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Magnesium in PDB 3ocm: The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis

Protein crystallography data

The structure of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis, PDB code: 3ocm was solved by K.Tan, C.Tesar, G.Cobb, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.62 / 1.80
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 152.289, 152.289, 46.888, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis (pdb code 3ocm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis, PDB code: 3ocm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3ocm

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Magnesium binding site 1 out of 7 in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:25.8
occ:1.00
 O A:HOH218 2.2 24.3 1.0
OE1 A:GLU460 2.2 22.1 1.0
O A:HOH217 2.2 21.9 1.0
O A:HOH222 2.2 27.3 1.0
O A:HOH219 2.2 25.0 1.0
O A:HOH216 2.2 18.6 1.0
CD A:GLU460 3.1 35.1 1.0
OE2 A:GLU460 3.2 39.3 1.0
OD2 A:ASP457 3.9 22.9 1.0
OE2 A:GLU449 3.9 26.8 1.0
O3' A:ADP470 4.0 18.1 1.0
OD1 A:ASP457 4.0 23.9 1.0
O A:HOH288 4.0 35.6 1.0
CG A:ASP457 4.1 23.1 1.0
O A:HOH58 4.2 34.9 1.0
N A:ASP457 4.2 20.4 1.0
O A:HOH247 4.2 33.2 1.0
CA A:PRO456 4.3 22.1 1.0
OE1 A:GLU449 4.3 23.1 1.0
O A:HOH123 4.3 30.0 1.0
O A:PHE455 4.3 19.9 1.0
CG A:GLU460 4.5 27.7 1.0
CD A:GLU449 4.5 22.6 1.0
C A:PRO456 4.7 20.4 1.0
O A:HOH287 4.8 50.6 1.0
C4' A:ADP470 4.8 16.9 1.0
C A:PHE455 4.9 22.7 1.0
CB A:ASP457 5.0 21.0 1.0
OE2 A:GLU454 5.0 49.6 1.0
CB A:GLU460 5.0 26.7 1.0

Magnesium binding site 2 out of 7 in 3ocm

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Magnesium binding site 2 out of 7 in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:20.5
occ:1.00
 O A:HOH227 2.1 17.0 1.0
O A:HOH210 2.2 17.4 1.0
O A:HOH201 2.2 18.9 1.0
NE2 A:HIS365 2.2 14.5 1.0
O A:HOH221 2.2 19.9 1.0
O A:HOH215 2.3 21.2 1.0
CE1 A:HIS365 3.1 15.9 1.0
CD2 A:HIS365 3.3 16.2 1.0
N3 A:ADP470 4.1 18.7 1.0
C2 A:ADP470 4.1 19.1 1.0
OD2 A:ASP457 4.1 22.9 1.0
OD2 A:ASP459 4.2 25.5 1.0
O A:ASP343 4.2 20.9 1.0
ND1 A:HIS365 4.2 16.5 1.0
OG A:SER345 4.3 22.7 1.0
O A:HOH16 4.3 37.5 1.0
O A:HOH123 4.3 30.0 1.0
O A:HOH108 4.3 36.9 1.0
O A:HOH245 4.4 40.6 1.0
CG A:HIS365 4.4 14.6 1.0
OD1 A:ASP459 4.4 21.8 1.0
CG A:PRO364 4.6 22.5 1.0
CD A:PRO364 4.6 20.5 1.0
CG A:ASP459 4.7 30.0 1.0
C4 A:ADP470 4.9 17.7 1.0
N1 A:ADP470 4.9 16.1 1.0

Magnesium binding site 3 out of 7 in 3ocm

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Magnesium binding site 3 out of 7 in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5

b:20.9
occ:1.00
 O2A B:ADP1 2.1 18.4 1.0
O2B B:ADP1 2.1 15.9 1.0
O B:HOH209 2.2 22.9 1.0
O B:HOH220 2.2 18.9 1.0
O A:HOH213 2.2 20.9 1.0
O B:HOH202 2.3 20.0 1.0
PB B:ADP1 3.3 18.7 1.0
PA B:ADP1 3.3 19.4 1.0
O3A B:ADP1 3.6 19.7 1.0
O B:HOH96 3.9 24.2 1.0
O A:HOH203 4.0 32.8 1.0
O3B B:ADP1 4.1 18.2 1.0
O A:HOH211 4.1 19.4 1.0
O A:HOH48 4.1 22.4 1.0
O B:HOH57 4.1 28.0 1.0
O B:HOH91 4.2 30.0 1.0
O A:HOH241 4.2 27.6 1.0
O5' B:ADP1 4.3 19.6 1.0
C5' B:ADP1 4.3 18.7 1.0
O1A B:ADP1 4.4 20.7 1.0
CA A:GLY426 4.4 28.7 1.0
O1B B:ADP1 4.4 20.1 1.0
O A:GLY426 4.4 25.7 1.0
O B:HOH204 4.6 41.8 1.0
C A:GLY426 4.9 24.5 1.0

