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Magnesium in PDB 6n7n: Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form I)

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

All present enzymatic activity of Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form I):
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 I) (pdb code 6n7n). 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 I), PDB code: 6n7n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6n7n

Go back to Magnesium Binding Sites List in 6n7n
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 I)


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

b:30.0
occ:1.00
 O1B B:TTP700 2.0 27.6 1.0
NE2 B:GLN343 2.0 36.6 1.0
OE1 B:GLN343 2.2 36.6 1.0
O1G B:TTP700 2.2 27.6 1.0
CD B:GLN343 2.4 36.6 1.0
OG B:SER319 2.6 27.5 1.0
PB B:TTP700 3.2 27.6 1.0
PG B:TTP700 3.4 27.6 1.0
O3B B:TTP700 3.6 27.6 1.0
CB B:SER319 3.6 27.5 1.0
O3A B:TTP700 3.6 27.6 1.0
O2A B:TTP700 3.9 27.6 1.0
CG B:GLN343 3.9 36.6 1.0
O2G B:TTP700 4.1 27.6 1.0
OD2 B:ASP424 4.2 34.8 1.0
PA B:TTP700 4.3 27.6 1.0
N B:SER319 4.4 27.5 1.0
O2B B:TTP700 4.4 27.6 1.0
OD1 B:ASP424 4.5 34.8 1.0
O3G B:TTP700 4.6 27.6 1.0
CA B:SER319 4.6 27.5 1.0
CB B:GLN343 4.8 36.6 1.0
CG B:ASP424 4.8 34.8 1.0
O1A B:TTP700 4.8 27.6 1.0
NH2 A:ARG522 4.9 34.5 1.0
CZ A:ARG522 5.0 34.5 1.0

Magnesium binding site 2 out of 5 in 6n7n

Go back to Magnesium Binding Sites List in 6n7n
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 I)


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

b:15.4
occ:1.00
 O1G C:TTP700 2.1 17.4 1.0
O1B C:TTP700 2.1 17.4 1.0
OE1 C:GLN343 2.2 25.1 1.0
OG C:SER319 2.5 15.9 1.0
PB C:TTP700 3.1 17.4 1.0
CD C:GLN343 3.1 25.1 1.0
PG C:TTP700 3.2 17.4 1.0
O3B C:TTP700 3.3 17.4 1.0
CB C:SER319 3.3 15.9 1.0
O2A C:TTP700 3.5 17.4 1.0
NE2 C:GLN343 3.5 25.1 1.0
O3A C:TTP700 3.6 17.4 1.0
PA C:TTP700 4.0 17.4 1.0
O2G C:TTP700 4.2 17.4 1.0
O3G C:TTP700 4.3 17.4 1.0
N C:SER319 4.3 15.9 1.0
CG C:GLN343 4.4 25.1 1.0
O1A C:TTP700 4.4 17.4 1.0
CA C:SER319 4.4 15.9 1.0
O2B C:TTP700 4.4 17.4 1.0
CG C:LYS318 4.4 15.1 1.0
OD1 C:ASP424 4.6 23.3 1.0
OD2 C:ASP424 4.8 23.3 1.0
CB C:GLN343 4.9 25.1 1.0
NE B:ARG522 4.9 19.7 1.0
C C:LYS318 5.0 15.1 1.0

Magnesium binding site 3 out of 5 in 6n7n

Go back to Magnesium Binding Sites List in 6n7n
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 I)


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

b:15.5
occ:1.00
 OE1 D:GLN343 2.0 21.1 1.0
O2G D:TTP700 2.3 14.3 1.0
O2B D:TTP700 2.3 14.3 1.0
OG D:SER319 2.5 14.1 1.0
CD D:GLN343 3.0 21.1 1.0
CB D:SER319 3.5 14.1 1.0
NE2 D:GLN343 3.5 21.1 1.0
PG D:TTP700 3.7 14.3 1.0
PB D:TTP700 3.7 14.3 1.0
OD1 D:ASP424 3.8 20.7 1.0
O3B D:TTP700 4.0 14.3 1.0
N D:SER319 4.2 14.1 1.0
O2A D:TTP700 4.2 14.3 1.0
OD2 D:ASP424 4.2 20.7 1.0
NZ D:LYS318 4.3 13.7 1.0
CG D:GLN343 4.4 21.1 1.0
CG D:ASP424 4.4 20.7 1.0
CA D:SER319 4.4 14.1 1.0
O3G D:TTP700 4.5 14.3 1.0
O1B D:TTP700 4.6 14.3 1.0
O1G D:TTP700 4.6 14.3 1.0
O3A D:TTP700 4.7 14.3 1.0
CB D:GLN343 4.8 21.1 1.0

Magnesium binding site 4 out of 5 in 6n7n

Go back to Magnesium Binding Sites List in 6n7n
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 I)


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

b:18.8
occ:1.00
 O2B E:TTP700 2.2 17.9 1.0
O2G E:TTP700 2.2 17.9 1.0
OE1 E:GLN343 2.3 21.4 1.0
OG E:SER319 2.4 15.8 1.0
CD E:GLN343 3.1 21.4 1.0
NE2 E:GLN343 3.3 21.4 1.0
CB E:SER319 3.4 15.8 1.0
OD2 E:ASP424 3.5 19.6 1.0
PB E:TTP700 3.6 17.9 1.0
PG E:TTP700 3.6 17.9 1.0
OD1 E:ASP424 3.8 19.6 1.0
O3B E:TTP700 4.0 17.9 1.0
O2A E:TTP700 4.0 17.9 1.0
CG E:ASP424 4.1 19.6 1.0
NZ E:LYS318 4.3 16.2 1.0
O1G E:TTP700 4.4 17.9 1.0
N E:SER319 4.4 15.8 1.0
O3A E:TTP700 4.5 17.9 1.0
CA E:SER319 4.5 15.8 1.0
O1B E:TTP700 4.5 17.9 1.0
CG E:GLN343 4.6 21.4 1.0
O3G E:TTP700 4.6 17.9 1.0
PA E:TTP700 4.7 17.9 1.0
O1A E:TTP700 4.9 17.9 1.0

Magnesium binding site 5 out of 5 in 6n7n

Go back to Magnesium Binding Sites List in 6n7n
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 I)


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

b:27.5
occ:1.00
 O2B F:TTP700 2.1 29.9 1.0
O1B F:TTP700 2.2 29.9 1.0
OG F:SER319 2.4 31.6 1.0
OE1 F:GLN343 2.5 38.6 1.0
PB F:TTP700 2.5 29.9 1.0
O2G F:TTP700 2.5 29.9 1.0
O3B F:TTP700 3.2 29.9 1.0
PG F:TTP700 3.4 29.9 1.0
CD F:GLN343 3.4 38.6 1.0
CB F:SER319 3.6 31.6 1.0
NZ F:LYS318 3.8 30.9 1.0
OD1 F:ASP424 3.9 40.0 1.0
OD2 F:ASP424 3.9 40.0 1.0
O3A F:TTP700 4.0 29.9 1.0
NE2 F:GLN343 4.1 38.6 1.0
O3G F:TTP700 4.2 29.9 1.0
N F:SER319 4.3 31.6 1.0
CG F:ASP424 4.3 40.0 1.0
CG F:GLN343 4.4 38.6 1.0
CA F:SER319 4.5 31.6 1.0
O1G F:TTP700 4.6 29.9 1.0
CB F:GLN343 4.9 38.6 1.0
PA F:TTP700 5.0 29.9 1.0
CB F:LYS318 5.0 30.9 1.0
O2A F:TTP700 5.0 29.9 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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