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: Mon Dec 14 23:39:59 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy