Atomistry » Magnesium » PDB 8dtw-8e23 » 8dvi
Atomistry »
  Magnesium »
    PDB 8dtw-8e23 »
      8dvi »

Magnesium in PDB 8dvi: T4 Bacteriophage Primosome with Single Strand Dna, State 2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T4 Bacteriophage Primosome with Single Strand Dna, State 2 (pdb code 8dvi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the T4 Bacteriophage Primosome with Single Strand Dna, State 2, PDB code: 8dvi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8dvi

Go back to Magnesium Binding Sites List in 8dvi
Magnesium binding site 1 out of 5 in the T4 Bacteriophage Primosome with Single Strand Dna, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T4 Bacteriophage Primosome with Single Strand Dna, State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:46.0
occ:1.00
O3B B:AGS501 2.0 58.7 1.0
OE2 B:GLU227 2.0 64.5 1.0
O3A B:AGS501 2.5 61.4 1.0
PB B:AGS501 2.7 54.6 1.0
OG B:SER204 2.8 56.3 1.0
CD B:GLU227 3.0 64.7 1.0
PG B:AGS501 3.1 73.5 1.0
OE1 B:GLU227 3.4 66.0 1.0
O3G B:AGS501 3.4 72.1 1.0
CB B:SER204 3.5 49.2 1.0
O2B B:AGS501 3.6 68.4 1.0
O2G B:AGS501 3.7 64.7 1.0
NZ B:LYS203 3.7 64.3 1.0
PA B:AGS501 3.9 58.5 1.0
O1B B:AGS501 3.9 57.3 1.0
O2A B:AGS501 4.1 65.3 1.0
CG B:GLU227 4.3 59.1 1.0
O B:GLY202 4.4 74.2 1.0
N B:SER204 4.5 48.0 1.0
O1A B:AGS501 4.6 66.6 1.0
CA B:SER204 4.6 43.1 1.0
C B:LYS203 4.7 56.7 1.0
O B:LYS203 4.7 65.2 1.0
CE B:LYS203 4.7 58.3 1.0
OD1 B:ASP311 4.7 66.8 1.0
S1G B:AGS501 4.8 67.2 1.0
O5' B:AGS501 5.0 52.4 1.0
OD2 B:ASP311 5.0 70.1 1.0

Magnesium binding site 2 out of 5 in 8dvi

Go back to Magnesium Binding Sites List in 8dvi
Magnesium binding site 2 out of 5 in the T4 Bacteriophage Primosome with Single Strand Dna, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T4 Bacteriophage Primosome with Single Strand Dna, State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:71.1
occ:1.00
O1B C:AGS501 1.9 52.9 1.0
OE2 C:GLU227 2.0 68.2 1.0
OG C:SER204 2.5 48.8 1.0
O3G C:AGS501 2.8 59.5 1.0
CD C:GLU227 3.0 68.1 1.0
PB C:AGS501 3.2 33.1 1.0
OE1 C:GLU227 3.6 69.3 1.0
CB C:SER204 3.6 44.3 1.0
O3B C:AGS501 3.7 47.2 1.0
PG C:AGS501 3.9 56.0 1.0
O1A C:AGS501 4.1 49.9 1.0
O3A C:AGS501 4.1 41.0 1.0
OD2 C:ASP311 4.1 71.7 1.0
CG C:GLU227 4.2 64.3 1.0
OD1 C:ASP311 4.2 68.2 1.0
O2B C:AGS501 4.3 60.1 1.0
CG C:ASP311 4.5 66.5 1.0
SD C:MET228 4.5 80.2 1.0
CE C:MET228 4.6 65.5 1.0
N C:SER204 4.6 36.7 1.0
NH2 B:ARG407 4.6 38.7 1.0
CA C:SER204 4.7 33.8 1.0
PA C:AGS501 4.7 35.8 1.0
CG C:MET228 4.7 62.5 1.0
O2G C:AGS501 4.7 54.8 1.0
CZ B:ARG407 4.8 42.2 1.0

Magnesium binding site 3 out of 5 in 8dvi

Go back to Magnesium Binding Sites List in 8dvi
Magnesium binding site 3 out of 5 in the T4 Bacteriophage Primosome with Single Strand Dna, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T4 Bacteriophage Primosome with Single Strand Dna, State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:72.8
occ:1.00
O2B D:AGS501 2.2 52.3 1.0
S1G D:AGS501 2.5 73.5 1.0
O2G D:AGS501 2.8 57.0 1.0
PG D:AGS501 2.9 76.3 1.0
O3B D:AGS501 3.1 62.1 1.0
PB D:AGS501 3.2 40.7 1.0
CB D:SER204 3.7 42.2 1.0
O1B D:AGS501 4.0 46.7 1.0
O2A D:AGS501 4.1 49.6 1.0
OD2 D:ASP311 4.2 65.6 1.0
OG D:SER204 4.3 47.3 1.0
OD1 D:ASP311 4.4 64.2 1.0
O3A D:AGS501 4.4 45.1 1.0
O3G D:AGS501 4.4 53.1 1.0
OE1 D:GLU227 4.5 67.0 1.0
NZ D:LYS203 4.6 49.7 1.0
PA D:AGS501 4.7 30.9 1.0
CG D:ASP311 4.7 62.3 1.0
NH2 C:ARG407 4.7 39.8 1.0
O1A D:AGS501 4.7 52.5 1.0
CA D:SER204 4.9 36.6 1.0
O D:GLY202 5.0 59.6 1.0
N D:SER204 5.0 42.5 1.0

Magnesium binding site 4 out of 5 in 8dvi

Go back to Magnesium Binding Sites List in 8dvi
Magnesium binding site 4 out of 5 in the T4 Bacteriophage Primosome with Single Strand Dna, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T4 Bacteriophage Primosome with Single Strand Dna, State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:54.5
occ:1.00
O2G E:AGS501 2.0 54.2 1.0
O2B E:AGS501 2.0 58.2 1.0
PB E:AGS501 3.2 56.6 1.0
PG E:AGS501 3.4 63.6 1.0
O1B E:AGS501 3.6 51.8 1.0
N E:ASN200 3.7 49.9 1.0
O3B E:AGS501 3.7 53.0 1.0
NZ E:LYS203 3.8 53.8 1.0
NH2 D:ARG407 3.8 48.1 1.0
NE2 E:GLN355 4.1 58.0 1.0
NZ D:LYS405 4.2 37.9 1.0
CG1 E:VAL199 4.2 51.3 1.0
O3G E:AGS501 4.4 50.9 1.0
CA E:VAL199 4.4 45.5 1.0
O D:ALA379 4.4 53.3 1.0
CA E:ASN200 4.5 46.5 1.0
O3A E:AGS501 4.5 50.8 1.0
C E:VAL199 4.5 50.0 1.0
S1G E:AGS501 4.6 64.8 1.0
CE D:LYS405 4.6 41.2 1.0
CA D:ALA379 4.7 43.9 1.0
CB E:VAL199 4.7 47.4 1.0
CE E:LYS203 4.7 46.2 1.0
CG2 E:VAL199 5.0 49.1 1.0
O1A E:AGS501 5.0 52.9 1.0

Magnesium binding site 5 out of 5 in 8dvi

Go back to Magnesium Binding Sites List in 8dvi
Magnesium binding site 5 out of 5 in the T4 Bacteriophage Primosome with Single Strand Dna, State 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of T4 Bacteriophage Primosome with Single Strand Dna, State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:60.9
occ:1.00
O2B F:AGS501 2.0 56.7 1.0
OG F:SER204 2.2 54.9 1.0
O3G F:AGS501 2.6 69.2 1.0
CB F:SER204 3.4 55.6 1.0
PB F:AGS501 3.5 59.2 1.0
OE1 F:GLU227 3.6 79.2 1.0
O2A F:AGS501 3.7 66.7 1.0
OD2 F:ASP311 3.8 73.3 1.0
OD1 F:ASP311 3.8 66.7 1.0
PG F:AGS501 3.8 76.0 1.0
O3B F:AGS501 3.9 69.4 1.0
CG F:ASP311 4.2 69.5 1.0
N F:SER204 4.2 58.0 1.0
O1B F:AGS501 4.3 62.9 1.0
O3A F:AGS501 4.4 62.2 1.0
CA F:SER204 4.4 52.0 1.0
CD F:GLU227 4.4 79.3 1.0
PA F:AGS501 4.4 48.6 1.0
SD F:MET228 4.6 78.3 1.0
O1A F:AGS501 4.6 61.0 1.0
CE F:MET228 4.6 63.9 1.0
CG F:MET228 4.8 72.0 1.0
O2G F:AGS501 4.8 69.7 1.0
OE2 F:GLU227 4.9 78.9 1.0

Reference:

X.Feng, M.M.Spiering, R.De Luna Almeida Santos, S.J.Benkovic, H.Li. Structural Basis of the T4 Bacteriophage Primosome Assembly and Primer Synthesis. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 37205424
DOI: 10.1101/2023.05.03.539249
Page generated: Fri Oct 4 00:55:46 2024

Last articles

Mn in 2LTN
Mn in 2MUC
Mn in 2LAL
Mn in 2JEC
Mn in 2MNR
Mn in 2KZM
Mn in 2JLA
Mn in 2JLY
Mn in 2JLZ
Mn in 2JLX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy