Atomistry » Magnesium » PDB 6n7n-6nk8 » 6n9x
Atomistry »
  Magnesium »
    PDB 6n7n-6nk8 »
      6n9x »

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

Go back to Magnesium Binding Sites List in 6n9x
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

Go back to Magnesium Binding Sites List in 6n9x
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

Go back to Magnesium Binding Sites List in 6n9x
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

Go back to Magnesium Binding Sites List in 6n9x
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

Last articles

Ca in 2Z56
Ca in 2Z5Z
Ca in 2Z5G
Ca in 2Z49
Ca in 2Z4E
Ca in 2Z48
Ca in 2Z2Y
Ca in 2Z30
Ca in 2Z2Z
Ca in 2Z2X
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy