Magnesium in PDB 6n7i: Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (GP4(5)-Dna)

Enzymatic activity of Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (GP4(5)-Dna)

All present enzymatic activity of Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (GP4(5)-Dna):
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 (GP4(5)-Dna) (pdb code 6n7i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 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 (GP4(5)-Dna), PDB code: 6n7i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6n7i

Go back to Magnesium Binding Sites List in 6n7i
Magnesium binding site 1 out of 4 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (GP4(5)-Dna)


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 (GP4(5)-Dna) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:37.8
occ:1.00
O1B B:TTP700 2.2 38.3 1.0
O1G B:TTP700 2.2 38.3 1.0
OG B:SER319 2.2 34.0 1.0
OE1 B:GLN343 2.2 48.0 1.0
CD B:GLN343 2.9 48.0 1.0
NE2 B:GLN343 2.9 48.0 1.0
CB B:SER319 3.3 34.0 1.0
PB B:TTP700 3.4 38.3 1.0
PG B:TTP700 3.5 38.3 1.0
O2A B:TTP700 3.7 38.3 1.0
O3B B:TTP700 3.8 38.3 1.0
O3A B:TTP700 4.1 38.3 1.0
N B:SER319 4.2 34.0 1.0
CA B:SER319 4.3 34.0 1.0
CG B:GLN343 4.4 48.0 1.0
O2G B:TTP700 4.4 38.3 1.0
O3G B:TTP700 4.5 38.3 1.0
PA B:TTP700 4.5 38.3 1.0
O2B B:TTP700 4.6 38.3 1.0
OD2 B:ASP424 4.6 42.5 1.0
OD1 B:ASP424 4.8 42.5 1.0
CB B:GLN343 5.0 48.0 1.0

Magnesium binding site 2 out of 4 in 6n7i

Go back to Magnesium Binding Sites List in 6n7i
Magnesium binding site 2 out of 4 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (GP4(5)-Dna)


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 (GP4(5)-Dna) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:25.9
occ:1.00
NE2 C:GLN343 2.2 34.8 1.0
O1G C:TTP700 2.2 24.3 1.0
OG C:SER319 2.3 23.2 1.0
OE1 C:GLN343 2.3 34.8 1.0
O1B C:TTP700 2.3 24.3 1.0
CD C:GLN343 2.5 34.8 1.0
CB C:SER319 3.3 23.2 1.0
PB C:TTP700 3.6 24.3 1.0
PG C:TTP700 3.6 24.3 1.0
O2A C:TTP700 3.9 24.3 1.0
O3B C:TTP700 3.9 24.3 1.0
CG C:GLN343 4.0 34.8 1.0
OD1 C:ASP424 4.1 31.5 1.0
O3A C:TTP700 4.3 24.3 1.0
CG C:LYS318 4.4 23.2 1.0
O2G C:TTP700 4.4 24.3 1.0
CA C:SER319 4.5 23.2 1.0
N C:SER319 4.5 23.2 1.0
OD2 C:ASP424 4.6 31.5 1.0
O3G C:TTP700 4.6 24.3 1.0
PA C:TTP700 4.7 24.3 1.0
O2B C:TTP700 4.7 24.3 1.0
CG C:ASP424 4.7 31.5 1.0
CB C:GLN343 4.9 34.8 1.0
CD C:LYS318 5.0 23.2 1.0

Magnesium binding site 3 out of 4 in 6n7i

Go back to Magnesium Binding Sites List in 6n7i
Magnesium binding site 3 out of 4 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (GP4(5)-Dna)


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 (GP4(5)-Dna) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:27.3
occ:1.00
O2G D:TTP700 2.3 24.3 1.0
O2B D:TTP700 2.3 24.3 1.0
OE1 D:GLN343 2.5 37.6 1.0
OG D:SER319 2.8 24.8 1.0
CD D:GLN343 3.4 37.6 1.0
CB D:SER319 3.4 24.8 1.0
OD1 D:ASP424 3.6 37.7 1.0
NE2 D:GLN343 3.6 37.6 1.0
PG D:TTP700 3.7 24.3 1.0
PB D:TTP700 3.7 24.3 1.0
O3B D:TTP700 4.0 24.3 1.0
N D:SER319 4.2 24.8 1.0
O2A D:TTP700 4.2 24.3 1.0
NZ D:LYS318 4.3 23.8 1.0
CA D:SER319 4.4 24.8 1.0
CG D:ASP424 4.4 37.7 1.0
OD2 D:ASP424 4.5 37.7 1.0
O3G D:TTP700 4.5 24.3 1.0
O1B D:TTP700 4.6 24.3 1.0
O1G D:TTP700 4.6 24.3 1.0
O3A D:TTP700 4.7 24.3 1.0
CG D:GLN343 4.8 37.6 1.0

Magnesium binding site 4 out of 4 in 6n7i

Go back to Magnesium Binding Sites List in 6n7i
Magnesium binding site 4 out of 4 in the Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (GP4(5)-Dna)


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 (GP4(5)-Dna) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:40.6
occ:1.00
O2B E:TTP700 2.2 37.3 1.0
OE1 E:GLN343 2.3 49.4 1.0
O2G E:TTP700 2.4 37.3 1.0
OG E:SER319 2.6 36.1 1.0
CD E:GLN343 3.0 49.4 1.0
NE2 E:GLN343 3.1 49.4 1.0
PB E:TTP700 3.6 37.3 1.0
CB E:SER319 3.6 36.1 1.0
PG E:TTP700 3.7 37.3 1.0
OD2 E:ASP424 4.0 45.4 1.0
O3B E:TTP700 4.0 37.3 1.0
OD1 E:ASP424 4.2 45.4 1.0
O3G E:TTP700 4.3 37.3 1.0
O2A E:TTP700 4.3 37.3 1.0
CG E:GLN343 4.4 49.4 1.0
CG E:ASP424 4.5 45.4 1.0
O1B E:TTP700 4.5 37.3 1.0
N E:SER319 4.5 36.1 1.0
O3A E:TTP700 4.6 37.3 1.0
NZ E:LYS318 4.7 35.6 1.0
O D:HOH801 4.7 36.7 1.0
CA E:SER319 4.7 36.1 1.0
O1G E:TTP700 4.8 37.3 1.0
PA E:TTP700 4.9 37.3 1.0
CB E:GLN343 5.0 49.4 1.0
O1A E:TTP700 5.0 37.3 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 23:39:40 2020

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