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Magnesium in PDB 3mmh: X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate

Enzymatic activity of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate

All present enzymatic activity of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate:
1.8.4.14;

Protein crystallography data

The structure of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate, PDB code: 3mmh was solved by A.Gruez, M.Libiad, S.Boschi-Muller, G.Branlant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.320, 39.480, 52.250, 104.17, 105.16, 100.50
R / Rfree (%) 11.8 / 15.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate (pdb code 3mmh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate, PDB code: 3mmh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3mmh

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Magnesium binding site 1 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg169

b:18.1
occ:1.00
 O A:ALA37 2.8 7.8 1.0
O B:PHE69 2.8 8.8 1.0
OE1 A:GLN70 2.9 11.8 1.0
O B:HOH173 3.2 16.4 1.0
C A:ALA37 3.6 7.7 1.0
CG A:GLN70 3.6 16.0 1.0
CD A:GLN70 3.6 9.4 1.0
CA A:ALA37 3.7 7.5 1.0
CE1 B:PHE69 3.8 8.5 1.0
CZ B:PHE69 3.9 8.7 1.0
CB A:ALA40 3.9 8.9 1.0
CD1 B:PHE69 3.9 8.8 1.0
C B:PHE69 3.9 8.2 1.0
N A:ALA41 3.9 7.7 1.0
O A:PHE69 4.0 8.5 1.0
CB A:ALA37 4.0 9.2 1.0
CE2 B:PHE69 4.0 8.5 1.0
CG B:PHE69 4.1 7.7 1.0
CD2 B:PHE69 4.2 8.9 1.0
N B:PHE69 4.3 8.1 1.0
C A:PHE69 4.3 7.4 1.0
CB A:ALA41 4.4 9.1 1.0
CA A:ALA41 4.5 8.1 1.0
C A:ALA40 4.5 7.3 1.0
N A:PHE69 4.5 7.9 1.0
CA B:PHE69 4.6 9.0 1.0
CA A:ALA40 4.7 7.8 1.0
CB A:PRO68 4.7 8.2 1.0
N A:ASN38 4.8 7.8 1.0
N B:GLN70 4.9 8.2 1.0
CA A:PHE69 4.9 8.0 1.0
N A:GLN70 4.9 7.8 1.0
NE2 A:GLN70 4.9 8.3 1.0
CA B:GLN70 4.9 8.2 0.3
CB A:GLN70 5.0 10.8 1.0

Magnesium binding site 2 out of 9 in 3mmh

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Magnesium binding site 2 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg170

b:18.2
occ:1.00
 OE1 A:GLU45 2.7 16.9 1.0
N B:LEU73 3.0 9.6 1.0
O A:ALA41 3.0 8.7 1.0
CD1 A:LEU4 3.4 24.2 0.7
C A:ALA41 3.4 8.1 1.0
CA B:PRO72 3.5 9.7 0.6
CA B:PRO72 3.5 10.1 0.4
CB A:GLU45 3.5 11.7 1.0
CB B:LEU73 3.7 16.6 1.0
CA A:VAL42 3.7 8.3 1.0
N A:VAL42 3.7 7.7 1.0
C B:PRO72 3.7 9.3 0.6
C B:PRO72 3.7 9.7 0.4
CD A:GLU45 3.8 17.3 1.0
CB B:PRO72 3.8 11.8 0.4
CA B:LEU73 3.9 11.5 1.0
CB B:PRO72 3.9 12.2 0.6
CB A:ALA41 4.0 9.1 1.0
O A:HOH346 4.1 26.6 1.0
O A:HOH321 4.1 16.6 1.0
CG A:GLU45 4.2 15.9 1.0
CG2 A:VAL42 4.3 10.8 1.0
CA A:ALA41 4.3 8.1 1.0
CB A:VAL42 4.6 9.2 1.0
C A:VAL42 4.7 8.2 1.0
N B:PRO72 4.8 9.8 0.6
O A:VAL42 4.8 8.5 1.0
N B:PRO72 4.8 10.0 0.4
CA A:GLU45 4.8 10.8 1.0
O B:GLY71 4.8 10.0 1.0
OE2 A:GLU45 4.9 24.9 1.0
O B:PRO72 4.9 10.7 0.6
CG B:PRO72 4.9 11.5 0.4
CZ A:PHE6 4.9 18.8 1.0
CG A:LEU4 4.9 19.6 0.7
O B:PRO72 4.9 10.7 0.4
N A:GLU45 4.9 9.5 1.0
CG B:LEU73 4.9 17.7 1.0

