Atomistry » Magnesium » PDB 3ig8-3irw » 3ijl
Atomistry »
  Magnesium »
    PDB 3ig8-3irw »
      3ijl »

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

Protein crystallography data

The structure of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding., PDB code: 3ijl 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) 24.91 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.897, 100.074, 60.075, 90.00, 90.34, 90.00
R / Rfree (%) 19.2 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding. (pdb code 3ijl). 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-Pro-D-Glu; Nonproductive Substrate Binding., PDB code: 3ijl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ijl

Go back to Magnesium Binding Sites List in 3ijl
Magnesium binding site 1 out of 2 in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-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-Pro-D-Glu; Nonproductive Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg386

b:15.5
occ:1.00
OE1 A:GLU251 2.0 15.4 1.0
O A:HOH451 2.0 15.4 1.0
OD2 A:ASP276 2.0 17.1 1.0
OD2 A:ASP224 2.1 15.2 1.0
O A:HOH536 2.1 17.2 1.0
O A:HOH471 2.2 17.5 1.0
CD A:GLU251 2.9 15.5 1.0
CG A:ASP276 3.1 16.9 1.0
CG A:ASP224 3.1 16.6 1.0
OD1 A:ASP224 3.5 16.0 1.0
CB A:ASP276 3.5 16.7 1.0
OE2 A:GLU251 3.6 16.9 1.0
CG A:GLU251 3.7 17.7 1.0
O A:HOH459 3.9 26.3 1.0
NZ A:LYS298 4.0 16.1 1.0
OE2 A:GLU277 4.0 27.3 1.0
OD1 A:ASN226 4.1 29.6 1.0
OD1 A:ASP276 4.2 16.6 1.0
OE1 A:GLU277 4.2 20.2 1.0
ND2 A:ASN296 4.2 15.2 1.0
O A:DGL385 4.3 17.7 1.0
O A:HOH452 4.4 16.9 1.0
CB A:ASP224 4.4 16.2 1.0
CD A:GLU277 4.6 23.1 1.0
OXT A:DGL385 4.6 17.8 1.0
CE A:LYS298 4.7 15.3 1.0
C A:DGL385 4.7 16.9 1.0
O A:HOH506 4.7 18.5 1.0
CB A:GLU251 4.9 18.9 1.0
CG A:ASN226 5.0 26.0 1.0

Magnesium binding site 2 out of 2 in 3ijl

Go back to Magnesium Binding Sites List in 3ijl
Magnesium binding site 2 out of 2 in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-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-Pro-D-Glu; Nonproductive Substrate Binding. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg386

b:12.4
occ:1.00
OE1 B:GLU251 2.0 15.2 1.0
OD2 B:ASP276 2.0 14.6 1.0
O B:HOH394 2.1 12.9 1.0
O B:HOH473 2.1 12.8 1.0
O B:HOH466 2.1 14.4 1.0
OD2 B:ASP224 2.1 12.9 1.0
CD B:GLU251 2.9 14.9 1.0
CG B:ASP276 3.1 14.1 1.0
CG B:ASP224 3.1 11.9 1.0
OD1 B:ASP224 3.5 13.7 1.0
CB B:ASP276 3.5 14.9 1.0
OE2 B:GLU251 3.6 14.4 1.0
CG B:GLU251 3.7 18.6 1.0
OD1 B:ASN226 3.8 30.8 1.0
O B:HOH616 3.9 19.6 1.0
NZ B:LYS298 4.0 13.1 1.0
OE2 B:GLU277 4.1 23.3 1.0
OD1 B:ASP276 4.2 16.1 1.0
ND2 B:ASN296 4.2 12.0 1.0
O B:DGL385 4.2 14.4 1.0
OE1 B:GLU277 4.2 17.9 1.0
O B:HOH424 4.4 14.0 1.0
CB B:ASP224 4.4 13.4 1.0
OXT B:DGL385 4.5 14.3 1.0
CD B:GLU277 4.6 21.4 1.0
C B:DGL385 4.6 13.8 1.0
CE B:LYS298 4.7 12.9 1.0
CB B:GLU251 4.8 18.7 1.0
CG B:ASN226 4.8 27.9 1.0
O B:HOH502 4.9 15.9 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: Mon Dec 14 08:17:05 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy