Magnesium in PDB 4yo7: Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol

Protein crystallography data

The structure of Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol, PDB code: 4yo7 was solved by U.Yadava, M.W.Vetting, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, J.Koss, S.R.Wasserman, J.D.Attonito, A.Scott Glenn, S.Chamala, S.Chowdhury, J.Lafleur, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.54 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.155, 79.845, 118.337, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 16.9

Other elements in 4yo7:

The structure of Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol (pdb code 4yo7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol, PDB code: 4yo7:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4yo7

Go back to Magnesium Binding Sites List in 4yo7
Magnesium binding site 1 out of 3 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol


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 An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:19.6
occ:1.00
O A:HOH568 2.1 20.6 1.0
O A:GLY38 2.1 19.1 1.0
O A:HOH559 2.1 23.7 1.0
C A:GLY38 3.2 15.6 1.0
HA3 A:GLY38 3.6 35.8 1.0
HB3 A:ASP39 3.7 24.3 1.0
CA A:GLY38 3.8 29.8 1.0
HA2 A:GLY38 3.9 35.8 1.0
HA A:ASP39 4.2 24.3 1.0
N A:ASP39 4.3 19.1 1.0
O A:HOH520 4.3 34.5 1.0
CB A:ASP39 4.5 20.3 1.0
CA A:ASP39 4.5 20.2 1.0
HB2 A:ASP39 4.9 24.3 1.0

Magnesium binding site 2 out of 3 in 4yo7

Go back to Magnesium Binding Sites List in 4yo7
Magnesium binding site 2 out of 3 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol


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 An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:37.9
occ:1.00
O A:HOH790 2.1 48.3 1.0
O A:HOH730 2.1 46.8 1.0
O A:HOH743 2.1 48.3 1.0
O A:LEU250 2.2 27.7 1.0
O A:VAL253 2.3 24.8 1.0
HG A:LEU250 3.4 32.1 1.0
HA A:ASP251 3.4 38.1 1.0
C A:LEU250 3.4 30.5 1.0
H A:VAL253 3.4 25.4 1.0
C A:VAL253 3.5 19.9 1.0
HD12 A:LEU250 3.6 29.8 1.0
OD2 A:ASP274 3.7 22.9 1.0
HA A:ILE254 3.7 22.6 1.0
HG23 A:VAL255 3.9 21.1 1.0
HD11 A:LEU250 4.0 29.8 1.0
CA A:ASP251 4.1 31.7 1.0
CD1 A:LEU250 4.1 24.8 1.0
N A:VAL253 4.1 21.2 1.0
CG A:LEU250 4.1 26.8 1.0
N A:ASP251 4.2 31.2 1.0
C A:ASP251 4.3 33.4 1.0
N A:ILE254 4.3 15.3 1.0
HA A:LEU250 4.3 28.9 1.0
H A:VAL255 4.3 16.3 1.0
CA A:VAL253 4.4 21.1 1.0
CA A:ILE254 4.4 18.9 1.0
CA A:LEU250 4.4 24.0 1.0
OD1 A:ASP274 4.5 27.0 1.0
CG A:ASP274 4.5 24.2 1.0
O A:ASP251 4.5 37.9 1.0
O A:LYS272 4.6 18.1 1.0
HB A:VAL253 4.6 26.0 1.0
N A:ASP252 4.7 26.5 1.0
N A:VAL255 4.8 13.6 1.0
CG2 A:VAL255 4.8 17.6 1.0
CB A:LEU250 4.8 25.9 1.0
H A:ASP252 4.9 31.8 1.0
C A:ILE254 4.9 18.6 1.0
HG21 A:VAL255 5.0 21.1 1.0

Magnesium binding site 3 out of 3 in 4yo7

Go back to Magnesium Binding Sites List in 4yo7
Magnesium binding site 3 out of 3 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol


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 An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi- 511484) with Bound Myo-Inositol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:19.9
occ:0.50
O A:HOH586 2.0 52.1 1.0
O A:HOH522 2.1 24.5 1.0
O A:HOH572 2.1 49.7 0.5
O A:HOH532 2.1 25.4 1.0
O A:HOH544 3.8 24.5 1.0
O A:THR140 4.0 8.4 1.0
O A:ALA139 4.2 10.9 1.0
O A:HOH638 4.4 14.7 1.0
O A:ASP137 4.4 10.2 1.0
HA A:ALA141 4.4 10.7 1.0
O A:HOH545 4.4 31.8 1.0
OD1 A:ASP303 4.5 13.5 1.0
HA A:ASP137 4.5 9.6 1.0
O A:HOH588 4.7 26.5 0.5
C A:THR140 4.7 8.3 1.0
HB2 A:ASP137 4.8 13.3 1.0
HA A:THR140 4.9 9.4 1.0

Reference:

U.Yadava, M.W.Vetting, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, J.Koss, S.R.Wasserman, J.D.Attonito, A.Scott Glenn, S.Chamala, S.Chowdhury, J.Lafleur, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Bacillus Halodurans C-125 (BH2323, Target Efi-511484) with Bound Myo-Inositol To Be Published.
Page generated: Mon Dec 14 19:55:11 2020

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