Magnesium binding site 3 out of 9 in 3mmh

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Magnesium binding site 3 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg171

b:18.9
occ:1.00
 O A:THR30 2.8 12.8 1.0
O A:ARG159 2.9 11.7 1.0
ND2 A:ASN35 3.0 11.2 1.0
CA A:TRP32 3.4 10.9 1.0
C A:THR30 3.5 12.1 1.0
C A:ARG159 3.5 11.1 1.0
N A:TRP32 3.6 11.3 1.0
CB A:ARG159 3.6 12.0 1.0
C A:ASP31 3.6 10.7 1.0
O A:ASP31 3.7 10.4 1.0
CB A:SER163 3.7 13.2 1.0
CE3 A:TRP32 3.8 12.7 1.0
CG A:ASN35 4.0 10.2 1.0
CA A:ARG159 4.1 11.5 1.0
CB A:TRP32 4.1 11.2 1.0
CA A:THR30 4.1 13.4 1.0
CB A:ASN35 4.2 9.3 1.0
N A:ASP31 4.2 11.7 1.0
N A:PHE160 4.3 11.1 1.0
O A:GLU29 4.3 12.9 1.0
CA A:SER163 4.5 13.5 1.0
CA A:ASP31 4.5 10.8 1.0
N A:SER163 4.5 13.3 1.0
C A:TRP32 4.6 9.5 1.0
OG A:SER163 4.6 14.6 1.0
CD2 A:TRP32 4.6 10.8 1.0
CZ3 A:TRP32 4.7 11.6 1.0
CA A:PHE160 4.7 11.9 1.0
NE A:ARG159 4.7 13.7 1.0
CG A:ARG159 4.8 12.9 1.0
CG A:TRP32 4.8 11.6 1.0
O A:TRP32 4.8 9.4 1.0
C A:GLU29 5.0 13.4 1.0
N A:THR30 5.0 13.2 1.0

Magnesium binding site 4 out of 9 in 3mmh

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Magnesium binding site 4 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg172

b:17.6
occ:1.00
 O A:HOH232 2.7 16.7 1.0
OD1 A:ASP145 2.8 10.5 1.0
O A:GLN140 2.9 13.3 1.0
NE1 A:TRP49 3.1 10.2 1.0
OD2 A:ASP145 3.4 11.3 1.0
CG A:ASP145 3.4 10.3 1.0
CE A:LYS11 3.6 14.2 1.0
CE2 A:TRP49 3.7 10.0 1.0
CZ2 A:TRP49 3.7 10.2 1.0
CD1 A:PHE141 3.7 10.0 1.0
NZ A:LYS11 3.8 14.2 1.0
C A:GLN140 3.9 13.1 1.0
CG A:GLN140 3.9 15.5 1.0
CD A:LYS11 4.0 13.7 1.0
CE1 A:PHE141 4.0 10.9 1.0
NE2 A:GLN140 4.2 17.1 1.0
CD1 A:TRP49 4.2 10.8 1.0
CG A:LYS11 4.4 12.1 1.0
CA A:PHE141 4.4 11.1 1.0
CG A:PHE141 4.6 10.5 1.0
N A:PHE141 4.6 11.9 1.0
CD A:GLN140 4.6 18.3 1.0
O A:HOH190 4.7 14.5 1.0
CB A:ASP145 4.8 10.2 1.0
CB A:GLN140 4.8 13.5 1.0
OH A:TYR15 4.8 10.2 1.0
O A:HOH241 4.8 15.8 1.0
CA A:GLN140 4.8 14.1 1.0
O A:HOH273 4.9 20.1 1.0
CD1 A:PHE47 4.9 11.6 1.0
CZ A:PHE141 4.9 10.6 1.0
CH2 A:TRP49 5.0 9.6 1.0

Magnesium binding site 5 out of 9 in 3mmh

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Magnesium binding site 5 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg173

b:20.5
occ:1.00
 O A:PHE141 2.7 13.5 1.0
O A:VAL97 2.9 15.0 1.0
N A:PHE141 3.0 11.9 1.0
CA A:ALA139 3.3 18.0 1.0
CA A:GLY98 3.4 18.1 1.0
N A:GLN140 3.5 15.0 1.0
CA A:PHE141 3.5 11.1 1.0
C A:VAL97 3.5 14.8 1.0
C A:PHE141 3.5 11.9 1.0
CB A:SER115 3.5 13.1 1.0
C A:ALA139 3.6 17.3 1.0
CB A:PHE141 3.6 10.9 1.0
N A:GLY98 3.7 16.9 1.0
OG A:SER115 3.9 14.0 1.0
CD2 A:PHE141 4.0 10.8 1.0
N A:ALA139 4.0 17.1 1.0
C A:GLN140 4.1 13.1 1.0
CG1 A:VAL96 4.2 18.2 1.0
CG A:PHE141 4.2 10.5 1.0
C A:GLY98 4.3 19.8 1.0
O A:ALA139 4.3 20.9 1.0
O A:GLY98 4.3 19.9 1.0
CA A:GLN140 4.4 14.1 1.0
O A:GLU116 4.4 12.2 1.0
N A:GLU116 4.4 10.8 1.0
N A:VAL97 4.5 13.4 1.0
CA A:SER115 4.6 12.7 1.0
CB A:ALA139 4.6 21.2 1.0
CA A:VAL97 4.7 14.4 1.0
N A:ASP142 4.8 11.7 1.0
C A:SER115 4.9 11.0 1.0

Magnesium binding site 6 out of 9 in 3mmh

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Magnesium binding site 6 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg174

b:18.3
occ:1.00
 OD1 A:ASN35 2.9 10.6 1.0
O A:HOH330 2.9 21.7 1.0
ND2 A:ASN38 3.1 7.1 1.0
CG2 B:THR76 3.4 12.7 1.0
CB A:ASN38 3.5 8.8 1.0
CG1 A:VAL25 3.5 18.5 1.0
O A:VAL25 3.7 17.8 1.0
CG A:ASN38 3.7 8.5 1.0
CG A:ASN35 4.0 10.2 1.0
CA A:ASN35 4.0 8.8 1.0
O A:ALA34 4.1 9.1 1.0
C A:VAL25 4.1 13.4 1.0
CB A:GLU29 4.2 12.9 1.0
CA A:VAL26 4.3 12.4 1.0
CG1 A:VAL26 4.3 12.8 1.0
N A:ASN35 4.4 8.6 1.0
N A:VAL26 4.4 11.3 1.0
C A:ALA34 4.4 8.7 1.0
CB A:ASN35 4.5 9.3 1.0
CG A:GLU29 4.7 12.1 1.0
O B:HOH224 4.7 28.8 1.0
CB B:THR76 4.8 11.5 1.0
CB A:VAL25 4.8 15.0 1.0
CB A:VAL26 4.8 11.1 1.0
O A:ASN35 4.8 8.6 1.0
CA A:ASN38 4.9 8.1 1.0
C A:ASN35 4.9 7.8 1.0

Magnesium binding site 7 out of 9 in 3mmh

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Magnesium binding site 7 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg175

b:45.4
occ:1.00
 OD1 A:ASP62 2.9 22.1 0.3
CD1 A:PHE80 3.6 18.6 1.0
CG A:ASP62 3.7 20.6 0.3
OD2 A:ASP62 3.7 25.5 0.3
CE1 A:PHE80 3.7 20.6 1.0
CG A:PHE80 4.0 15.0 1.0
CZ A:PHE80 4.2 20.9 1.0
OD1 A:ASP62 4.3 28.5 0.7
CD2 A:PHE80 4.4 18.0 1.0
CZ2 A:TRP89 4.4 15.8 1.0
CE2 A:PHE80 4.5 20.5 1.0
CB A:PHE80 4.6 15.1 1.0
CG A:ASP62 4.7 25.1 0.7
O A:HOH345 4.7 34.4 1.0
O A:HOH233 4.8 38.1 1.0
CE2 A:TRP89 4.8 14.8 1.0
NE1 A:TRP89 4.9 17.1 1.0
CB A:ASP62 5.0 21.9 0.7

