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Magnesium in PDB 7p0h: Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)

Protein crystallography data

The structure of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2), PDB code: 7p0h was solved by L.Celma, H.Walbott, P.Legrand, S.Quevillon-Cheruel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.88, 87.98, 122.79, 80.23, 76.44, 76.39
R / Rfree (%) 22.1 / 24.5

Other elements in 7p0h:

The structure of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) (pdb code 7p0h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2), PDB code: 7p0h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7p0h

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Magnesium binding site 1 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:62.8
occ:1.00
 O A:HOH646 2.2 44.5 1.0
O1B A:PRP502 2.6 82.5 1.0
O2 A:PRP502 2.7 67.1 1.0
O A:HOH627 3.0 43.1 1.0
O3A A:PRP502 3.1 78.3 1.0
O1 A:PRP502 3.3 71.5 1.0
PB A:PRP502 3.6 82.0 1.0
O3 A:PRP502 3.6 66.6 1.0
C2 A:PRP502 3.8 67.4 1.0
PA A:PRP502 3.9 74.8 1.0
OH A:TYR289 4.1 77.0 1.0
C1 A:PRP502 4.1 68.7 1.0
C3 A:PRP502 4.3 66.6 1.0
O2B A:PRP502 4.4 82.6 1.0
NZ A:LYS288 4.5 74.6 1.0
OD1 A:ASP394 4.5 56.1 1.0
OD2 A:ASP394 4.7 59.3 1.0
O1A A:PRP502 4.7 75.0 1.0
O3B A:PRP502 4.8 82.0 1.0
OD1 A:ASP393 4.8 59.2 1.0

Magnesium binding site 2 out of 8 in 7p0h

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Magnesium binding site 2 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg510

b:57.1
occ:1.00
 O A:HOH609 2.0 28.9 1.0
O A:LYS342 2.2 51.7 1.0
O A:CYS345 2.5 50.5 1.0
O A:HOH667 3.3 52.8 1.0
C A:LYS342 3.4 50.8 1.0
O A:GLY343 3.4 49.1 1.0
C A:CYS345 3.7 49.9 1.0
C A:GLY343 3.8 48.3 1.0
CA A:GLY343 3.8 48.8 1.0
N A:GLY343 4.1 49.4 1.0
N A:CYS345 4.3 47.6 1.0
CA A:CYS345 4.4 48.3 1.0
CA A:LYS342 4.6 51.2 1.0
N A:PHE344 4.7 46.9 1.0
N A:GLN346 4.7 50.2 1.0
CB A:CYS345 4.8 48.5 1.0
CG A:LYS342 4.8 58.6 1.0
C A:PHE344 4.8 47.1 1.0
CB A:GLN346 5.0 53.0 1.0

Magnesium binding site 3 out of 8 in 7p0h

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Magnesium binding site 3 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:114.0
occ:1.00
 O2 B:PRP502 2.6 106.3 1.0
O3B B:PRP502 2.7 114.0 1.0
O3A B:PRP502 3.1 112.2 1.0
O1 B:PRP502 3.4 108.7 1.0
PB B:PRP502 3.6 113.7 1.0
O3 B:PRP502 3.6 105.3 1.0
C2 B:PRP502 3.8 106.3 1.0
PA B:PRP502 3.9 110.7 1.0
C1 B:PRP502 4.1 107.0 1.0
OH B:TYR289 4.1 90.3 1.0
C3 B:PRP502 4.3 105.6 1.0
O2B B:PRP502 4.4 113.8 1.0
OD1 B:ASP394 4.5 76.0 1.0
NZ B:LYS288 4.5 90.5 1.0
OD2 B:ASP394 4.6 77.0 1.0
O1B B:PRP502 4.8 113.9 1.0
OD1 B:ASP393 4.8 69.2 1.0
O2A B:PRP502 4.8 110.9 1.0
CG B:ASP394 5.0 74.6 1.0

Magnesium binding site 4 out of 8 in 7p0h

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Magnesium binding site 4 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:41.5
occ:1.00
 O B:HOH630 1.9 56.5 1.0
O B:LYS342 2.7 64.2 1.0
O B:GLY343 2.7 61.5 1.0
O B:CYS345 2.7 58.6 1.0
O B:HOH638 3.2 55.5 1.0
C B:GLY343 3.2 61.1 1.0
CA B:GLY343 3.5 62.1 1.0
C B:LYS342 3.7 63.7 1.0
C B:CYS345 3.8 58.1 1.0
N B:GLY343 4.0 62.6 1.0
N B:CYS345 4.2 57.8 1.0
N B:PHE344 4.3 59.4 1.0
C B:PHE344 4.4 58.1 1.0
CA B:CYS345 4.5 57.5 1.0
OE1 B:GLN346 4.5 66.2 1.0
CB B:GLN346 4.7 59.7 1.0
N B:GLN346 4.8 58.1 1.0
O B:PHE344 4.8 58.0 1.0
CA B:PHE344 4.9 58.3 1.0
NE2 B:GLN302 4.9 72.1 1.0
CG B:GLN302 4.9 62.5 1.0

