Iron in PDB 5dqr: The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)

All present enzymatic activity of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar):
1.17.7.2;

The structure of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar), PDB code: 5dqr was solved by X.Wang, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.61 / 2.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	89.105, 89.105, 273.312, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) (pdb code 5dqr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar), PDB code: 5dqr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.1 occ:1.00 FE1 A:SF4501 0.0 19.1 1.0 S4 A:SF4501 2.3 15.8 1.0 SG A:CYS80 2.3 16.9 1.0 S2 A:SF4501 2.3 17.0 1.0 S3 A:SF4501 2.3 22.9 1.0 CB A:CYS80 3.0 17.8 1.0 FE3 A:SF4501 3.2 20.3 1.0 FE2 A:SF4501 3.2 24.8 1.0 FE4 A:SF4501 3.2 28.2 1.0 CA A:CYS80 3.8 17.7 1.0 S1 A:SF4501 4.0 13.6 1.0 CB A:ALA58 4.1 18.6 1.0 CG2 A:VAL76 4.5 21.6 1.0 CD2 A:PHE82 4.6 18.4 1.0 C A:CYS80 4.6 21.0 1.0 N A:ALA81 4.6 18.1 1.0

Iron binding site 2 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:24.8 occ:1.00 FE2 A:SF4501 0.0 24.8 1.0 SG A:CYS65 2.3 15.3 1.0 S4 A:SF4501 2.3 15.8 1.0 S1 A:SF4501 2.3 13.6 1.0 S3 A:SF4501 2.3 22.9 1.0 FE3 A:SF4501 3.2 20.3 1.0 FE1 A:SF4501 3.2 19.1 1.0 FE4 A:SF4501 3.2 28.2 1.0 CB A:CYS65 3.4 19.3 1.0 N A:CYS65 3.5 17.1 1.0 CA A:CYS65 3.9 15.7 1.0 S2 A:SF4501 4.0 17.0 1.0 CB A:LEU67 4.1 23.7 1.0 N A:GLY66 4.1 21.8 1.0 N A:LEU67 4.2 17.9 1.0 C A:CYS65 4.4 20.8 1.0 C A:GLN64 4.6 17.8 1.0 OG A:SER63 4.6 13.2 1.0 N A:GLN64 4.7 19.4 1.0 CA A:LEU67 4.8 20.8 1.0 CA A:GLN64 4.8 19.3 1.0

Iron binding site 3 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.3 occ:1.00 FE3 A:SF4501 0.0 20.3 1.0 SG A:CYS68 2.3 26.4 1.0 S2 A:SF4501 2.3 17.0 1.0 S4 A:SF4501 2.3 15.8 1.0 S1 A:SF4501 2.3 13.6 1.0 FE1 A:SF4501 3.2 19.1 1.0 FE4 A:SF4501 3.2 28.2 1.0 FE2 A:SF4501 3.2 24.8 1.0 CB A:CYS68 3.3 28.1 1.0 N A:CYS68 3.7 22.7 1.0 CG2 A:VAL76 3.9 21.6 1.0 S3 A:SF4501 4.0 22.9 1.0 CA A:CYS68 4.1 25.7 1.0 CB A:LEU67 4.2 23.7 1.0 CD1 A:TYR56 4.4 26.0 1.0 C A:LEU67 4.6 23.7 1.0 CD A:PRO57 4.6 23.6 1.0 CA A:LEU67 4.8 20.8 1.0 N A:LEU67 4.8 17.9 1.0 CD2 A:LEU67 4.8 21.2 1.0 CG A:LEU67 4.9 23.1 1.0 CG A:PRO57 4.9 18.7 1.0 CB A:VAL76 4.9 22.1 1.0

Iron binding site 4 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.2 occ:1.00 FE4 A:SF4501 0.0 28.2 1.0 SG A:CYS62 2.3 22.4 1.0 S2 A:SF4501 2.3 17.0 1.0 S3 A:SF4501 2.3 22.9 1.0 S1 A:SF4501 2.3 13.6 1.0 CB A:CYS62 3.2 19.5 1.0 FE3 A:SF4501 3.2 20.3 1.0 FE1 A:SF4501 3.2 19.1 1.0 FE2 A:SF4501 3.2 24.8 1.0 CA A:CYS62 3.7 19.0 1.0 N A:GLN64 3.9 19.4 1.0 S4 A:SF4501 4.0 15.8 1.0 CB A:TYR56 4.1 30.1 1.0 N A:SER63 4.1 17.3 1.0 C A:CYS62 4.2 17.6 1.0 CD1 A:TYR56 4.2 26.0 1.0 CA A:GLN64 4.2 19.3 1.0 CG A:TYR56 4.3 29.5 1.0 CB A:ALA58 4.6 18.6 1.0 N A:CYS65 4.7 17.1 1.0 C A:SER63 4.9 16.4 1.0