Magnesium binding site 8 out of 9 in 3mmh

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Magnesium binding site 8 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg169

b:17.9
occ:1.00
 O B:ALA37 2.8 9.2 1.0
O A:PHE69 2.8 8.5 1.0
NE2 B:GLN70 2.9 5.7 0.3
NE2 B:GLN70 3.0 10.7 0.7
O B:HOH173 3.2 16.4 1.0
CG B:GLN70 3.3 8.4 0.3
C B:ALA37 3.6 8.7 1.0
CD B:GLN70 3.6 7.0 0.3
CA B:ALA37 3.7 8.9 1.0
CE1 A:PHE69 3.8 9.2 1.0
CD B:GLN70 3.9 10.8 0.7
CG B:GLN70 3.9 17.1 0.7
CZ A:PHE69 3.9 9.4 1.0
C A:PHE69 3.9 7.4 1.0
O B:PHE69 4.0 8.8 1.0
N B:ALA41 4.0 8.8 1.0
CD1 A:PHE69 4.0 8.6 1.0
CB B:ALA37 4.0 9.3 1.0
CE2 A:PHE69 4.1 10.1 1.0
CB B:ALA40 4.1 10.2 1.0
CG A:PHE69 4.2 7.9 1.0
CD2 A:PHE69 4.2 8.5 1.0
C B:PHE69 4.3 8.2 1.0
N A:PHE69 4.3 7.9 1.0
CB B:ALA41 4.3 10.3 1.0
CA B:ALA41 4.5 9.2 1.0
C B:ALA40 4.5 8.9 1.0
N B:PHE69 4.5 8.1 1.0
CA A:PHE69 4.6 8.0 1.0
CB B:PRO68 4.8 9.3 1.0
N B:ASN38 4.8 10.1 1.0
CA B:ALA40 4.8 9.5 1.0
CB B:GLN70 4.8 7.6 0.3
OE1 B:GLN70 4.8 6.5 0.3
N A:GLN70 4.8 7.8 1.0
CA B:PHE69 4.8 9.0 1.0
N B:GLN70 4.9 8.2 1.0
CA A:GLN70 5.0 7.8 1.0
OE1 B:GLN70 5.0 12.8 0.7

Magnesium binding site 9 out of 9 in 3mmh

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Magnesium binding site 9 out of 9 in the X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of X-Ray Structure of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg170

b:19.9
occ:1.00
 OD1 B:ASN35 2.9 13.5 1.0
ND2 B:ASN38 3.0 8.8 1.0
O B:HOH260 3.0 29.9 1.0
O B:VAL25 3.3 21.6 1.0
CG2 A:THR76 3.4 15.3 1.0
CB B:ASN38 3.5 10.8 1.0
CG1 B:VAL25 3.5 21.4 1.0
CG B:ASN38 3.7 10.9 1.0
C B:VAL25 3.9 17.6 1.0
CA B:ASN35 4.0 10.8 1.0
CG B:ASN35 4.0 11.0 1.0
O B:ALA34 4.1 10.7 1.0
CA B:VAL26 4.1 15.3 1.0
CG1 B:VAL26 4.2 14.9 1.0
N B:VAL26 4.3 15.0 1.0
CB B:GLU29 4.4 15.4 1.0
N B:ASN35 4.4 10.0 1.0
C B:ALA34 4.5 10.2 1.0
CB B:ASN35 4.6 11.8 1.0
CB B:VAL26 4.7 14.5 1.0
CB B:VAL25 4.7 17.5 1.0
O B:ASN35 4.8 10.6 1.0
CB A:THR76 4.8 13.1 1.0
CG B:GLU29 4.8 15.7 1.0
CA B:ASN38 4.9 9.7 1.0
C B:ASN35 4.9 10.2 1.0
CA B:VAL25 4.9 17.9 1.0
OD1 B:ASN38 4.9 14.8 1.0
O A:HOH282 5.0 28.8 1.0

Reference:

A.Gruez, M.Libiad, S.Boschi-Muller, G.Branlant. Structural and Biochemical Characterization of Free Methionine-R-Sulfoxide Reductase From Neisseria Meningitidis. J.Biol.Chem. V. 285 25033 2010.
ISSN: ISSN 0021-9258
PubMed: 20489204
DOI: 10.1074/JBC.M110.134528
Page generated: Wed Aug 14 19:21:59 2024

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