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Magnesium in PDB 6n7v: Structure of Bacteriophage T7 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes)

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

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Bacteriophage T7 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes) (pdb code 6n7v). 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 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes), PDB code: 6n7v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6n7v

Go back to Magnesium Binding Sites List in 6n7v
Magnesium binding site 1 out of 5 in the Structure of Bacteriophage T7 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes)


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

b:69.3
occ:1.00
 OG B:SER319 2.2 66.5 1.0
O1B B:TTP700 2.2 74.4 1.0
O1G B:TTP700 2.3 74.4 1.0
OE1 B:GLN343 2.3 87.2 1.0
CB B:SER319 3.0 66.5 1.0
CD B:GLN343 3.1 87.2 1.0
NE2 B:GLN343 3.1 87.2 1.0
PG B:TTP700 3.2 74.4 1.0
O2A B:TTP700 3.2 74.4 1.0
PB B:TTP700 3.3 74.4 1.0
O3G B:TTP700 3.3 74.4 1.0
O3B B:TTP700 3.5 74.4 1.0
N B:SER319 3.9 66.5 1.0
CA B:SER319 4.1 66.5 1.0
O3A B:TTP700 4.1 74.4 1.0
PA B:TTP700 4.3 74.4 1.0
OD2 B:ASP424 4.4 82.5 1.0
CG B:GLN343 4.5 87.2 1.0
O2B B:TTP700 4.5 74.4 1.0
O2G B:TTP700 4.6 74.4 1.0
OD1 B:ASP424 4.7 82.5 1.0
CB B:LYS318 4.9 68.7 1.0
NE A:ARG522 5.0 84.8 1.0

Magnesium binding site 2 out of 5 in 6n7v

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Magnesium binding site 2 out of 5 in the Structure of Bacteriophage T7 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes)


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

b:60.5
occ:1.00
 O1G C:TTP700 2.1 68.0 1.0
O1B C:TTP700 2.2 68.0 1.0
OE1 C:GLN343 2.2 70.0 1.0
OG C:SER319 2.4 60.4 1.0
O2A C:TTP700 3.0 68.0 1.0
CD C:GLN343 3.0 70.0 1.0
PB C:TTP700 3.1 68.0 1.0
NE2 C:GLN343 3.1 70.0 1.0
CB C:SER319 3.2 60.4 1.0
O3A C:TTP700 3.3 68.0 1.0
PG C:TTP700 3.4 68.0 1.0
O3B C:TTP700 3.5 68.0 1.0
PA C:TTP700 3.7 68.0 1.0
O1A C:TTP700 4.2 68.0 1.0
O2G C:TTP700 4.3 68.0 1.0
CA C:SER319 4.4 60.4 1.0
O3G C:TTP700 4.4 68.0 1.0
N C:SER319 4.4 60.4 1.0
CG C:GLN343 4.5 70.0 1.0
O2B C:TTP700 4.5 68.0 1.0
NE B:ARG522 4.6 67.9 1.0
CG C:LYS318 4.8 61.4 1.0
CZ B:ARG522 4.9 67.9 1.0
NH2 B:ARG522 5.0 67.9 1.0
CB C:GLN343 5.0 70.0 1.0

Magnesium binding site 3 out of 5 in 6n7v

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Magnesium binding site 3 out of 5 in the Structure of Bacteriophage T7 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes)


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

b:60.3
occ:1.00
 O2B D:TTP700 2.3 60.1 1.0
OE1 D:GLN343 2.4 64.5 1.0
O2G D:TTP700 2.4 60.1 1.0
OG D:SER319 2.5 60.5 1.0
CD D:GLN343 3.3 64.5 1.0
CB D:SER319 3.4 60.5 1.0
NE2 D:GLN343 3.6 64.5 1.0
PB D:TTP700 3.7 60.1 1.0
PG D:TTP700 3.7 60.1 1.0
O3B D:TTP700 4.1 60.1 1.0
OD1 D:ASP424 4.2 68.7 1.0
O1G D:TTP700 4.3 60.1 1.0
N D:SER319 4.4 60.5 1.0
CA D:SER319 4.5 60.5 1.0
O1B D:TTP700 4.5 60.1 1.0
O2A D:TTP700 4.6 60.1 1.0
OD2 D:ASP424 4.6 68.7 1.0
CG D:GLN343 4.7 64.5 1.0
O3A D:TTP700 4.7 60.1 1.0
CG D:ASP424 4.8 68.7 1.0
NZ D:LYS318 4.8 56.9 1.0
O3G D:TTP700 4.9 60.1 1.0
O1A D:TTP700 4.9 60.1 1.0

Magnesium binding site 4 out of 5 in 6n7v

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Magnesium binding site 4 out of 5 in the Structure of Bacteriophage T7 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes)


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

b:81.8
occ:1.00
 OE1 E:GLN343 2.1 89.7 1.0
OG E:SER319 2.2 77.0 1.0
O2G E:TTP700 2.2 75.8 1.0
O2B E:TTP700 2.3 75.8 1.0
CD E:GLN343 2.8 89.7 1.0
NE2 E:GLN343 2.9 89.7 1.0
CB E:SER319 3.3 77.0 1.0
PG E:TTP700 3.6 75.8 1.0
PB E:TTP700 3.7 75.8 1.0
O3B E:TTP700 4.0 75.8 1.0
NZ E:LYS318 4.0 77.0 1.0
N E:SER319 4.1 77.0 1.0
OD1 E:ASP424 4.2 84.3 1.0
CG E:GLN343 4.3 89.7 1.0
CA E:SER319 4.3 77.0 1.0
O3G E:TTP700 4.4 75.8 1.0
OD2 E:ASP424 4.4 84.3 1.0
O1B E:TTP700 4.4 75.8 1.0
O1G E:TTP700 4.6 75.8 1.0
CG E:ASP424 4.7 84.3 1.0
O3A E:TTP700 4.8 75.8 1.0
O2A E:TTP700 4.8 75.8 1.0
CB E:GLN343 4.9 89.7 1.0
CB E:LYS318 5.0 77.0 1.0

Magnesium binding site 5 out of 5 in 6n7v

Go back to Magnesium Binding Sites List in 6n7v
Magnesium binding site 5 out of 5 in the Structure of Bacteriophage T7 GP4 (Helicase-Primase, E343Q Mutant) in Complex with Ssdna, Dttp, Ac Dinucleotide, and Ctp (From Multiple Lead Complexes)


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

b:0.3
occ:1.00
 O2G F:TTP700 2.1 0.0 1.0
OE1 F:GLN343 2.2 0.2 1.0
OG F:SER319 2.2 1.0 1.0
O2B F:TTP700 2.4 0.0 1.0
O1B F:TTP700 2.5 0.0 1.0
PB F:TTP700 2.8 0.0 1.0
NE2 F:GLN343 2.8 0.2 1.0
CD F:GLN343 2.8 0.2 1.0
PG F:TTP700 3.2 0.0 1.0
O3B F:TTP700 3.2 0.0 1.0
CB F:SER319 3.3 1.0 1.0
OD2 F:ASP424 3.7 0.4 1.0
OD1 F:ASP424 3.9 0.4 1.0
NZ F:LYS318 4.0 0.5 1.0
N F:SER319 4.0 1.0 1.0
O3G F:TTP700 4.0 0.0 1.0
CG F:ASP424 4.2 0.4 1.0
CA F:SER319 4.2 1.0 1.0
CG F:GLN343 4.3 0.2 1.0
O3A F:TTP700 4.3 0.0 1.0
O1G F:TTP700 4.4 0.0 1.0
CB F:LYS318 4.8 0.5 1.0
CB F:GLN343 4.9 0.2 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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