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Magnesium in PDB 6n7s: Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form II)

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

All present enzymatic activity of Structure of Bacteriophage T7 E343Q Mutant GP4 Helicase-Primase in Complex with Ssdna, Dttp, Ac Dinucleotide and Ctp (Form II):
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 II) (pdb code 6n7s). 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 (Form II), PDB code: 6n7s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6n7s

Go back to Magnesium Binding Sites List in 6n7s
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 (Form II)


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

b:48.9
occ:1.00
 O3A B:TTP700 2.2 57.6 1.0
O1G B:TTP700 2.3 57.6 1.0
OG B:SER319 2.4 58.5 1.0
OE1 B:GLN343 2.5 76.8 1.0
O1B B:TTP700 2.6 57.6 1.0
PB B:TTP700 2.7 57.6 1.0
O3B B:TTP700 3.2 57.6 1.0
CD B:GLN343 3.2 76.8 1.0
CB B:SER319 3.2 58.5 1.0
O2A B:TTP700 3.2 57.6 1.0
PA B:TTP700 3.2 57.6 1.0
PG B:TTP700 3.3 57.6 1.0
NE2 B:GLN343 3.3 76.8 1.0
O1A B:TTP700 3.9 57.6 1.0
O2B B:TTP700 4.2 57.6 1.0
O3G B:TTP700 4.2 57.6 1.0
O2G B:TTP700 4.4 57.6 1.0
N B:SER319 4.4 58.5 1.0
CA B:SER319 4.4 58.5 1.0
CG B:GLN343 4.6 76.8 1.0
O5' B:TTP700 4.7 57.6 1.0
NE A:ARG522 4.7 72.8 1.0
CZ A:ARG522 4.8 72.8 1.0
CD A:ARG522 4.9 72.8 1.0
NH1 A:ARG522 4.9 72.8 1.0
C B:LYS318 5.0 54.1 1.0

Magnesium binding site 2 out of 4 in 6n7s

Go back to Magnesium Binding Sites List in 6n7s
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 (Form II)


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

b:33.3
occ:1.00
 OE1 C:GLN343 1.8 42.6 1.0
O1G C:TTP700 2.1 36.5 1.0
O1B C:TTP700 2.3 36.5 1.0
CD C:GLN343 2.4 42.6 1.0
NE2 C:GLN343 2.4 42.6 1.0
OG C:SER319 3.1 40.1 1.0
O2A C:TTP700 3.2 36.5 1.0
PB C:TTP700 3.3 36.5 1.0
O3A C:TTP700 3.3 36.5 1.0
O1A C:TTP700 3.4 36.5 1.0
PG C:TTP700 3.4 36.5 1.0
PA C:TTP700 3.5 36.5 1.0
CB C:SER319 3.6 40.1 1.0
O3B C:TTP700 3.7 36.5 1.0
CG C:GLN343 3.9 42.6 1.0
O3G C:TTP700 4.2 36.5 1.0
N C:SER319 4.3 40.1 1.0
CG C:LYS318 4.5 39.8 1.0
OD1 C:ASP424 4.5 53.1 1.0
O2G C:TTP700 4.5 36.5 1.0
CA C:SER319 4.6 40.1 1.0
O2B C:TTP700 4.6 36.5 1.0
C C:LYS318 4.8 39.8 1.0
CB C:GLN343 4.8 42.6 1.0

Magnesium binding site 3 out of 4 in 6n7s

Go back to Magnesium Binding Sites List in 6n7s
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 (Form II)


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

b:47.8
occ:1.00
 O2G D:TTP700 2.0 41.9 1.0
O2B D:TTP700 2.2 41.9 1.0
OE1 D:GLN343 2.3 53.0 1.0
OG D:SER319 2.7 45.2 1.0
O2A D:TTP700 2.8 41.9 1.0
CD D:GLN343 2.8 53.0 1.0
PB D:TTP700 2.9 41.9 1.0
PG D:TTP700 3.0 41.9 1.0
CB D:SER319 3.1 45.2 1.0
O3B D:TTP700 3.2 41.9 1.0
O3A D:TTP700 3.2 41.9 1.0
NE2 D:GLN343 3.3 53.0 1.0
PA D:TTP700 3.4 41.9 1.0
O1G D:TTP700 3.5 41.9 1.0
CG D:GLN343 3.7 53.0 1.0
O1A D:TTP700 3.8 41.9 1.0
N D:SER319 3.9 45.2 1.0
CA D:SER319 4.1 45.2 1.0
O3G D:TTP700 4.3 41.9 1.0
C D:LYS318 4.4 47.7 1.0
O1B D:TTP700 4.4 41.9 1.0
CB D:GLN343 4.6 53.0 1.0
O D:LYS318 4.7 47.7 1.0
N D:LYS318 4.9 47.7 1.0
OD1 D:ASP424 5.0 51.1 1.0
O5' D:TTP700 5.0 41.9 1.0

Magnesium binding site 4 out of 4 in 6n7s

Go back to Magnesium Binding Sites List in 6n7s
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 (Form II)


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

b:85.0
occ:1.00
 OE1 E:GLN343 1.9 80.1 1.0
O1B E:TTP700 2.0 61.8 1.0
O2B E:TTP700 2.3 61.8 1.0
CD E:GLN343 2.5 80.1 1.0
NE2 E:GLN343 2.6 80.1 1.0
PB E:TTP700 2.6 61.8 1.0
O2G E:TTP700 3.2 61.8 1.0
OG E:SER319 3.3 61.4 1.0
O3B E:TTP700 3.4 61.8 1.0
OD2 E:ASP424 3.4 77.7 1.0
OD1 E:ASP424 3.5 77.7 1.0
CG E:ASP424 3.7 77.7 1.0
PG E:TTP700 3.9 61.8 1.0
CG E:GLN343 3.9 80.1 1.0
O3A E:TTP700 4.0 61.8 1.0
CB E:SER319 4.1 61.4 1.0
NZ E:LYS318 4.4 65.9 1.0
CB E:GLN343 4.5 80.1 1.0
O1G E:TTP700 4.7 61.8 1.0
O1A E:TTP700 4.8 61.8 1.0
PA E:TTP700 4.9 61.8 1.0
N E:SER319 5.0 61.4 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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