Atomistry » Manganese » PDB 5dcd-5ekd » 5dnx
Atomistry »
  Manganese »
    PDB 5dcd-5ekd »
      5dnx »

Manganese in PDB 5dnx: Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348

Enzymatic activity of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348

All present enzymatic activity of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348:
4.2.1.19;

Protein crystallography data

The structure of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348, PDB code: 5dnx was solved by C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.C.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.98 / 1.80
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 140.430, 140.430, 136.720, 90.00, 90.00, 90.00
R / Rfree (%) 13.1 / 15.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348 (pdb code 5dnx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348, PDB code: 5dnx:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5dnx

Go back to Manganese Binding Sites List in 5dnx
Manganese binding site 1 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:14.4
occ:1.00
 OE1 A:GLU121 2.2 16.7 1.0
OE1 A:GLU56 2.2 16.6 1.0
NE2 A:HIS52 2.3 15.5 1.0
N4 A:5LD203 2.3 13.0 1.0
CD A:GLU121 3.2 22.4 1.0
CD A:GLU56 3.2 24.6 1.0
CE1 A:HIS52 3.2 14.6 1.0
C3 A:5LD203 3.2 15.8 1.0
CD2 A:HIS52 3.3 15.3 1.0
C5 A:5LD203 3.3 13.4 1.0
OE2 A:GLU56 3.6 19.0 1.0
CG A:GLU121 3.8 17.8 1.0
OE2 A:GLU121 4.2 23.7 1.0
ND1 A:HIS52 4.3 13.6 1.0
O A:HOH348 4.4 17.9 1.0
N2 A:5LD203 4.4 17.4 1.0
CG A:HIS52 4.4 14.3 1.0
N1 A:5LD203 4.5 13.9 1.0
CG A:GLU56 4.5 16.4 1.0
CB A:GLU121 4.6 16.9 1.0
CB A:GLU56 4.7 15.6 1.0

Manganese binding site 2 out of 6 in 5dnx

Go back to Manganese Binding Sites List in 5dnx
Manganese binding site 2 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:14.6
occ:1.00
 N1 A:5LD203 2.3 13.9 1.0
O13 A:5LD203 2.3 14.9 1.0
NE2 A:HIS53 2.3 13.7 1.0
CE1 A:HIS53 3.2 14.9 1.0
C5 A:5LD203 3.2 13.4 1.0
C7 A:5LD203 3.3 15.7 1.0
N2 A:5LD203 3.3 17.4 1.0
CD2 A:HIS53 3.4 15.8 1.0
C6 A:5LD203 3.6 14.7 1.0
OE2 A:GLU7 4.3 22.2 1.0
ND1 A:HIS53 4.4 16.2 1.0
N4 A:5LD203 4.4 13.0 1.0
C3 A:5LD203 4.4 15.8 1.0
CG A:HIS53 4.5 13.5 1.0
C8 A:5LD203 4.6 16.8 1.0
CD A:GLU7 4.9 19.9 1.0

Manganese binding site 3 out of 6 in 5dnx

Go back to Manganese Binding Sites List in 5dnx
Manganese binding site 3 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:14.8
occ:1.00
 OE1 C:GLU56 2.1 16.8 1.0
OE1 C:GLU121 2.1 17.2 1.0
O B:HOH304 2.2 14.8 1.0
NE2 C:HIS52 2.3 17.6 1.0
NE2 B:HIS146 2.3 14.5 1.0
N4 B:5LD201 2.3 14.6 1.0
CD C:GLU56 3.2 22.9 1.0
CE1 B:HIS146 3.2 16.2 1.0
CD C:GLU121 3.2 21.4 1.0
CE1 C:HIS52 3.2 13.8 1.0
C3 B:5LD201 3.2 16.0 1.0
CD2 C:HIS52 3.3 14.5 1.0
C5 B:5LD201 3.3 13.3 1.0
CD2 B:HIS146 3.3 14.5 1.0
OE2 C:GLU56 3.6 17.4 1.0
CG C:GLU121 3.9 17.0 1.0
OD2 B:ASP85 4.0 26.8 1.0
OE2 C:GLU121 4.2 22.6 1.0
O C:HOH350 4.3 16.8 1.0
ND1 B:HIS146 4.3 14.0 1.0
ND1 C:HIS52 4.3 14.8 1.0
N2 B:5LD201 4.4 18.2 1.0
CG C:HIS52 4.4 15.3 1.0
CG B:HIS146 4.4 11.6 1.0
CG C:GLU56 4.4 16.3 1.0
N1 B:5LD201 4.5 16.3 1.0
O B:HOH301 4.5 26.8 1.0
CB C:GLU121 4.5 15.9 1.0
CB C:GLU56 4.7 16.0 1.0
CG B:ASP85 4.9 31.7 1.0