Magnesium binding site 4 out of 7 in 3ocm

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Magnesium binding site 4 out of 7 in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:51.5
occ:1.00
 OE1 A:GLU449 2.3 23.1 1.0
O A:HOH286 2.3 32.4 1.0
O A:HOH289 2.4 41.0 1.0
O A:HOH287 2.4 50.6 1.0
O A:HOH288 2.4 35.6 1.0
O A:HOH285 2.6 42.8 1.0
CD A:GLU449 3.5 22.6 1.0
O A:HOH219 3.5 25.0 1.0
O A:ILE337 3.9 21.9 1.0
CB A:GLU449 4.0 23.2 1.0
OD1 A:ASP446 4.2 21.0 1.0
OE1 A:GLU454 4.3 44.6 1.0
OE2 A:GLU449 4.3 26.8 1.0
CG A:GLU449 4.3 22.9 1.0
OE2 A:GLU454 4.4 49.6 1.0
O A:HOH164 4.4 47.2 1.0
O A:ASP446 4.4 19.6 1.0
O A:HOH58 4.5 34.9 1.0
CA A:ASP446 4.6 21.6 1.0
O A:HOH222 4.7 27.3 1.0
C A:ILE337 4.8 19.0 1.0
CD A:GLU454 4.8 44.9 1.0
O A:HOH217 4.9 21.9 1.0
CB A:ASP446 4.9 21.1 1.0
CA A:ILE337 4.9 22.7 1.0

Magnesium binding site 5 out of 7 in 3ocm

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Magnesium binding site 5 out of 7 in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3

b:23.4
occ:1.00
 O B:HOH231 2.1 20.5 1.0
O B:HOH233 2.2 20.9 1.0
O B:HOH224 2.2 19.0 1.0
O B:HOH239 2.2 22.5 1.0
NE2 B:HIS365 2.2 17.3 1.0
O B:HOH279 2.3 23.8 1.0
CE1 B:HIS365 3.1 18.2 1.0
CD2 B:HIS365 3.3 19.3 1.0
OD2 B:ASP457 4.1 31.1 1.0
O B:HOH261 4.2 46.1 1.0
N3 B:ADP1 4.2 18.1 1.0
OD2 B:ASP459 4.2 32.7 1.0
C2 B:ADP1 4.2 18.6 1.0
O B:ASP343 4.2 22.9 1.0
ND1 B:HIS365 4.3 18.2 1.0
OG B:SER345 4.3 25.0 1.0
O B:HOH66 4.4 43.0 1.0
OD1 B:ASP459 4.4 28.1 1.0
O B:HOH140 4.4 44.6 1.0
CG B:HIS365 4.4 17.0 1.0
O B:HOH94 4.5 39.0 1.0
CG B:PRO364 4.5 21.4 1.0
CD B:PRO364 4.6 24.6 1.0
CG B:ASP459 4.7 37.8 1.0
O B:HOH275 4.8 56.9 1.0
C4 B:ADP1 4.9 19.2 1.0
N1 B:ADP1 5.0 20.0 1.0

Magnesium binding site 6 out of 7 in 3ocm

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Magnesium binding site 6 out of 7 in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4

b:33.8
occ:1.00
 O B:HOH240 2.2 23.4 1.0
O B:HOH252 2.2 36.8 1.0
O B:HOH268 2.3 29.0 1.0
OE1 B:GLU460 2.3 32.4 1.0
O B:HOH229 2.3 32.0 1.0
O B:HOH248 2.3 30.6 1.0
CD B:GLU460 3.1 51.4 1.0
OE2 B:GLU460 3.2 56.7 1.0
OD2 B:ASP457 3.8 31.1 1.0
OE2 B:GLU449 3.9 30.1 1.0
O3' B:ADP1 4.0 20.9 1.0
CG B:ASP457 4.1 32.0 1.0
O B:HOH272 4.1 44.0 1.0
OD1 B:ASP457 4.1 27.2 1.0
N B:ASP457 4.2 26.8 1.0
OE1 B:GLU449 4.3 32.8 1.0
O B:HOH94 4.3 39.0 1.0
O B:PHE455 4.4 25.2 1.0
O B:HOH162 4.4 36.2 1.0
CG B:GLU460 4.5 52.3 1.0
CD B:GLU449 4.5 29.1 1.0
CA B:PRO456 4.6 28.9 1.0
OE2 B:GLU454 4.8 64.3 1.0
C4' B:ADP1 4.8 19.6 1.0
C B:PRO456 4.9 28.6 1.0
CB B:ASP457 4.9 26.1 1.0

Magnesium binding site 7 out of 7 in 3ocm

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Magnesium binding site 7 out of 7 in the The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6

b:19.0
occ:1.00
 O2A A:ADP470 2.0 17.9 1.0
O1B A:ADP470 2.1 16.9 1.0
O A:HOH199 2.2 19.3 1.0
O A:HOH211 2.2 19.4 1.0
O B:HOH207 2.2 21.2 1.0
O A:HOH291 2.2 21.6 1.0
PA A:ADP470 3.3 19.1 1.0
PB A:ADP470 3.3 18.2 1.0
O3A A:ADP470 3.5 16.3 1.0
O A:HOH54 3.9 24.1 1.0
O B:HOH196 4.0 34.2 1.0
O3B A:ADP470 4.0 16.9 1.0
O B:HOH220 4.1 18.9 1.0
O B:HOH205 4.1 22.1 1.0
O A:HOH65 4.1 28.2 1.0
O B:HOH225 4.1 31.9 1.0
O A:HOH41 4.2 24.4 1.0
O B:HOH122 4.2 31.2 1.0
O5' A:ADP470 4.3 18.6 1.0
O1A A:ADP470 4.3 19.5 1.0
C5' A:ADP470 4.3 16.8 1.0
CA B:GLY426 4.4 25.2 1.0
O B:GLY426 4.4 23.4 1.0
O2B A:ADP470 4.5 18.1 1.0
O A:HOH61 4.7 32.3 1.0
C B:GLY426 4.9 21.9 1.0
O A:HOH203 4.9 32.8 1.0

Reference:

K.Tan, C.Tesar, G.Cobb, A.Joachimiak. The Crystal Structure of A Domain From A Possible Membrane Protein of Bordetella Parapertussis To Be Published.
Page generated: Mon Aug 11 01:06:42 2025

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