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Magnesium in PDB 6n7t: Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III)

Enzymatic activity of Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III)

All present enzymatic activity of Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III):
3.6.4.12;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III) (pdb code 6n7t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III), PDB code: 6n7t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6n7t

Go back to Magnesium Binding Sites List in 6n7t
Magnesium binding site 1 out of 5 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III)


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 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:51.6
occ:1.00
 O1G A:TTP700 2.0 53.8 1.0
O1B A:TTP700 2.0 53.8 1.0
OG A:SER319 2.2 45.8 1.0
OE1 A:GLN343 2.7 62.1 1.0
PB A:TTP700 3.1 53.8 1.0
PG A:TTP700 3.2 53.8 1.0
O3B A:TTP700 3.3 53.8 1.0
CD A:GLN343 3.4 62.1 1.0
O2A A:TTP700 3.4 53.8 1.0
CG A:GLN343 3.4 62.1 1.0
CB A:SER319 3.5 45.8 1.0
O3A A:TTP700 3.8 53.8 1.0
CB A:GLN343 4.0 62.1 1.0
O2G A:TTP700 4.1 53.8 1.0
PA A:TTP700 4.2 53.8 1.0
O3G A:TTP700 4.2 53.8 1.0
N A:SER319 4.3 45.8 1.0
O2B A:TTP700 4.3 53.8 1.0
NH2 F:ARG522 4.4 62.0 1.0
CA A:SER319 4.5 45.8 1.0
NE F:ARG522 4.5 62.0 1.0
O1A A:TTP700 4.6 53.8 1.0
NE2 A:GLN343 4.7 62.1 1.0
CZ F:ARG522 4.7 62.0 1.0
OD1 A:ASP424 4.8 58.0 1.0
OD2 A:ASP424 4.8 58.0 1.0

Magnesium binding site 2 out of 5 in 6n7t

Go back to Magnesium Binding Sites List in 6n7t
Magnesium binding site 2 out of 5 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III)


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 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:32.8
occ:1.00
 OE1 B:GLN343 2.2 40.1 1.0
O1G B:TTP700 2.2 32.7 1.0
OG B:SER319 2.3 30.6 1.0
O1B B:TTP700 2.5 32.7 1.0
O2A B:TTP700 2.6 32.7 1.0
O3A B:TTP700 2.8 32.7 1.0
CD B:GLN343 2.8 40.1 1.0
NE2 B:GLN343 2.8 40.1 1.0
PB B:TTP700 3.0 32.7 1.0
CB B:SER319 3.0 30.6 1.0
PA B:TTP700 3.1 32.7 1.0
PG B:TTP700 3.4 32.7 1.0
O3B B:TTP700 3.4 32.7 1.0
O1A B:TTP700 3.6 32.7 1.0
N B:SER319 4.0 30.6 1.0
CA B:SER319 4.1 30.6 1.0
O2G B:TTP700 4.2 32.7 1.0
CG B:GLN343 4.3 40.1 1.0
O2B B:TTP700 4.4 32.7 1.0
O3G B:TTP700 4.5 32.7 1.0
O5' B:TTP700 4.6 32.7 1.0
OD2 B:ASP424 4.6 35.7 1.0
NE A:ARG522 4.7 41.8 1.0
CB B:GLN343 4.9 40.1 1.0
CD A:ARG522 5.0 41.8 1.0

Magnesium binding site 3 out of 5 in 6n7t

Go back to Magnesium Binding Sites List in 6n7t
Magnesium binding site 3 out of 5 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III)


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 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:26.2
occ:1.00
 O1G C:TTP700 1.9 27.8 1.0
OG C:SER319 2.3 25.0 1.0
O1B C:TTP700 2.3 27.8 1.0
OE1 C:GLN343 2.5 36.8 1.0
CB C:SER319 3.1 25.0 1.0
O2A C:TTP700 3.1 27.8 1.0
PG C:TTP700 3.2 27.8 1.0
NE2 C:GLN343 3.2 36.8 1.0
CD C:GLN343 3.2 36.8 1.0
PB C:TTP700 3.4 27.8 1.0
O3B C:TTP700 3.6 27.8 1.0
O3G C:TTP700 3.8 27.8 1.0
O3A C:TTP700 4.0 27.8 1.0
PA C:TTP700 4.1 27.8 1.0
N C:SER319 4.1 25.0 1.0
CA C:SER319 4.2 25.0 1.0
O2G C:TTP700 4.3 27.8 1.0
CG C:LYS318 4.5 23.9 1.0
OD1 C:ASP424 4.5 34.0 1.0
O1A C:TTP700 4.6 27.8 1.0
CG C:GLN343 4.7 36.8 1.0
O2B C:TTP700 4.7 27.8 1.0
C C:LYS318 4.9 23.9 1.0

Magnesium binding site 4 out of 5 in 6n7t

Go back to Magnesium Binding Sites List in 6n7t
Magnesium binding site 4 out of 5 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III)


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 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:32.5
occ:1.00
 O2B D:TTP700 2.0 31.1 1.0
O2G D:TTP700 2.3 31.1 1.0
OE1 D:GLN343 2.5 40.6 1.0
OG D:SER319 2.6 28.5 1.0
NE2 D:GLN343 3.0 40.6 1.0
CD D:GLN343 3.1 40.6 1.0
PB D:TTP700 3.3 31.1 1.0
PG D:TTP700 3.4 31.1 1.0
CB D:SER319 3.5 28.5 1.0
O3B D:TTP700 3.7 31.1 1.0
O3G D:TTP700 4.0 31.1 1.0
O3A D:TTP700 4.1 31.1 1.0
O1A D:TTP700 4.4 31.1 1.0
N D:SER319 4.4 28.5 1.0
NZ D:LYS318 4.4 28.0 1.0
O1B D:TTP700 4.5 31.1 1.0
OD1 D:ASP424 4.5 33.2 1.0
CG D:GLN343 4.6 40.6 1.0
CA D:SER319 4.6 28.5 1.0
O2A D:TTP700 4.6 31.1 1.0
PA D:TTP700 4.6 31.1 1.0
O1G D:TTP700 4.7 31.1 1.0

Magnesium binding site 5 out of 5 in 6n7t

Go back to Magnesium Binding Sites List in 6n7t
Magnesium binding site 5 out of 5 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III)


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 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:50.1
occ:1.00
 O2B E:TTP700 2.1 46.5 1.0
O2G E:TTP700 2.3 46.5 1.0
OE1 E:GLN343 2.3 61.8 1.0
OG E:SER319 2.4 51.8 1.0
CD E:GLN343 3.1 61.8 1.0
PB E:TTP700 3.2 46.5 1.0
NE2 E:GLN343 3.3 61.8 1.0
PG E:TTP700 3.5 46.5 1.0
O3B E:TTP700 3.5 46.5 1.0
CB E:SER319 3.6 51.8 1.0
O1B E:TTP700 3.7 46.5 1.0
OD2 E:ASP424 3.9 61.6 1.0
OD1 E:ASP424 4.2 61.6 1.0
NZ E:LYS318 4.3 48.5 1.0
O3G E:TTP700 4.4 46.5 1.0
CG E:ASP424 4.4 61.6 1.0
O1G E:TTP700 4.5 46.5 1.0
CG E:GLN343 4.5 61.8 1.0
O3A E:TTP700 4.6 46.5 1.0
N E:SER319 4.6 51.8 1.0
CA E:SER319 4.6 51.8 1.0
O1A E:TTP700 4.8 46.5 1.0
CB E:GLN343 5.0 61.8 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 12:34:29 2024

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