Atomistry » Iron » PDB 5li6-5m2g » 5lun
Atomistry »
  Iron »
    PDB 5li6-5m2g »
      5lun »

Iron in PDB 5lun: Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine

Enzymatic activity of Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine

All present enzymatic activity of Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine:
1.13.12.19; 1.14.11.34;

Protein crystallography data

The structure of Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine, PDB code: 5lun was solved by M.A.Mcdonough, Z.Zhang, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.60 / 1.08
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.839, 79.056, 97.859, 91.56, 93.42, 100.80
R / Rfree (%) 16.2 / 18.5

Iron Binding Sites:

The binding sites of Iron atom in the Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine (pdb code 5lun). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine, PDB code: 5lun:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5lun

Go back to Iron Binding Sites List in 5lun
Iron binding site 1 out of 4 in the Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:11.4
occ:1.00
 OD2 A:ASP191 2.0 14.3 0.5
O1 A:OGA402 2.0 11.0 0.5
NE2 A:HIS268 2.0 10.9 1.0
O2' A:OGA402 2.1 12.1 0.5
O1 A:OGA402 2.1 17.8 0.5
NE2 A:HIS189 2.1 10.4 1.0
O A:HOH1405 2.2 16.3 1.0
OD1 A:ASP191 2.2 11.1 0.5
O2' A:OGA402 2.2 18.8 0.5
C2 A:OGA402 2.7 11.9 0.5
C1 A:OGA402 2.7 11.6 0.5
C1 A:OGA402 2.9 15.8 0.5
CG A:ASP191 2.9 14.6 0.5
C2 A:OGA402 2.9 16.9 0.5
CD2 A:HIS268 3.0 10.1 1.0
CG A:ASP191 3.0 9.9 0.5
CE1 A:HIS268 3.0 10.6 1.0
CE1 A:HIS189 3.0 11.2 1.0
OD2 A:ASP191 3.1 11.3 0.5
OD1 A:ASP191 3.1 14.1 0.5
CD2 A:HIS189 3.2 9.9 1.0
O2 A:OGA402 4.0 12.6 0.5
NE A:ARG403 4.0 15.4 0.5
N1 A:OGA402 4.0 12.9 0.5
O2 A:OGA402 4.1 14.6 0.5
NH1 A:ARG403 4.1 15.8 0.5
ND1 A:HIS268 4.1 10.6 1.0
CG A:HIS268 4.2 9.2 1.0
ND1 A:HIS189 4.2 9.7 1.0
CB A:ASP191 4.3 13.0 0.5
CG A:HIS189 4.3 9.6 1.0
N1 A:OGA402 4.3 16.7 0.5
O A:HOH1533 4.3 23.3 1.0
CD A:ARG403 4.5 9.3 0.5
CZ A:ARG403 4.5 15.1 0.5
CB A:ASP191 4.5 10.6 0.5
CE1 A:PHE283 4.7 10.7 1.0
CZ A:PHE283 4.7 10.3 1.0
C4 A:OGA402 4.8 13.4 0.5
C4 A:OGA402 4.9 17.1 0.5
NH2 A:ARG403 5.0 11.1 0.5

Iron binding site 2 out of 4 in 5lun

Go back to Iron Binding Sites List in 5lun
Iron binding site 2 out of 4 in the Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:13.6
occ:1.00
 O2 B:OGA402 2.0 14.5 0.5
NE2 B:HIS268 2.0 12.0 1.0
OD2 B:ASP191 2.0 14.0 0.5
O B:HOH506 2.2 19.8 1.0
O2' B:OGA402 2.2 16.1 0.5
O2 B:OGA402 2.2 19.9 0.5
NE2 B:HIS189 2.2 12.0 1.0
O2' B:OGA402 2.2 22.1 0.5
OD1 B:ASP191 2.3 15.0 0.5
C1 B:OGA402 2.7 17.0 0.5
C2 B:OGA402 2.7 17.7 0.5
C1 B:OGA402 2.9 19.4 0.5
C2 B:OGA402 2.9 21.3 0.5
CG B:ASP191 2.9 14.7 0.5
OD2 B:ASP191 3.0 12.3 0.5
CG B:ASP191 3.0 12.9 0.5
CD2 B:HIS268 3.0 11.8 1.0
CE1 B:HIS268 3.0 11.5 1.0
OD1 B:ASP191 3.1 15.7 0.5
CE1 B:HIS189 3.1 11.3 1.0
CD2 B:HIS189 3.2 12.1 1.0
O1 B:OGA402 3.9 18.0 0.5
N1 B:OGA402 4.1 18.5 0.5
O1 B:OGA402 4.1 16.3 0.5
ND1 B:HIS268 4.1 10.9 1.0
NE B:ARG403 4.1 20.9 0.5
CG B:HIS268 4.1 10.8 1.0
O B:HOH595 4.2 32.2 1.0
ND1 B:HIS189 4.2 11.3 1.0
N1 B:OGA402 4.3 20.4 0.5
CB B:ASP191 4.3 13.6 0.5
CG B:HIS189 4.3 10.7 1.0
CD B:ARG403 4.3 11.0 0.5
CB B:ASP191 4.5 13.8 0.5
NH2 B:ARG403 4.5 23.9 0.5
CZ B:ARG403 4.7 22.7 0.5
CE1 B:PHE283 4.7 11.7 1.0
CZ B:PHE283 4.8 12.6 1.0
C4 B:OGA402 4.8 19.1 0.5
CD B:ARG403 4.9 18.4 0.5
C4 B:OGA402 4.9 19.4 0.5

Iron binding site 3 out of 4 in 5lun

Go back to Iron Binding Sites List in 5lun
Iron binding site 3 out of 4 in the Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:16.1
occ:1.00
 O2' C:OGA402 2.0 20.9 0.5
OD2 C:ASP191 2.0 16.7 0.5
O1 C:OGA402 2.0 21.4 0.5
O1 C:OGA402 2.0 17.2 0.5
NE2 C:HIS268 2.0 14.9 1.0
NE2 C:HIS189 2.2 15.3 1.0
OD1 C:ASP191 2.2 14.4 0.5
O C:HOH510 2.2 20.7 1.0
O2' C:OGA402 2.4 23.4 0.5
C2 C:OGA402 2.6 21.4 0.5
C1 C:OGA402 2.6 19.9 0.5
C1 C:OGA402 2.8 21.6 0.5
CG C:ASP191 2.9 15.9 0.5
C2 C:OGA402 2.9 23.3 0.5
CG C:ASP191 3.0 14.9 0.5
CD2 C:HIS268 3.0 14.2 1.0
CE1 C:HIS268 3.0 13.4 1.0
OD2 C:ASP191 3.1 15.6 0.5
CE1 C:HIS189 3.1 14.3 1.0
OD1 C:ASP191 3.1 16.4 0.5
CD2 C:HIS189 3.2 13.8 1.0
O2 C:OGA402 3.9 20.2 0.5
N1 C:OGA402 4.0 22.2 0.5
O2 C:OGA402 4.0 20.4 0.5
NE C:ARG403 4.0 20.4 0.5
ND1 C:HIS268 4.1 13.6 1.0
CG C:HIS268 4.2 13.1 1.0
ND1 C:HIS189 4.2 13.4 1.0
O C:HOH664 4.2 28.9 1.0
NH1 C:ARG403 4.2 21.7 0.5
CG C:HIS189 4.3 13.6 1.0
CD C:ARG403 4.3 12.5 0.5
CB C:ASP191 4.3 14.6 0.5
N1 C:OGA402 4.3 23.2 0.5
CB C:ASP191 4.5 15.4 0.5
CZ C:ARG403 4.5 20.7 0.5
CE1 C:PHE283 4.7 15.6 1.0
C4 C:OGA402 4.7 22.7 0.5
CZ C:PHE283 4.7 16.1 1.0
NH2 C:ARG403 5.0 14.0 0.5
CD C:ARG403 5.0 18.9 0.5
C4 C:OGA402 5.0 23.7 0.5

Iron binding site 4 out of 4 in 5lun

Go back to Iron Binding Sites List in 5lun
Iron binding site 4 out of 4 in the Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ethylene Forming Enzyme From Pseudomonas Syringae Pv. Phaseolicola - P1 Ultra-High Resolution Crystal Form in Complex with Iron, N- Oxalylglycine and Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:20.1
occ:1.00
 O2 D:OGA402 1.9 23.0 0.5
OD2 D:ASP191 2.0 16.2 0.5
NE2 D:HIS268 2.0 17.2 1.0
NE2 D:HIS189 2.1 19.0 1.0
O2' D:OGA402 2.1 25.4 0.5
O2 D:OGA402 2.1 27.9 0.5
O D:HOH519 2.2 22.6 1.0
OD1 D:ASP191 2.3 17.5 0.5
O2' D:OGA402 2.3 28.3 0.5
C1 D:OGA402 2.6 25.0 0.5
C2 D:OGA402 2.6 25.3 0.5
C1 D:OGA402 2.9 26.9 0.5
OD2 D:ASP191 2.9 17.5 0.5
CG D:ASP191 2.9 17.4 0.5
C2 D:OGA402 2.9 27.4 0.5
CG D:ASP191 3.0 16.6 0.5
CD2 D:HIS268 3.0 16.3 1.0
CE1 D:HIS268 3.0 16.3 1.0
CE1 D:HIS189 3.0 19.2 1.0
CD2 D:HIS189 3.1 17.9 1.0
OD1 D:ASP191 3.3 19.3 0.5
O1 D:OGA402 3.8 25.7 0.5
N1 D:OGA402 4.0 25.3 0.5
O1 D:OGA402 4.1 25.8 0.5
ND1 D:HIS268 4.1 16.1 1.0
CG D:HIS268 4.2 15.5 1.0
ND1 D:HIS189 4.2 18.7 1.0
NE D:ARG403 4.2 24.3 0.5
CG D:HIS189 4.2 16.6 1.0
O D:HOH623 4.3 28.8 1.0
CB D:ASP191 4.3 17.6 0.5
N1 D:OGA402 4.3 27.0 0.5
NH2 D:ARG403 4.4 25.4 0.5
CD D:ARG403 4.4 20.0 0.5
CB D:ASP191 4.5 17.1 0.5
CE1 D:PHE283 4.7 15.4 1.0
CZ D:PHE283 4.7 16.4 1.0
CZ D:ARG403 4.7 24.9 0.5
C4 D:OGA402 4.8 25.2 0.5
CZ D:PHE250 5.0 17.9 1.0
C4 D:OGA402 5.0 25.3 0.5

Reference:

Z.Zhang, T.J.Smart, H.Choi, F.Hardy, C.T.Lohans, M.I.Abboud, M.S.W.Richardson, R.S.Paton, M.A.Mcdonough, C.J.Schofield. Structural and Stereoelectronic Insights Into Oxygenase-Catalyzed Formation of Ethylene From 2-Oxoglutarate. Proc. Natl. Acad. Sci. V. 114 4667 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28420789
DOI: 10.1073/PNAS.1617760114
Page generated: Tue Aug 6 04:48:21 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