Magnesium binding site 5 out of 8 in 7p0h

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Magnesium binding site 5 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:102.7
occ:1.00
 O C:HOH676 2.4 72.0 1.0
O2 C:PRP502 2.6 94.3 1.0
O1B C:PRP502 2.7 103.5 1.0
O3A C:PRP502 3.1 101.5 1.0
O C:HOH658 3.1 54.2 1.0
O1 C:PRP502 3.3 97.5 1.0
PB C:PRP502 3.6 103.2 1.0
O3 C:PRP502 3.6 93.0 1.0
C2 C:PRP502 3.8 94.4 1.0
PA C:PRP502 3.9 99.7 1.0
C1 C:PRP502 4.1 95.4 1.0
OH C:TYR289 4.1 81.2 1.0
C3 C:PRP502 4.3 93.4 1.0
O2B C:PRP502 4.4 103.3 1.0
NZ C:LYS288 4.5 82.5 1.0
OD1 C:ASP394 4.5 69.8 1.0
OD2 C:ASP394 4.6 71.7 1.0
O3B C:PRP502 4.8 103.2 1.0
O1A C:PRP502 4.8 100.0 1.0
OD1 C:ASP393 4.8 70.3 1.0
CG C:ASP394 5.0 69.4 1.0

Magnesium binding site 6 out of 8 in 7p0h

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Magnesium binding site 6 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg508

b:49.7
occ:1.00
 O C:CYS345 2.7 53.6 1.0
O C:LYS342 2.8 58.4 1.0
O C:GLY343 2.8 55.0 1.0
O C:HOH659 2.8 51.9 1.0
C C:GLY343 3.4 54.5 1.0
CA C:GLY343 3.7 55.4 1.0
C C:CYS345 3.8 53.4 1.0
C C:LYS342 3.9 57.5 1.0
N C:GLY343 4.2 56.2 1.0
N C:CYS345 4.3 52.5 1.0
NE2 C:GLN346 4.4 62.8 1.0
N C:PHE344 4.4 53.2 1.0
C C:PHE344 4.5 52.6 1.0
CA C:CYS345 4.6 52.4 1.0
CB C:GLN346 4.6 56.1 1.0
N C:GLN346 4.7 53.7 1.0
O C:PHE344 4.9 52.9 1.0
CG C:GLN302 5.0 60.6 1.0
NE2 C:GLN302 5.0 69.9 1.0
CA C:GLN346 5.0 54.6 1.0

Magnesium binding site 7 out of 8 in 7p0h

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Magnesium binding site 7 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:109.0
occ:1.00
 O2 D:PRP502 2.6 97.8 1.0
O3B D:PRP502 2.7 104.7 1.0
O D:HOH626 3.0 73.8 1.0
O3A D:PRP502 3.2 103.1 1.0
O1 D:PRP502 3.3 100.3 1.0
O3 D:PRP502 3.6 97.5 1.0
PB D:PRP502 3.6 104.4 1.0
C2 D:PRP502 3.7 98.0 1.0
PA D:PRP502 4.0 101.7 1.0
C1 D:PRP502 4.0 98.8 1.0
OH D:TYR289 4.1 93.3 1.0
C3 D:PRP502 4.3 97.5 1.0
NZ D:LYS288 4.4 87.9 1.0
OD1 D:ASP394 4.5 67.4 1.0
O1B D:PRP502 4.6 104.5 1.0
OD2 D:ASP394 4.7 68.5 1.0
O2B D:PRP502 4.8 104.4 1.0
O2A D:PRP502 4.8 101.9 1.0
OD1 D:ASP393 4.8 66.1 1.0
CG D:ASP394 5.0 66.6 1.0

Magnesium binding site 8 out of 8 in 7p0h

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Magnesium binding site 8 out of 8 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg506

b:41.2
occ:1.00
 O D:HOH649 2.5 50.7 1.0
O D:CYS345 2.7 53.6 1.0
O D:LYS342 2.7 56.2 1.0
O D:GLY343 2.8 53.5 1.0
C D:GLY343 3.4 53.1 1.0
CA D:GLY343 3.7 53.5 1.0
C D:CYS345 3.7 52.9 1.0
C D:LYS342 3.8 55.2 1.0
N D:GLY343 4.2 54.1 1.0
N D:CYS345 4.3 51.5 1.0
N D:PHE344 4.4 52.1 1.0
NE2 D:GLN346 4.5 59.6 1.0
C D:PHE344 4.5 51.3 1.0
CA D:CYS345 4.5 52.1 1.0
CB D:GLN346 4.6 54.5 1.0
N D:GLN346 4.7 52.6 1.0
O D:PHE344 4.9 51.0 1.0
NE2 D:GLN302 5.0 65.2 1.0

Reference:

P.P.Damke, L.Celma, S.M.Kondekar, A.M.Di Guilmi, S.Marsin, J.Depagne, X.Veaute, P.Legrand, H.Walbott, J.Vercruyssen, R.Guerois, S.Quevillon-Cheruel, J.P.Radicella. Comfc Mediates Transport and Handling of Single-Stranded Dna During Natural Transformation. Nat Commun V. 13 1961 2022.
ISSN: ESSN 2041-1723
PubMed: 35414142
DOI: 10.1038/S41467-022-29494-Z
Page generated: Thu Oct 3 03:57:20 2024

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