Manganese binding site 4 out of 6 in 5dnx

Go back to Manganese Binding Sites List in 5dnx
Manganese binding site 4 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:14.3
occ:1.00
 OE1 B:GLU149 2.2 15.2 1.0
N1 B:5LD201 2.2 16.3 1.0
O13 B:5LD201 2.2 16.6 1.0
NE2 B:HIS29 2.3 16.4 1.0
NE2 B:HIS145 2.3 14.6 1.0
NE2 C:HIS53 2.3 15.8 1.0
CD B:GLU149 3.1 21.6 1.0
CE1 B:HIS145 3.2 16.0 1.0
CD2 B:HIS29 3.2 14.6 1.0
C5 B:5LD201 3.2 13.3 1.0
C7 B:5LD201 3.2 14.0 1.0
CE1 B:HIS29 3.2 18.9 1.0
CE1 C:HIS53 3.2 14.8 1.0
CD2 B:HIS145 3.3 18.0 1.0
N2 B:5LD201 3.3 18.2 1.0
CD2 C:HIS53 3.4 14.2 1.0
OE2 B:GLU149 3.5 20.4 1.0
C6 B:5LD201 3.6 14.3 1.0
OE2 C:GLU7 4.2 23.6 1.0
ND1 B:HIS145 4.3 14.6 1.0
ND1 B:HIS29 4.4 18.3 1.0
CG B:HIS29 4.4 15.4 1.0
CE B:MET84 4.4 19.0 1.0
ND1 C:HIS53 4.4 15.0 1.0
N4 B:5LD201 4.4 14.6 1.0
CG B:HIS145 4.4 16.9 1.0
C3 B:5LD201 4.4 16.0 1.0
CG B:GLU149 4.5 16.7 1.0
CG C:HIS53 4.5 13.8 1.0
C8 B:5LD201 4.6 15.2 1.0
CD C:GLU7 4.9 21.4 1.0
CB B:GLU149 4.9 16.6 1.0

Manganese binding site 5 out of 6 in 5dnx

Go back to Manganese Binding Sites List in 5dnx
Manganese binding site 5 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:14.1
occ:1.00
 O13 B:5LD205 2.2 16.6 1.0
N1 B:5LD205 2.3 13.9 1.0
C5 B:5LD205 3.3 15.6 1.0
C7 B:5LD205 3.3 17.0 1.0
N2 B:5LD205 3.3 15.0 1.0
C6 B:5LD205 3.6 15.0 1.0
N4 B:5LD205 4.4 12.6 1.0
C3 B:5LD205 4.4 14.0 1.0
C8 B:5LD205 4.6 16.7 1.0

Manganese binding site 6 out of 6 in 5dnx

Go back to Manganese Binding Sites List in 5dnx
Manganese binding site 6 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (R)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn204

b:14.5
occ:1.00
 N4 B:5LD205 2.3 12.6 1.0
C3 B:5LD205 3.2 14.0 1.0
C5 B:5LD205 3.3 15.6 1.0
N2 B:5LD205 4.3 15.0 1.0
N1 B:5LD205 4.4 13.9 1.0

Reference:

C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.C.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice. Mirror-Image Packing Provides A Molecular Basis For the Nanomolar Equipotency of Enantiomers of An Experimental Herbicide. Angew.Chem.Int.Ed.Engl. V. 55 13485 2016.
ISSN: ESSN 1521-3773
PubMed: 27717128
DOI: 10.1002/ANIE.201607185
Page generated: Sat Oct 5 23:56:52 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy