Atomistry » Magnesium » PDB 8dr6-8e1f » 8dw6
Atomistry »
  Magnesium »
    PDB 8dr6-8e1f »
      8dw6 »

Magnesium in PDB 8dw6: T4 Bacteriophage Primosome with Single-Strand Dna, State 3

Other elements in 8dw6:

The structure of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3 (pdb code 8dw6). 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 3, PDB code: 8dw6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8dw6

Go back to Magnesium Binding Sites List in 8dw6
Magnesium binding site 1 out of 5 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


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 3 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
CE B:LYS203 4.7 58.3 1.0
O B:LYS203 4.7 65.2 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 8dw6

Go back to Magnesium Binding Sites List in 8dw6
Magnesium binding site 2 out of 5 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


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 3 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
OD1 C:ASP311 4.2 68.2 1.0
CG C:GLU227 4.2 64.3 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 8dw6

Go back to Magnesium Binding Sites List in 8dw6
Magnesium binding site 3 out of 5 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


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 3 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 8dw6

Go back to Magnesium Binding Sites List in 8dw6
Magnesium binding site 4 out of 5 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


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 3 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 8dw6

Go back to Magnesium Binding Sites List in 8dw6
Magnesium binding site 5 out of 5 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


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 3 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 00:56:12 2024

Last articles

F in 5WNY
F in 5WN8
F in 5WMJ
F in 5WL0
F in 5WIN
F in 5WJJ
F in 5WIL
F in 5WIK
F in 5WI0
F in 5WH6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy