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

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

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

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

Protein crystallography data

The structure of Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-C348, PDB code: 5dnl 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) 49.25 / 1.53
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 141.270, 141.270, 137.410, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 14.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-C348 (pdb code 5dnl). 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 (S)-C348, PDB code: 5dnl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5dnl

Go back to Manganese Binding Sites List in 5dnl
Manganese binding site 1 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-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 (S)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:11.8
occ:1.00
 OE1 A:GLU121 2.2 14.5 1.0
OE1 A:GLU56 2.2 13.1 1.0
O A:HOH314 2.2 13.6 1.0
NE2 A:HIS52 2.3 12.9 1.0
N4 A:5DL203 2.3 13.7 1.0
CD A:GLU56 3.2 14.9 1.0
CE1 A:HIS52 3.2 12.5 1.0
CD A:GLU121 3.2 14.9 1.0
CD2 A:HIS52 3.3 11.3 1.0
C5 A:5DL203 3.3 12.1 1.0
C3 A:5DL203 3.3 12.9 1.0
OE2 A:GLU56 3.6 14.0 1.0
CG A:GLU121 3.9 13.9 1.0
OE2 A:GLU121 4.2 17.2 1.0
ND1 A:HIS52 4.3 12.5 1.0
N2 A:5DL203 4.4 13.1 1.0
CG A:HIS52 4.4 11.7 1.0
CG A:GLU56 4.4 14.6 1.0
O A:HOH360 4.4 17.4 1.0
N1 A:5DL203 4.4 12.0 1.0
CB A:GLU121 4.6 13.3 1.0
CB A:GLU56 4.6 12.2 1.0
O A:HOH398 4.6 18.9 1.0

Manganese binding site 2 out of 6 in 5dnl

Go back to Manganese Binding Sites List in 5dnl
Manganese binding site 2 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-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 (S)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:12.2
occ:1.00
 N1 A:5DL203 2.2 12.0 1.0
O13 A:5DL203 2.3 14.2 1.0
NE2 A:HIS53 2.4 12.7 1.0
N2 A:5DL203 3.2 13.1 1.0
CE1 A:HIS53 3.2 13.5 1.0
C5 A:5DL203 3.3 12.1 1.0
CD2 A:HIS53 3.4 11.7 1.0
C7 A:5DL203 3.4 12.1 1.0
C6 A:5DL203 3.5 12.5 1.0
OE2 A:GLU7 4.2 16.7 1.0
C3 A:5DL203 4.4 12.9 1.0
ND1 A:HIS53 4.4 13.3 1.0
N4 A:5DL203 4.4 13.7 1.0
CG A:HIS53 4.5 13.0 1.0
C8 A:5DL203 4.5 13.2 1.0
CD A:GLU7 4.9 15.9 1.0
O A:HOH331 5.0 21.4 1.0

Manganese binding site 3 out of 6 in 5dnl

Go back to Manganese Binding Sites List in 5dnl
Manganese binding site 3 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-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 (S)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:12.0
occ:1.00
 OE1 C:GLU121 2.1 14.6 1.0
OE1 C:GLU56 2.2 13.1 1.0
O B:HOH305 2.2 13.7 1.0
NE2 C:HIS52 2.3 13.5 1.0
NE2 B:HIS146 2.3 10.9 1.0
N4 C:5DL203 2.3 12.1 1.0
CD C:GLU121 3.2 15.1 1.0
CD C:GLU56 3.2 15.2 1.0
CE1 B:HIS146 3.2 11.3 1.0
CE1 C:HIS52 3.2 11.4 1.0
C5 C:5DL203 3.3 10.7 1.0
CD2 C:HIS52 3.3 12.6 1.0
C3 C:5DL203 3.3 12.6 1.0
CD2 B:HIS146 3.3 10.9 1.0
OE2 C:GLU56 3.6 14.2 1.0
CG C:GLU121 3.9 13.4 1.0
OD2 B:ASP85 4.0 17.5 1.0
OE2 C:GLU121 4.1 16.9 1.0
ND1 C:HIS52 4.3 11.7 1.0
ND1 B:HIS146 4.4 11.2 1.0
N2 C:5DL203 4.4 12.1 1.0
O C:HOH386 4.4 15.8 1.0
CG C:GLU56 4.4 13.4 1.0
CG C:HIS52 4.4 11.6 1.0
CG B:HIS146 4.5 10.6 1.0
N1 C:5DL203 4.5 13.4 1.0
CB C:GLU121 4.6 12.6 1.0
O C:HOH411 4.6 18.3 1.0
CB C:GLU56 4.6 12.6 1.0
O B:HOH308 4.7 17.9 1.0
CG B:ASP85 5.0 17.4 1.0

Manganese binding site 4 out of 6 in 5dnl

Go back to Manganese Binding Sites List in 5dnl
Manganese binding site 4 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-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 (S)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn202

b:12.2
occ:1.00
 OE1 B:GLU149 2.1 12.9 1.0
N1 C:5DL203 2.2 13.4 1.0
NE2 B:HIS29 2.2 12.8 1.0
O13 C:5DL203 2.3 16.0 1.0
NE2 B:HIS145 2.3 11.2 1.0
NE2 C:HIS53 2.3 12.9 1.0
CD B:GLU149 3.1 14.8 1.0
N2 C:5DL203 3.2 12.1 1.0
CD2 B:HIS29 3.2 13.3 1.0
CE1 B:HIS29 3.2 13.4 1.0
CE1 C:HIS53 3.2 13.6 1.0
CE1 B:HIS145 3.3 10.8 1.0
C5 C:5DL203 3.3 10.7 1.0
CD2 B:HIS145 3.3 11.3 1.0
CD2 C:HIS53 3.4 14.0 1.0
C7 C:5DL203 3.4 13.1 1.0
OE2 B:GLU149 3.4 14.2 1.0
C6 C:5DL203 3.4 11.9 1.0
OE2 C:GLU7 4.2 16.4 1.0
ND1 B:HIS29 4.3 13.5 1.0
CG B:HIS29 4.4 12.6 1.0
ND1 B:HIS145 4.4 12.2 1.0
ND1 C:HIS53 4.4 12.9 1.0
C3 C:5DL203 4.4 12.6 1.0
N4 C:5DL203 4.4 12.1 1.0
CG B:GLU149 4.4 11.5 1.0
CG B:HIS145 4.4 12.6 1.0
CG C:HIS53 4.5 11.6 1.0
C8 C:5DL203 4.5 12.6 1.0
CB B:GLU149 4.8 11.4 1.0
CD C:GLU7 4.9 15.3 1.0
CE B:MET30 5.0 13.7 1.0

Manganese binding site 5 out of 6 in 5dnl

Go back to Manganese Binding Sites List in 5dnl
Manganese binding site 5 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-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 (S)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:11.8
occ:1.00
 N1 B:5DL203 2.2 11.0 1.0
O13 B:5DL203 2.3 15.2 1.0
N2 B:5DL203 3.2 12.9 1.0
C5 B:5DL203 3.3 10.8 1.0
C7 B:5DL203 3.4 12.5 1.0
C6 B:5DL203 3.5 12.6 1.0
C3 B:5DL203 4.4 13.1 1.0
N4 B:5DL203 4.4 11.6 1.0
C8 B:5DL203 4.5 13.0 1.0

Manganese binding site 6 out of 6 in 5dnl

Go back to Manganese Binding Sites List in 5dnl
Manganese binding site 6 out of 6 in the Crystal Structure of Igpd From Pyrococcus Furiosus in Complex with (S)-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 (S)-C348 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:11.5
occ:1.00
 N4 B:5DL203 2.3 11.6 1.0
C5 B:5DL203 3.3 10.8 1.0
C3 B:5DL203 3.3 13.1 1.0
N2 B:5DL203 4.4 12.9 1.0
N1 B:5DL203 4.5 11.0 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 23:56:18 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy