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Magnesium in PDB 2oux: Crystal Structure of the Soluble Part of A Magnesium Transporter

Protein crystallography data

The structure of Crystal Structure of the Soluble Part of A Magnesium Transporter, PDB code: 2oux was solved by R.Sugadev, S.K.Burley, S.Swaminathan, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.61 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.215, 79.662, 105.886, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 30.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Soluble Part of A Magnesium Transporter (pdb code 2oux). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of the Soluble Part of A Magnesium Transporter, PDB code: 2oux:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2oux

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Magnesium binding site 1 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:28.2
occ:1.00
 O A:ARG227 2.0 25.3 1.0
O B:HOH462 2.1 26.7 1.0
O B:HOH461 2.1 24.1 1.0
OD1 A:ASP230 2.2 29.1 1.0
O B:HOH409 2.2 22.8 1.0
O A:HOH487 2.4 24.9 1.0
C A:ARG227 3.1 27.1 1.0
CG A:ASP230 3.4 28.7 1.0
CA A:ARG227 3.7 28.0 1.0
OD2 A:ASP230 4.0 27.6 1.0
O B:ASP250 4.0 20.8 1.0
OD1 B:ASP254 4.1 26.2 1.0
N A:ASP228 4.2 27.7 1.0
CG A:ARG227 4.3 36.4 1.0
O B:HOH432 4.3 29.7 1.0
OD2 B:ASP254 4.3 24.1 1.0
N A:ASP230 4.4 28.4 1.0
CA A:ASP230 4.5 26.6 1.0
CB A:ASP230 4.5 28.0 1.0
O B:HOH456 4.5 26.8 1.0
O A:ILE226 4.5 24.1 1.0
CB A:ARG227 4.6 31.2 1.0
CA A:ASP228 4.6 27.6 1.0
CG B:ASP254 4.6 28.9 1.0
O A:ASP228 4.6 28.4 1.0
CB B:ASP250 4.6 20.4 1.0
C A:ASP228 4.6 27.6 1.0
C B:ASP250 4.8 20.6 1.0
N A:ARG227 4.9 26.5 1.0

Magnesium binding site 2 out of 10 in 2oux

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Magnesium binding site 2 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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 the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:33.0
occ:1.00
 O A:HOH470 2.1 23.3 1.0
O A:ALA140 2.1 29.1 1.0
O A:HOH471 2.1 32.0 1.0
OD1 A:ASP102 2.2 23.1 1.0
O A:HOH481 2.3 21.7 1.0
O A:HOH472 2.4 24.4 1.0
CG A:ASP102 3.2 26.6 1.0
C A:ALA140 3.3 29.1 1.0
OD2 A:ASP102 3.4 22.6 1.0
O A:HOH424 4.0 25.3 1.0
O A:ASP98 4.0 28.4 1.0
CA A:ALA140 4.2 29.2 1.0
N A:ILE141 4.3 27.1 1.0
CA A:ILE141 4.3 27.1 1.0
O A:HOH417 4.5 24.4 1.0
CB A:ASP102 4.5 27.7 1.0
CB A:ALA140 4.5 29.0 1.0
CG1 A:VAL101 4.5 29.4 1.0
N A:ASP102 4.7 29.0 1.0
O A:HOH447 4.8 39.9 1.0
CA A:ASP102 4.8 29.8 1.0
C A:ASP98 4.9 28.6 1.0
CG2 A:ILE141 4.9 32.0 1.0
O A:HOH450 5.0 45.5 1.0

Magnesium binding site 3 out of 10 in 2oux

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Magnesium binding site 3 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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 the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:35.6
occ:1.00
 O A:HOH411 2.3 31.2 1.0
OH A:TYR176 2.7 20.2 1.0
O A:HOH473 2.7 18.4 1.0
O A:ALA233 2.8 24.3 1.0
CD A:PRO235 3.4 25.0 1.0
CE1 A:TYR176 3.5 17.1 1.0
CZ A:TYR176 3.5 20.8 1.0
CD2 A:TYR174 3.5 29.2 1.0
C A:ALA233 3.6 24.9 1.0
CG A:TYR174 3.7 29.1 1.0
CE2 A:TYR174 3.8 31.2 1.0
CA A:VAL234 3.8 23.9 1.0
N A:VAL234 4.0 24.4 1.0
CD1 A:TYR174 4.2 32.2 1.0
CB A:TYR174 4.3 26.4 1.0
CZ A:TYR174 4.3 34.1 1.0
N A:PRO235 4.4 25.7 1.0
CE1 A:TYR174 4.4 34.5 1.0
O A:HOH485 4.5 27.4 1.0
C A:VAL234 4.6 24.7 1.0
CG A:PRO235 4.6 25.9 1.0
CA A:ALA233 4.7 25.1 1.0
CB A:ALA233 4.7 24.0 1.0
CD2 A:PHE231 4.8 28.5 1.0
CD1 A:TYR176 4.8 22.1 1.0
CG A:PHE231 4.8 27.7 1.0
CE2 A:TYR176 4.9 20.6 1.0
CB A:VAL234 4.9 26.2 1.0
CG2 A:VAL187 4.9 25.6 1.0
O A:ILE211 5.0 30.4 1.0

Magnesium binding site 4 out of 10 in 2oux

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Magnesium binding site 4 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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 the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:28.5
occ:1.00
 O A:HOH413 2.1 29.2 1.0
OD2 A:ASP98 2.1 26.9 1.0
OD2 A:ASP251 2.2 17.6 1.0
O A:HOH423 2.2 22.8 1.0
O A:HOH430 2.3 18.7 1.0
O A:HOH425 2.4 26.0 1.0
CG A:ASP251 3.1 20.3 1.0
CG A:ASP98 3.2 27.5 1.0
OD1 A:ASP251 3.4 21.4 1.0
O A:HOH415 3.4 18.4 1.0
OD1 A:ASP98 3.6 22.9 1.0
OG1 A:THR248 3.7 22.0 1.0
O A:HOH447 3.9 39.9 1.0
OE2 A:GLU170 4.0 41.3 1.0
OE1 A:GLU170 4.1 35.9 1.0
CD A:GLU170 4.2 34.1 1.0
O A:HOH458 4.2 21.7 1.0
OD1 A:ASP250 4.4 23.7 1.0
OD1 A:ASN99 4.4 27.2 1.0
CB A:ASP98 4.4 27.1 1.0
CB A:ASP251 4.4 18.3 1.0
ND2 A:ASN99 4.7 25.3 1.0
CB A:THR143 4.8 21.9 1.0
CG2 A:THR143 4.9 18.3 1.0
CG A:ASN99 4.9 28.8 1.0
O A:HOH443 4.9 26.9 1.0
OD2 A:ASP250 4.9 23.8 1.0

Magnesium binding site 5 out of 10 in 2oux

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Magnesium binding site 5 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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 the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:34.0
occ:1.00
 O A:HOH479 2.1 34.5 1.0
OE1 A:GLU71 2.2 48.5 1.0
O A:HOH456 2.2 31.8 1.0
O A:HOH477 2.2 33.9 1.0
O A:HOH478 2.4 39.4 1.0
O A:HOH476 2.4 30.9 1.0
CD A:GLU71 3.0 47.8 1.0
OE2 A:GLU71 3.2 48.7 1.0
O A:HOH435 3.9 32.3 1.0
O A:HOH427 4.1 20.0 1.0
N A:GLU71 4.2 46.3 1.0
OD2 A:ASP102 4.2 22.6 1.0
CG A:GLU71 4.3 48.6 1.0
OD1 A:ASN99 4.4 27.2 1.0
O A:ILE69 4.4 27.9 1.0
CB A:GLU71 4.5 49.0 1.0
CA A:GLU70 4.8 41.5 1.0
O A:ASP67 4.9 28.8 1.0
CA A:GLU71 5.0 50.0 1.0

Magnesium binding site 6 out of 10 in 2oux

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Magnesium binding site 6 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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 the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg400

b:23.2
occ:1.00
 O B:ARG227 2.1 22.3 1.0
OD1 B:ASP230 2.2 21.9 1.0
O A:HOH480 2.2 23.5 1.0
O A:HOH469 2.3 31.6 1.0
O B:HOH420 2.4 22.1 1.0
O A:HOH410 2.4 22.9 1.0
C B:ARG227 3.3 23.0 1.0
CG B:ASP230 3.3 21.1 1.0
OD2 B:ASP230 3.9 25.3 1.0
CA B:ARG227 4.1 22.3 1.0
OD1 A:ASP254 4.2 24.2 1.0
O A:ASP250 4.2 21.5 1.0
O A:HOH443 4.3 26.9 1.0
N B:ASP228 4.3 23.7 1.0
O B:HOH424 4.4 21.9 1.0
O B:ASP228 4.4 29.5 1.0
OD2 A:ASP254 4.4 24.9 1.0
N B:ASP230 4.4 23.8 1.0
CA B:ASP228 4.5 26.1 1.0
CB B:ASP230 4.5 22.4 1.0
CG B:ARG227 4.5 31.6 1.0
CA B:ASP230 4.5 22.6 1.0
C B:ASP228 4.5 26.9 1.0
CB A:ASP250 4.7 22.5 1.0
CG A:ASP254 4.7 24.3 1.0
O B:ILE226 4.8 20.1 1.0
CB B:ARG227 4.9 26.6 1.0
C A:ASP250 5.0 22.0 1.0

