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Magnesium in PDB 4hqs: Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4

Protein crystallography data

The structure of Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4, PDB code: 4hqs was solved by S.G.Bartual, M.Saleh, M.R.Abdullah, I.Jensch, T.M.Asmat, L.Petruschka, T.Pribyl, J.A.Hermoso, S.Hammerschmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.11 / 1.48
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.850, 62.850, 89.600, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 (pdb code 4hqs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4, PDB code: 4hqs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4hqs

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Magnesium binding site 1 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:17.1
occ:1.00
 HG A:SER112 2.7 12.7 1.0
OG A:SER112 2.8 10.6 1.0
HA A:VAL111 2.8 9.3 1.0
HD22 A:LEU147 2.8 18.3 1.0
OH A:TYR155 2.8 10.7 1.0
HD2 A:PHE79 2.9 15.3 1.0
HH A:TYR155 2.9 12.8 1.0
O A:VAL110 3.0 8.6 1.0
HG12 A:VAL110 3.2 16.1 1.0
HE1 A:TYR155 3.2 11.7 1.0
HB2 A:SER112 3.3 11.4 1.0
H A:SER112 3.4 10.1 1.0
N A:SER112 3.5 8.4 1.0
CB A:SER112 3.5 9.5 1.0
CA A:VAL111 3.5 7.8 1.0
O A:TRP80 3.5 7.7 1.0
C A:VAL111 3.6 8.2 1.0
H A:TRP80 3.6 9.6 1.0
HB3 A:PHE79 3.6 12.1 1.0
CZ A:TYR155 3.6 8.3 1.0
C A:VAL110 3.7 9.4 1.0
CD2 A:LEU147 3.7 15.3 1.0
CE1 A:TYR155 3.7 9.7 1.0
CD2 A:PHE79 3.8 12.7 1.0
HD21 A:LEU147 3.9 18.3 1.0
O A:HOH328 3.9 9.4 1.0
N A:VAL111 3.9 8.2 1.0
HG A:LEU147 4.0 17.9 1.0
HD11 A:LEU147 4.0 17.2 1.0
HA A:PHE79 4.1 10.6 1.0
CG1 A:VAL110 4.1 13.4 1.0
CA A:SER112 4.1 9.8 1.0
N A:TRP80 4.2 8.0 1.0
HB A:VAL110 4.2 14.0 1.0
MG A:MG210 4.2 20.6 1.0
O A:VAL111 4.3 8.4 1.0
CG A:LEU147 4.3 14.9 1.0
HG11 A:VAL110 4.3 16.1 1.0
CB A:PHE79 4.4 10.1 1.0
HD23 A:LEU147 4.4 18.3 1.0
HB3 A:SER112 4.4 11.4 1.0
C A:TRP80 4.6 7.4 1.0
CA A:PHE79 4.6 8.8 1.0
CG A:PHE79 4.6 9.5 1.0
CB A:VAL110 4.6 11.7 1.0
HA A:SER112 4.6 11.8 1.0
HE2 A:PHE79 4.6 15.2 1.0
CD1 A:LEU147 4.7 14.4 1.0
H A:VAL111 4.7 9.8 1.0
HG13 A:VAL110 4.7 16.1 1.0
CE2 A:PHE79 4.7 12.7 1.0
C A:PHE79 4.7 8.7 1.0
CA A:VAL110 4.8 9.1 1.0
CE2 A:TYR155 4.8 10.7 1.0
O A:HOH330 4.8 13.3 1.0
CB A:VAL111 4.9 8.7 1.0
CD1 A:TYR155 4.9 8.7 1.0
HB A:VAL111 4.9 10.4 1.0
CA A:TRP80 5.0 7.8 1.0
HG12 A:VAL111 5.0 10.3 1.0

Magnesium binding site 2 out of 9 in 4hqs

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Magnesium binding site 2 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:24.0
occ:1.00
 H A:GLU121 2.5 14.5 1.0
HA A:SER120 2.9 14.1 1.0
HB2 A:PRO113 3.1 14.9 1.0
O A:HOH465 3.2 37.4 1.0
N A:GLU121 3.3 12.1 1.0
O A:HOH348 3.3 23.3 1.0
HB3 A:PRO142 3.3 17.7 1.0
HB3 A:PRO113 3.5 14.9 1.0
HB2 A:SER120 3.5 16.6 1.0
HB2 A:GLU121 3.6 18.6 1.0
CA A:SER120 3.7 11.7 1.0
CB A:PRO113 3.7 12.4 1.0
O A:HOH352 3.7 27.1 1.0
HA3 A:GLY114 3.9 15.8 1.0
C A:SER120 3.9 12.0 1.0
C A:PRO113 4.0 12.7 1.0
O A:PRO113 4.0 12.8 1.0
HB3 A:GLU121 4.0 18.6 1.0
CB A:SER120 4.1 13.8 1.0
CB A:GLU121 4.1 15.5 1.0
N A:GLY114 4.2 11.9 1.0
CA A:GLU121 4.2 12.7 1.0
CB A:PRO142 4.3 14.7 1.0
CA A:PRO113 4.4 10.6 1.0
CA A:GLY114 4.5 13.2 1.0
O A:HOH336 4.5 19.1 1.0
HB3 A:SER120 4.5 16.6 1.0
H A:GLY114 4.6 14.2 1.0
HB2 A:PRO142 4.6 17.7 1.0
HA A:GLU121 4.6 15.3 1.0
HA2 A:GLY114 4.6 15.8 1.0
HA A:PRO142 4.7 15.5 1.0
O A:HOH444 4.8 36.3 1.0
O A:GLN119 4.8 11.2 1.0
HG3 A:PRO142 4.8 25.1 1.0
N A:SER120 4.9 10.6 1.0
HA A:PRO113 5.0 12.7 1.0
HG2 A:PRO113 5.0 13.7 1.0
CG A:PRO113 5.0 11.4 1.0

Magnesium binding site 3 out of 9 in 4hqs

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Magnesium binding site 3 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:23.4
occ:1.00
 HD3 A:LYS129 2.6 33.3 1.0
O A:HOH479 2.9 22.0 1.0
HD2 A:TYR128 2.9 11.1 1.0
O A:HOH393 3.0 24.3 1.0
CD A:LYS129 3.5 27.7 1.0
HD2 A:LYS129 3.6 33.3 1.0
HA A:LYS129 3.7 11.9 1.0
CD2 A:TYR128 3.7 9.2 1.0
HE2 A:TYR128 3.8 11.2 1.0
HZ3 A:LYS129 4.0 31.9 1.0
HB A:VAL60 4.0 15.7 1.0
HG23 A:VAL60 4.0 17.5 1.0
HG21 A:VAL60 4.1 17.5 1.0
CE2 A:TYR128 4.2 9.4 1.0
HE3 A:LYS129 4.2 34.4 1.0
O A:HOH438 4.3 29.2 1.0
CE A:LYS129 4.3 28.7 1.0
HB3 A:TYR128 4.4 11.6 1.0
HG2 A:LYS129 4.4 18.7 1.0
CG2 A:VAL60 4.4 14.6 1.0
CA A:LYS129 4.5 9.9 1.0
CG A:LYS129 4.5 15.6 1.0
NZ A:LYS129 4.6 26.6 1.0
N A:LYS129 4.6 10.4 1.0
O A:TYR128 4.6 10.9 1.0
C A:TYR128 4.7 9.4 1.0
CB A:VAL60 4.7 13.1 1.0
O A:HOH362 4.8 21.6 1.0
CG A:TYR128 4.8 9.5 1.0
H A:LYS129 4.9 12.4 1.0
HZ1 A:LYS129 4.9 31.9 1.0
O A:VAL60 5.0 15.5 1.0

Magnesium binding site 4 out of 9 in 4hqs

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Magnesium binding site 4 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:18.6
occ:1.00
 OG1 A:THR64 2.7 12.8 1.0
O A:GLY62 2.7 11.2 1.0
HE1 A:MET58 2.9 18.6 1.0
H A:THR64 3.0 12.8 1.0
HA A:LYS63 3.1 12.8 1.0
HG1 A:THR64 3.2 15.3 1.0
N A:THR64 3.3 10.7 1.0
HB A:THR64 3.5 15.2 1.0
CB A:THR64 3.6 12.6 1.0
C A:LYS63 3.7 12.1 1.0
CA A:LYS63 3.8 10.7 1.0
CE A:MET58 3.8 15.5 1.0
C A:GLY62 3.9 11.8 1.0
CA A:THR64 4.0 12.0 1.0
HE2 A:MET58 4.1 18.6 1.0
HG3 A:MET58 4.1 13.8 1.0
HE3 A:MET58 4.2 18.6 1.0
N A:LYS63 4.4 11.0 1.0
HA A:THR64 4.4 14.4 1.0
O A:LYS63 4.6 12.6 1.0
O A:HOH333 4.8 16.4 1.0
CG2 A:THR64 4.9 13.6 1.0
CG A:MET58 5.0 11.5 1.0

Magnesium binding site 5 out of 9 in 4hqs

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Magnesium binding site 5 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:21.8
occ:1.00
 HG A:SER82 2.8 11.3 1.0
OG A:SER82 2.8 9.4 1.0
HB3 A:TRP83 3.1 11.9 1.0
HE22 A:GLN119 3.1 17.8 1.0
HA A:TRP83 3.3 11.0 1.0
HB2 A:SER82 3.4 11.6 1.0
N A:TRP83 3.6 10.1 1.0
NE2 A:GLN119 3.6 14.8 1.0
CB A:SER82 3.6 9.7 1.0
C A:SER82 3.7 9.5 1.0
CA A:TRP83 3.7 9.1 1.0
HG3 A:GLN119 3.8 13.3 1.0
CB A:TRP83 3.8 10.0 1.0
O A:SER82 3.9 10.7 1.0
H A:TRP83 3.9 12.1 1.0
HE21 A:GLN119 4.0 17.8 1.0
MG A:MG213 4.0 26.8 1.0
CA A:SER82 4.3 9.1 1.0
CD A:GLN119 4.4 12.1 1.0
HD1 A:TRP83 4.4 12.6 1.0
HB2 A:TRP83 4.4 11.9 1.0
CG A:GLN119 4.4 11.1 1.0
HB3 A:SER82 4.4 11.6 1.0
O A:HOH413 4.5 30.6 1.0
HG2 A:GLN119 4.5 13.3 1.0
CG A:TRP83 4.8 10.8 1.0
OE1 A:GLU118 4.9 10.3 1.0
CD1 A:TRP83 4.9 10.5 1.0

Magnesium binding site 6 out of 9 in 4hqs

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Magnesium binding site 6 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:20.6
occ:1.00
 OH A:TYR155 2.5 10.7 1.0
HB2 A:LYS116 2.6 16.0 1.0
HB2 A:GLU118 2.8 10.6 1.0
O A:HIS115 2.8 10.6 1.0
O A:HOH328 2.8 9.4 1.0
HE2 A:TYR155 2.8 12.8 1.0
HB2 A:SER112 2.8 11.4 1.0
HH A:TYR155 3.1 12.8 1.0
CZ A:TYR155 3.3 8.3 1.0
CE2 A:TYR155 3.4 10.7 1.0
HB3 A:ALA81 3.4 11.0 1.0
H A:SER112 3.5 10.1 1.0
O A:SER112 3.5 10.9 1.0
CB A:GLU118 3.6 8.8 1.0
CB A:LYS116 3.6 13.3 1.0
HB3 A:GLU118 3.6 10.6 1.0
C A:HIS115 3.7 14.0 1.0
CB A:SER112 3.8 9.5 1.0
HD11 A:LEU147 3.8 17.2 1.0
HB2 A:HIS115 3.9 15.2 1.0
H A:GLU118 3.9 13.3 1.0
HB3 A:LYS116 4.0 16.0 1.0
HD3 A:LYS116 4.0 25.6 1.0
N A:SER112 4.1 8.4 1.0
HG2 A:GLU118 4.1 11.4 1.0
C A:SER112 4.2 10.4 1.0
HB2 A:ALA81 4.2 11.0 1.0
O A:LYS116 4.2 13.8 1.0
CB A:ALA81 4.2 9.2 1.0
CA A:SER112 4.2 9.8 1.0
MG A:MG205 4.2 17.1 1.0
CA A:LYS116 4.3 12.8 1.0
HB3 A:SER112 4.3 11.4 1.0
N A:LYS116 4.3 12.9 1.0
C A:LYS116 4.4 11.7 1.0
HG3 A:LYS116 4.4 19.1 1.0
H A:HIS115 4.4 13.8 1.0
CG A:GLU118 4.4 9.5 1.0
HE1 A:TRP83 4.5 12.9 1.0
CG A:LYS116 4.5 15.9 1.0
N A:GLU118 4.5 11.1 1.0
CB A:HIS115 4.5 12.7 1.0
OG A:SER112 4.6 10.6 1.0
O A:TRP80 4.6 7.7 1.0
HB3 A:HIS115 4.6 15.2 1.0
CA A:HIS115 4.6 11.8 1.0
CA A:GLU118 4.6 11.0 1.0
CE1 A:TYR155 4.6 9.7 1.0
HD22 A:LEU147 4.7 18.3 1.0
CD2 A:TYR155 4.7 11.4 1.0
CD1 A:LEU147 4.7 14.4 1.0
OE2 A:GLU118 4.7 9.2 1.0
CD A:LYS116 4.7 21.3 1.0
HA A:ALA81 4.7 10.2 1.0
HD13 A:LEU147 4.8 17.2 1.0
HB1 A:ALA81 4.9 11.0 1.0
HA A:GLU118 4.9 13.2 1.0
N A:HIS115 4.9 11.5 1.0
HA A:VAL111 4.9 9.3 1.0
HG A:SER112 5.0 12.7 1.0
HE1 A:TYR155 5.0 11.7 1.0
CD A:GLU118 5.0 8.4 1.0

Magnesium binding site 7 out of 9 in 4hqs

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Magnesium binding site 7 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:29.8
occ:1.00
 O A:HOH519 2.6 35.5 1.0
HA2 A:GLY117 2.9 15.1 1.0
HA3 A:GLY117 3.2 15.1 1.0
CA A:GLY117 3.5 12.6 1.0
N A:GLY117 4.1 13.1 1.0
H A:GLY117 4.2 15.7 1.0
O A:HOH368 4.6 21.0 1.0
C A:GLY117 4.7 13.1 1.0
O A:HOH354 4.8 24.0 1.0
C A:LYS116 4.9 11.7 1.0
O A:GLY117 5.0 11.7 1.0

Magnesium binding site 8 out of 9 in 4hqs

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Magnesium binding site 8 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:33.7
occ:1.00
 O A:HOH497 2.5 37.6 1.0
O A:HOH436 2.6 30.6 1.0
HG A:SER85 3.2 29.3 1.0
HB2 A:SER85 3.6 22.7 1.0
HB3 A:SER85 3.6 22.7 1.0
CB A:SER85 3.9 18.9 1.0
OG A:SER85 3.9 24.4 1.0
O A:HOH458 3.9 37.0 1.0
O A:HOH460 4.9 27.8 1.0

Magnesium binding site 9 out of 9 in 4hqs

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Magnesium binding site 9 out of 9 in the Crystal Structure of the Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4


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 Pneumoccocal Exposed Lipoprotein Thioredoxin SP_0659 (ETRX1) From Streptococcus Pneumoniae Strain TIGR4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:26.8
occ:1.00
 O A:SER82 2.7 10.7 1.0
O A:HOH404 2.7 34.7 1.0
O A:HOH521 2.7 33.5 1.0
HD12 A:LEU88 2.9 17.4 1.0
HA A:TRP83 3.2 11.0 1.0
HZ2 A:TRP127 3.4 13.1 1.0
CD1 A:LEU88 3.7 14.5 1.0
HD13 A:LEU88 3.7 17.4 1.0
C A:SER82 3.7 9.5 1.0
HE1 A:TRP127 3.9 14.8 1.0
HD11 A:LEU88 4.0 17.4 1.0
MG A:MG209 4.0 21.8 1.0
CZ2 A:TRP127 4.1 10.9 1.0
O A:HOH359 4.1 23.6 1.0
CA A:TRP83 4.1 9.1 1.0
HB2 A:SER82 4.3 11.6 1.0
N A:TRP83 4.3 10.1 1.0
NE1 A:TRP127 4.4 12.3 1.0
CE2 A:TRP127 4.5 10.6 1.0
C A:TRP83 4.6 11.8 1.0
O A:HOH394 4.8 24.6 1.0
HD21 A:LEU88 4.8 18.4 1.0
CA A:SER82 4.8 9.1 1.0
HG A:LEU88 4.9 15.3 1.0
CG A:LEU88 4.9 12.7 1.0
HA A:SER82 4.9 10.9 1.0
O A:TRP83 4.9 13.1 1.0
CB A:SER82 5.0 9.7 1.0

Reference:

M.Saleh, S.G.Bartual, M.R.Abdullah, I.Jensch, T.M.Asmat, L.Petruschka, T.Pribyl, M.Gellert, C.H.Lillig, H.Antelmann, J.A.Hermoso, S.Hammerschmidt. Molecular Architecture of Streptococcus Pneumoniae Surface Thioredoxin-Fold Lipoproteins Crucial For Extracellular Oxidative Stress Resistance and Maintenance of Virulence. Embo Mol Med V. 5 1852 2013.
ISSN: ISSN 1757-4676
PubMed: 24136784
DOI: 10.1002/EMMM.201202435
Page generated: Fri Aug 16 16:23:08 2024

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