Iron in PDB 6npc: X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate

Protein crystallography data

The structure of X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate, PDB code: 6npc was solved by L.J.Rajakovich, A.J.Mitchell, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.901, 86.901, 220.613, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate (pdb code 6npc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate, PDB code: 6npc:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6npc

Go back to Iron Binding Sites List in 6npc
Iron binding site 1 out of 2 in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:8.0
occ:1.00
OD1 A:ASP200 2.0 5.3 1.0
O1 A:AKG402 2.0 12.3 1.0
O5 A:AKG402 2.2 13.2 1.0
NE2 A:HIS341 2.3 7.9 1.0
NE2 A:HIS198 2.3 5.7 1.0
C1 A:AKG402 2.8 12.6 1.0
C2 A:AKG402 2.9 12.7 1.0
CE1 A:HIS341 3.0 7.9 1.0
CG A:ASP200 3.0 5.3 1.0
CD2 A:HIS198 3.2 5.7 1.0
CE1 A:HIS198 3.3 5.8 1.0
CD2 A:HIS341 3.3 7.8 1.0
OD2 A:ASP200 3.4 5.2 1.0
OE1 A:GLN211 4.0 8.3 1.0
O2 A:AKG402 4.0 12.6 1.0
ND1 A:HIS341 4.1 7.8 1.0
C1 A:KVV403 4.2 6.2 1.0
NE2 A:GLN211 4.2 7.5 1.0
CG A:HIS341 4.3 7.7 1.0
CB A:ASP200 4.4 5.3 1.0
ND1 A:HIS198 4.4 5.7 1.0
CG A:HIS198 4.4 5.7 1.0
C3 A:AKG402 4.4 12.7 1.0
O11 A:KVV403 4.4 6.1 1.0
CD A:GLN211 4.5 7.7 1.0
C5 A:KVV403 4.6 6.6 1.0
NH2 A:ARG288 4.8 6.8 1.0
CA A:ASP200 4.8 5.2 1.0
P4 A:KVV403 4.9 6.1 1.0
C4 A:AKG402 5.0 12.5 1.0

Iron binding site 2 out of 2 in 6npc

Go back to Iron Binding Sites List in 6npc
Iron binding site 2 out of 2 in the X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Tmpa, 2-Trimethylaminoethylphosphonate Hydroxylase, with Fe, 2OG, and 2-Trimethylaminoethylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:15.2
occ:0.65
O B:HOH660 2.0 17.0 0.7
O B:HOH616 2.1 13.7 0.7
OD1 B:ASP200 2.2 11.2 1.0
O B:HOH694 2.3 16.6 0.7
NE2 B:HIS198 2.4 12.3 1.0
NE2 B:HIS341 2.5 14.1 1.0
CE1 B:HIS341 3.0 14.1 1.0
CG B:ASP200 3.1 11.1 1.0
OD2 B:ASP200 3.3 11.7 1.0
CD2 B:HIS198 3.3 12.1 1.0
CE1 B:HIS198 3.4 12.3 1.0
CD2 B:HIS341 3.6 14.0 1.0
OE1 B:GLN211 4.2 14.6 1.0
ND1 B:HIS341 4.2 13.9 1.0
O3 B:SO4402 4.3 19.6 1.0
CG B:HIS198 4.5 11.9 1.0
ND1 B:HIS198 4.5 12.1 1.0
O4 B:SO4402 4.5 17.8 1.0
CB B:ASP200 4.5 10.7 1.0
NE2 B:GLN211 4.5 13.9 1.0
CG B:HIS341 4.5 13.7 1.0
CD B:GLN211 4.8 13.2 1.0
NH2 B:ARG288 4.9 22.7 1.0
S B:SO4402 5.0 17.8 1.0

Reference:

L.J.Rajakovich, M.E.Pandelia, A.J.Mitchell, W.C.Chang, B.Zhang, A.K.Boal, C.Krebs, J.M.Bollinger Jr.. A New Microbial Pathway For Organophosphonate Degradation Catalyzed By Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry V. 58 1627 2019.
ISSN: ISSN 1520-4995
PubMed: 30789718
DOI: 10.1021/ACS.BIOCHEM.9B00044
Page generated: Sun Dec 13 16:46:26 2020

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