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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

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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

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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

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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

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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

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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: Tue Dec 15 04:37:35 2020

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