Atomistry » Magnesium » PDB 6n7e-6njv » 6n7v
Atomistry »
  Magnesium »
    PDB 6n7e-6njv »
      6n7v »

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

Go back to Magnesium Binding Sites List in 6n7v
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

Go back to Magnesium Binding Sites List in 6n7v
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

Go back to Magnesium Binding Sites List in 6n7v
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy