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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

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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

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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

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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

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