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Magnesium in PDB 8qbk: Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment) (pdb code 8qbk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment), PDB code: 8qbk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8qbk

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Magnesium binding site 1 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:89.2
occ:1.00
OP1 B:DG85 2.4 98.0 1.0
OD2 A:ASP119 3.2 119.4 1.0
P B:DG85 3.7 110.2 1.0
C5' B:DG85 4.0 94.4 1.0
O5' B:DG85 4.0 101.8 1.0
CG A:ASP119 4.1 116.5 1.0
OD1 A:ASP119 4.1 121.0 1.0
CB A:ASP198 4.3 93.8 1.0
OD1 A:ASN117 4.4 106.0 1.0
CE A:LYS231 4.4 162.5 1.0
OP2 B:DG85 4.6 94.8 1.0
OD2 A:ASP198 4.7 118.5 1.0
NZ A:LYS231 4.8 169.6 1.0
CG A:ASP198 4.8 111.1 1.0
O3' B:DA84 4.8 91.8 1.0
OP1 C:G69 4.9 201.7 1.0
O3' B:DG85 4.9 94.1 1.0

Magnesium binding site 2 out of 4 in 8qbk

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Magnesium binding site 2 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg101

b:119.8
occ:1.00
OP1 L:DG85 2.4 126.0 1.0
P L:DG85 3.8 140.7 1.0
ND2 K:ASN117 4.3 127.3 1.0
OD2 K:ASP119 4.5 135.6 1.0
O3' L:DA84 4.6 113.8 1.0
OP2 L:DG85 4.6 127.1 1.0
OD1 K:ASP119 4.7 142.0 1.0
O5' L:DG85 4.7 122.5 1.0
C5' L:DG85 4.9 117.0 1.0

Magnesium binding site 3 out of 4 in 8qbk

Go back to Magnesium Binding Sites List in 8qbk
Magnesium binding site 3 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg101

b:108.8
occ:1.00
OP1 Q:DG85 2.4 111.2 1.0
P Q:DG85 3.8 126.4 1.0
OD1 P:ASP119 4.1 135.5 1.0
O5' Q:DG85 4.4 116.9 1.0
C5' Q:DG85 4.5 106.4 1.0
OP1 R:G69 4.5 222.5 1.0
OD1 P:ASN117 4.5 115.7 1.0
OP2 Q:DG85 4.5 111.2 1.0
OP2 R:G69 4.6 223.6 1.0
CD P:LYS231 4.8 167.1 1.0
O3' Q:DA84 4.8 107.7 1.0
CB P:ASP198 4.9 105.0 1.0

Magnesium binding site 4 out of 4 in 8qbk

Go back to Magnesium Binding Sites List in 8qbk
Magnesium binding site 4 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment) within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg401

b:114.4
occ:1.00
OP1 V:DG85 2.6 110.3 1.0
OD2 U:ASP198 3.1 123.8 1.0
P V:DG85 4.1 128.4 1.0
OD1 U:ASN117 4.1 103.0 1.0
CE U:LYS231 4.3 152.8 1.0
CG U:ASP198 4.3 130.3 1.0
N U:THR244 4.3 105.4 1.0
CA U:THR244 4.6 105.8 1.0
O3' V:DA84 4.7 96.1 1.0
ND2 U:ASN117 4.7 105.4 1.0
CG U:ASN117 4.7 104.5 1.0
OD2 U:ASP119 4.8 137.7 1.0
NZ U:LYS231 4.9 152.2 1.0
O5' V:DG85 4.9 112.0 1.0
C5' V:DG85 5.0 101.2 1.0
OP2 V:DG85 5.0 108.3 1.0

Reference:

A.Carabias, S.Camara-Wilpert, M.R.Mestre, B.Lopez-Mendez, I.A.Hendriks, R.Zhao, T.Pape, A.Fuglsang, S.H.Luk, M.L.Nielsen, R.Pinilla-Redondo, G.Montoya. Retron-ECO1 Assembles Nad + -Hydrolyzing Filaments That Provide Immunity Against Bacteriophages. Mol.Cell 2024.
ISSN: ISSN 1097-2765
PubMed: 38788717
DOI: 10.1016/J.MOLCEL.2024.05.001
Page generated: Fri Oct 4 16:40:14 2024

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