.6 1.0
PG E:TTP602 3.6 57.6 1.0
OD2 E:ASP424 3.9 61.7 1.0
O3B E:TTP602 3.9 57.6 1.0
OD1 E:ASP424 4.2 61.7 1.0
O1B E:TTP602 4.3 57.6 1.0
O1G E:TTP602 4.4 57.6 1.0
CG E:ASP424 4.5 61.7 1.0
CG E:GLN343 4.5 68.4 1.0
CA E:SER319 4.5 42.2 1.0
N E:SER319 4.6 42.2 1.0
O3G E:TTP602 4.6 57.6 1.0
NZ E:LYS318 4.6 41.7 1.0
O2A E:TTP602 4.7 57.6 1.0
O3A E:TTP602 4.7 57.6 1.0

Magnesium binding site 5 out of 7 in 6n9v

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Magnesium binding site 5 out of 7 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 (LAGS1)


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 (LAGS1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg701

b:57.5
occ:1.00
 O2B F:TTP700 2.1 63.7 1.0
OG F:SER319 2.2 56.3 1.0
OE1 F:GLN343 2.2 64.5 1.0
O1B F:TTP700 2.2 63.7 1.0
O2G F:TTP700 2.3 63.7 1.0
PB F:TTP700 2.5 63.7 1.0
CD F:GLN343 3.2 64.5 1.0
O3B F:TTP700 3.2 63.7 1.0
PG F:TTP700 3.3 63.7 1.0
CB F:SER319 3.4 56.3 1.0
NE2 F:GLN343 3.5 64.5 1.0
O3A F:TTP700 4.1 63.7 1.0
N F:SER319 4.2 56.3 1.0
O3G F:TTP700 4.3 63.7 1.0
OD1 F:ASP424 4.3 66.8 1.0
CA F:SER319 4.4 56.3 1.0
O1G F:TTP700 4.4 63.7 1.0
NZ F:LYS318 4.6 54.1 1.0
CG F:GLN343 4.6 64.5 1.0
OD2 F:ASP424 4.8 66.8 1.0
O1A F:TTP700 4.9 63.7 1.0
CB F:GLN343 4.9 64.5 1.0
PA F:TTP700 4.9 63.7 1.0
CG F:ASP424 5.0 66.8 1.0

Magnesium binding site 6 out of 7 in 6n9v

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Magnesium binding site 6 out of 7 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 (LAGS1)


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 (LAGS1) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg802

b:0.1
occ:1.00
 OD2 H:ASP654 2.2 0.9 1.0
O H:ALA476 2.3 0.2 1.0
O2B H:TTP801 2.4 0.8 1.0
O1G H:TTP801 2.4 0.8 1.0
OD1 H:ASP475 2.5 0.2 1.0
O2A H:TTP801 2.6 0.8 1.0
OD2 H:ASP475 3.0 0.2 1.0
CG H:ASP475 3.0 0.2 1.0
CG H:ASP654 3.4 0.9 1.0
C H:ALA476 3.5 0.2 1.0
PB H:TTP801 3.6 0.8 1.0
PG H:TTP801 3.7 0.8 1.0
PA H:TTP801 3.9 0.8 1.0
O3B H:TTP801 4.0 0.8 1.0
O3A H:TTP801 4.1 0.8 1.0
OD1 H:ASP654 4.1 0.9 1.0
N H:ALA476 4.3 0.2 1.0
CB H:ASP654 4.3 0.9 1.0
N H:SER477 4.4 0.8 1.0
CA H:SER477 4.4 0.8 1.0
CB H:ASP475 4.4 0.2 1.0
CA H:ALA476 4.5 0.2 1.0
O3G H:TTP801 4.5 0.8 1.0
O2G H:TTP801 4.8 0.8 1.0
C5' H:TTP801 4.8 0.8 1.0
C H:ASP475 4.8 0.2 1.0
O1B H:TTP801 4.8 0.8 1.0
O1A H:TTP801 4.8 0.8 1.0
O5' H:TTP801 4.9 0.8 1.0
N H:GLY478 5.0 1.0 1.0

Magnesium binding site 7 out of 7 in 6n9v

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Magnesium binding site 7 out of 7 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 (LAGS1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 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 (LAGS1) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg803

b:84.2
occ:1.00
 O H:HIS59 3.6 0.8 1.0
OD2 H:ASP65 4.4 0.8 1.0
OD2 H:ASP174 4.4 0.6 1.0
C H:HIS59 4.7 0.8 1.0
O H:ILE6 4.8 0.0 1.0
CG2 H:ILE6 4.9 0.0 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 12:36:36 2024

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