Magnesium binding site 7 out of 10 in 2oux

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Magnesium binding site 7 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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 the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:39.1
occ:1.00
 O B:ALA140 2.2 29.8 1.0
O B:HOH464 2.2 26.8 1.0
OD1 B:ASP102 2.3 26.8 1.0
O B:HOH465 2.4 37.9 1.0
O B:HOH463 2.4 23.6 1.0
CG B:ASP102 3.0 29.7 1.0
OD2 B:ASP102 3.1 26.0 1.0
C B:ALA140 3.4 31.4 1.0
O B:HOH423 3.9 27.2 1.0
O B:ASP98 4.0 33.1 1.0
CA B:ILE141 4.1 27.7 1.0
N B:ILE141 4.2 29.5 1.0
CA B:ALA140 4.4 31.1 1.0
O B:HOH421 4.4 16.9 1.0
O B:HOH443 4.4 28.1 1.0
O B:HOH448 4.4 35.3 1.0
CB B:ASP102 4.5 28.6 1.0
CG2 B:ILE141 4.7 28.8 1.0
CB B:ALA140 4.8 32.9 1.0
C B:ASP98 4.8 31.5 1.0
N B:ASP102 4.8 29.1 1.0
CA B:ASP102 4.9 31.1 1.0
CB B:ASP98 5.0 27.2 1.0
C B:ILE141 5.0 26.7 1.0

Magnesium binding site 8 out of 10 in 2oux

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Magnesium binding site 8 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


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 the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:38.6
occ:1.00
 O B:HOH477 2.1 21.3 1.0
O B:HOH410 2.1 18.9 1.0
O B:HOH468 2.2 38.6 1.0
O B:HOH466 2.2 38.4 1.0
O B:HOH467 2.2 31.7 1.0
OE1 B:GLU71 2.3 53.2 1.0
CD B:GLU71 3.1 51.5 1.0
OE2 B:GLU71 3.1 51.3 1.0
O B:HOH430 3.8 19.5 1.0
OD2 B:ASP102 4.0 26.0 1.0
OD1 B:ASN99 4.0 29.2 1.0
O B:HOH444 4.3 22.7 1.0
N B:GLU71 4.4 51.9 1.0
CG B:GLU71 4.5 52.7 1.0
O B:ILE69 4.6 34.4 1.0
CB B:ASP102 4.8 28.6 1.0
CG B:ASP102 4.8 29.7 1.0
CA B:GLU70 4.9 47.8 1.0
O B:ASP67 4.9 27.6 1.0
CB B:GLU71 5.0 53.8 1.0

Magnesium binding site 9 out of 10 in 2oux

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Magnesium binding site 9 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:49.5
occ:1.00
 O B:HOH412 2.3 43.4 1.0
OE2 B:GLU259 2.5 41.0 1.0
O B:HOH469 2.8 35.4 1.0
OE1 B:GLU136 3.1 48.9 1.0
CD B:GLU136 3.4 48.5 1.0
OE2 B:GLU136 3.5 49.0 1.0
CD B:GLU259 3.6 43.3 1.0
NE2 B:GLN219 3.8 26.4 1.0
OD1 B:ASP218 3.9 34.4 1.0
OE1 B:GLU259 3.9 44.0 1.0
CG B:GLN219 4.1 27.1 1.0
CB B:GLU136 4.2 43.2 1.0
CD B:GLN219 4.3 27.6 1.0
CG B:GLU136 4.3 46.1 1.0
OD2 B:ASP218 4.3 32.6 1.0
CG B:ASP218 4.5 29.9 1.0
CG B:GLU259 4.9 42.8 1.0

Magnesium binding site 10 out of 10 in 2oux

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Magnesium binding site 10 out of 10 in the Crystal Structure of the Soluble Part of A Magnesium Transporter


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Soluble Part of A Magnesium Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:28.7
occ:1.00
 OD2 B:ASP251 2.1 19.5 1.0
O B:HOH470 2.1 23.8 1.0
O B:HOH415 2.2 21.0 1.0
OD2 B:ASP98 2.2 25.1 1.0
O B:HOH416 2.2 21.6 1.0
O B:HOH471 2.3 29.7 1.0
CG B:ASP251 3.1 20.7 1.0
CG B:ASP98 3.2 27.3 1.0
OD1 B:ASP251 3.4 15.2 1.0
OD1 B:ASP98 3.5 22.6 1.0
O B:HOH422 3.6 16.5 1.0
OG1 B:THR248 3.8 24.4 1.0
OE1 B:GLU170 3.9 23.6 1.0
OE2 B:GLU170 4.1 28.7 1.0
O B:HOH421 4.1 16.9 1.0
CD B:GLU170 4.1 27.1 1.0
O B:HOH476 4.2 22.3 1.0
OD2 B:ASP250 4.4 21.4 1.0
CB B:ASP251 4.4 19.5 1.0
ND2 B:ASN99 4.5 27.4 1.0
CB B:ASP98 4.5 27.2 1.0
OD1 B:ASN99 4.6 29.2 1.0
OD1 B:ASP250 4.8 19.5 1.0
CG B:ASN99 4.9 30.2 1.0
CB B:THR143 5.0 27.8 1.0
CG B:ASP250 5.0 20.2 1.0

Reference:

S.Ragumani, J.M.Sauder, S.K.Burley, S.Swaminathan. Structural Studies on Cytosolic Domain of Magnesium Transporter Mgte From Enterococcus Faecalis. Proteins V. 78 487 2010.
ISSN: ISSN 0887-3585
PubMed: 19787770
DOI: 10.1002/PROT.22585
Page generated: Wed Aug 14 01:57:27 2024

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