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Magnesium in PDB 8dzg: Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp

Other elements in 8dzg:

The structure of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp (pdb code 8dzg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp, PDB code: 8dzg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8dzg

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:43.4
occ:1.00
O2B A:ADP602 2.1 20.0 1.0
OG A:SER267 2.2 43.8 1.0
PB A:ADP602 3.4 20.0 1.0
O1B A:ADP602 3.6 20.0 1.0
CB A:SER267 3.6 43.8 1.0
OE2 A:GLU295 3.7 73.0 1.0
O3B A:ADP602 4.3 20.0 1.0
N A:SER267 4.4 43.8 1.0
O3A A:ADP602 4.4 20.0 1.0
CA A:SER267 4.5 43.8 1.0
CD A:GLU295 4.9 73.0 1.0

Magnesium binding site 2 out of 6 in 8dzg

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:41.8
occ:1.00
O2B B:ADP602 2.1 20.0 1.0
OG B:SER267 2.2 43.1 1.0
PB B:ADP602 3.4 20.0 1.0
O1B B:ADP602 3.6 20.0 1.0
CB B:SER267 3.6 43.1 1.0
OE2 B:GLU295 3.7 71.6 1.0
O3B B:ADP602 4.3 20.0 1.0
N B:SER267 4.4 43.1 1.0
O3A B:ADP602 4.4 20.0 1.0
CA B:SER267 4.5 43.1 1.0
CD B:GLU295 4.9 71.6 1.0

Magnesium binding site 3 out of 6 in 8dzg

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:40.0
occ:1.00
O2B C:ADP602 2.1 20.0 1.0
OG C:SER267 2.2 42.8 1.0
PB C:ADP602 3.4 20.0 1.0
O1B C:ADP602 3.6 20.0 1.0
CB C:SER267 3.6 42.8 1.0
OE2 C:GLU295 3.7 72.5 1.0
O3B C:ADP602 4.3 20.0 1.0
N C:SER267 4.4 42.8 1.0
O3A C:ADP602 4.4 20.0 1.0
CA C:SER267 4.5 42.8 1.0
CD C:GLU295 4.9 72.5 1.0

Magnesium binding site 4 out of 6 in 8dzg

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:43.3
occ:1.00
O2B D:ADP602 2.1 20.0 1.0
OG D:SER267 2.2 43.2 1.0
PB D:ADP602 3.4 20.0 1.0
O1B D:ADP602 3.6 20.0 1.0
CB D:SER267 3.6 43.2 1.0
OE2 D:GLU295 3.7 72.2 1.0
O3B D:ADP602 4.3 20.0 1.0
N D:SER267 4.4 43.2 1.0
O3A D:ADP602 4.4 20.0 1.0
CA D:SER267 4.5 43.2 1.0
CD D:GLU295 4.9 72.2 1.0

Magnesium binding site 5 out of 6 in 8dzg

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:41.4
occ:1.00
O2B E:ADP602 2.1 20.0 1.0
OG E:SER267 2.2 43.3 1.0
PB E:ADP602 3.4 20.0 1.0
O1B E:ADP602 3.6 20.0 1.0
CB E:SER267 3.6 43.3 1.0
OE2 E:GLU295 3.7 71.6 1.0
O3B E:ADP602 4.3 20.0 1.0
N E:SER267 4.4 43.3 1.0
O3A E:ADP602 4.4 20.0 1.0
CA E:SER267 4.5 43.3 1.0
CD E:GLU295 4.9 71.6 1.0

Magnesium binding site 6 out of 6 in 8dzg

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:40.2
occ:1.00
O2B F:ADP602 2.1 20.0 1.0
OG F:SER267 2.2 42.5 1.0
PB F:ADP602 3.4 20.0 1.0
O1B F:ADP602 3.6 20.0 1.0
CB F:SER267 3.6 42.5 1.0
OE2 F:GLU295 3.7 72.6 1.0
O3B F:ADP602 4.3 20.0 1.0
N F:SER267 4.4 42.5 1.0
O3A F:ADP602 4.4 20.0 1.0
CA F:SER267 4.5 42.5 1.0
CD F:GLU295 4.9 72.6 1.0

Reference:

A.R.Nayak, P.K.Singh, J.Zhao, M.Samso, M.S.Donnenberg. Cryo-Em Structure of the Type IV Pilus Extension Atpase From Enteropathogenic Escherichia Coli. Mbio V. 13 2022.
ISSN: ESSN 2150-7511
PubMed: 36326250
DOI: 10.1128/MBIO.02270-22
Page generated: Fri Oct 4 00:58:56 2024

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