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Magnesium in PDB 3iji: Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding.

Protein crystallography data

The structure of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding., PDB code: 3iji was solved by A.A.Fedorov, E.V.Fedorov, T.Lukk, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.83 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.432, 100.079, 60.000, 90.00, 90.25, 90.00
R / Rfree (%) 18.9 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding. (pdb code 3iji). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding., PDB code: 3iji:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3iji

Go back to Magnesium Binding Sites List in 3iji
Magnesium binding site 1 out of 2 in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg386

b:17.4
occ:1.00
OE1 A:GLU251 2.0 19.1 1.0
OD2 A:ASP276 2.0 20.3 1.0
O A:HOH538 2.0 22.1 1.0
O A:HOH470 2.1 19.0 1.0
OD2 A:ASP224 2.1 19.0 1.0
O A:HOH449 2.1 20.8 1.0
CD A:GLU251 3.0 19.6 1.0
CG A:ASP276 3.1 21.1 1.0
CG A:ASP224 3.1 20.1 1.0
OD1 A:ASP224 3.5 19.8 1.0
CB A:ASP276 3.5 19.7 1.0
CG A:GLU251 3.8 19.6 1.0
OE2 A:GLU251 3.8 19.9 1.0
O A:HOH457 3.9 25.6 1.0
NZ A:LYS298 4.0 21.1 1.0
OE2 A:GLU277 4.1 28.7 1.0
OD1 A:ASP276 4.2 21.7 1.0
OD1 A:ASN226 4.2 39.3 1.0
OE1 A:GLU277 4.2 26.0 1.0
O A:DGL385 4.2 18.5 1.0
ND2 A:ASN296 4.3 19.3 1.0
O A:HOH451 4.3 19.6 1.0
OXT A:DGL385 4.4 19.3 1.0
CB A:ASP224 4.4 20.2 1.0
CD A:GLU277 4.6 26.3 1.0
C A:DGL385 4.6 20.0 1.0
O A:HOH506 4.6 21.8 1.0
CE A:LYS298 4.7 19.0 1.0
NZ A:LYS198 4.9 20.5 1.0
CB A:GLU251 5.0 20.8 1.0

Magnesium binding site 2 out of 2 in 3iji

Go back to Magnesium Binding Sites List in 3iji
Magnesium binding site 2 out of 2 in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Nonproductive Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg386

b:13.7
occ:1.00
OE1 B:GLU251 2.0 17.0 1.0
O B:HOH397 2.0 14.6 1.0
OD2 B:ASP276 2.1 14.9 1.0
OD2 B:ASP224 2.1 15.6 1.0
O B:HOH489 2.1 14.0 1.0
O B:HOH485 2.1 15.4 1.0
CD B:GLU251 2.8 17.3 1.0
CG B:ASP224 3.1 14.9 1.0
CG B:ASP276 3.1 13.7 1.0
OD1 B:ASP224 3.5 15.7 1.0
CB B:ASP276 3.5 14.5 1.0
CG B:GLU251 3.6 20.9 1.0
OE2 B:GLU251 3.7 17.6 1.0
NZ B:LYS298 3.9 15.7 1.0
O B:HOH682 4.0 24.1 1.0
OE2 B:GLU277 4.1 19.4 1.0
O B:DGL385 4.1 18.8 1.0
OE1 B:GLU277 4.2 16.3 1.0
ND2 B:ASN296 4.2 12.4 1.0
OD1 B:ASP276 4.2 14.9 1.0
O B:HOH430 4.3 16.6 1.0
OXT B:DGL385 4.4 18.8 1.0
CB B:ASP224 4.4 13.6 1.0
CD B:GLU277 4.6 18.1 1.0
C B:DGL385 4.6 18.9 1.0
CE B:LYS298 4.7 16.5 1.0
CB B:GLU251 4.7 18.9 1.0
O B:HOH518 4.8 19.5 1.0

Reference:

T.Lukk, A.Sakai, C.Kalyanaraman, S.D.Brown, H.J.Imker, L.Song, A.A.Fedorov, E.V.Fedorov, R.Toro, B.Hillerich, R.Seidel, Y.Patskovsky, M.W.Vetting, S.K.Nair, P.C.Babbitt, S.C.Almo, J.A.Gerlt, M.P.Jacobson. Homology Models Guide Discovery of Diverse Enzyme Specificities Among Dipeptide Epimerases in the Enolase Superfamily. Proc.Natl.Acad.Sci.Usa V. 109 4122 2012.
ISSN: ISSN 0027-8424
PubMed: 22392983
DOI: 10.1073/PNAS.1112081109
Page generated: Wed Aug 14 16:09:34 2024

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