Iron binding site 5 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:16.8 occ:1.00 FE1 A:SF4502 0.0 16.8 1.0 SG A:CYS302 2.3 10.3 1.0 S3 A:SF4502 2.3 5.9 1.0 S2 A:SF4502 2.3 8.4 1.0 S4 A:SF4502 2.3 11.3 1.0 CB A:CYS302 2.7 13.3 1.0 FE4 A:SF4502 3.2 18.7 1.0 FE2 A:SF4502 3.2 12.8 1.0 FE3 A:SF4502 3.2 19.0 1.0 S1 A:SF4502 3.9 17.4 1.0 CA A:CYS302 4.1 15.1 1.0 CE A:MET87 4.3 18.2 1.0 O A:CYS235 4.7 12.0 1.0 CA A:CYS299 4.7 15.2 1.0 CB A:CYS211 4.8 14.9 1.0 O A:SER298 4.9 15.1 1.0 C A:CYS302 4.9 12.3 1.0 N A:CYS302 5.0 15.2 1.0

Iron binding site 6 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:12.8 occ:1.00 FE2 A:SF4502 0.0 12.8 1.0 SG A:CYS235 2.2 11.7 1.0 S4 A:SF4502 2.3 11.3 1.0 S1 A:SF4502 2.3 17.4 1.0 S3 A:SF4502 2.3 5.9 1.0 CB A:CYS235 3.1 10.6 1.0 FE3 A:SF4502 3.2 19.0 1.0 FE1 A:SF4502 3.2 16.8 1.0 FE4 A:SF4502 3.2 18.7 1.0 S2 A:SF4502 3.9 8.4 1.0 C A:CYS235 4.0 10.2 1.0 CG2 A:VAL209 4.0 13.7 1.0 CB A:VAL209 4.1 16.4 1.0 CA A:CYS235 4.1 10.7 1.0 N A:VAL236 4.2 10.7 1.0 O A:CYS235 4.2 12.0 1.0 CB A:ASN238 4.3 12.7 1.0 CG1 A:VAL209 4.4 21.1 1.0 ND2 A:ASN238 4.6 11.4 1.0 CA A:VAL236 4.7 12.7 1.0

Iron binding site 7 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.0 occ:1.00 FE3 A:SF4502 0.0 19.0 1.0 SG A:CYS211 2.3 22.1 1.0 S1 A:SF4502 2.3 17.4 1.0 S4 A:SF4502 2.3 11.3 1.0 S2 A:SF4502 2.3 8.4 1.0 CB A:CYS211 3.0 14.9 1.0 FE2 A:SF4502 3.2 12.8 1.0 FE1 A:SF4502 3.2 16.8 1.0 FE4 A:SF4502 3.2 18.7 1.0 CG2 A:VAL209 3.7 13.7 1.0 N A:CYS211 3.9 17.0 1.0 S3 A:SF4502 4.0 5.9 1.0 CB A:SER63 4.1 14.3 1.0 CA A:CYS211 4.1 19.9 1.0 OG A:SER63 4.2 13.2 1.0 O A:HOH617 4.5 14.4 1.0 CB A:VAL209 4.7 16.4 1.0 C A:CYS211 5.0 18.1 1.0

Iron binding site 8 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.7 occ:1.00 FE4 A:SF4502 0.0 18.7 1.0 SG A:CYS299 2.3 12.4 1.0 S3 A:SF4502 2.3 5.9 1.0 S2 A:SF4502 2.3 8.4 1.0 S1 A:SF4502 2.3 17.4 1.0 CB A:CYS299 3.1 14.1 1.0 FE1 A:SF4502 3.2 16.8 1.0 FE2 A:SF4502 3.2 12.8 1.0 FE3 A:SF4502 3.2 19.0 1.0 CA A:CYS299 3.4 15.2 1.0 N A:CYS299 3.8 14.6 1.0 S4 A:SF4502 4.0 11.3 1.0 CB A:ASN238 4.0 12.7 1.0 OG A:SER298 4.1 14.2 1.0 C A:SER298 4.3 17.3 1.0 O A:SER298 4.5 15.1 1.0 N A:ASN238 4.6 15.9 1.0 C A:CYS299 4.8 17.3 1.0 CB A:CYS302 4.8 13.3 1.0 CA A:ASN238 4.8 15.5 1.0 CB A:SER63 4.8 14.3 1.0 CB A:SER298 4.9 16.1 1.0

Iron binding site 9 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:14.3 occ:1.00 FE1 B:SF4501 0.0 14.3 1.0 SG B:CYS80 2.2 17.3 1.0 S2 B:SF4501 2.3 5.8 1.0 S4 B:SF4501 2.3 6.0 1.0 S3 B:SF4501 2.3 4.8 1.0 CB B:CYS80 3.1 8.9 1.0 FE4 B:SF4501 3.2 14.2 1.0 FE3 B:SF4501 3.2 20.7 1.0 FE2 B:SF4501 3.2 12.2 1.0 CB B:ALA58 3.8 8.8 1.0 S1 B:SF4501 3.9 12.3 1.0 CA B:CYS80 4.0 7.7 1.0 CD2 B:PHE82 4.4 6.7 1.0 CG2 B:VAL76 4.5 12.2 1.0 C B:CYS80 4.7 8.7 1.0 N B:ALA81 4.7 6.9 1.0 N B:ALA58 4.8 13.7 1.0 CA B:ALA58 4.9 10.9 1.0

Iron binding site 10 out of 48 in the The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Crystal Structure of Arabidopsis 7-Hydroxymethyl Chlorophyll A Reductase (Hcar) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:12.2 occ:1.00 FE2 B:SF4501 0.0 12.2 1.0 SG B:CYS65 2.2 4.9 1.0 S3 B:SF4501 2.3 4.8 1.0 S4 B:SF4501 2.3 6.0 1.0 S1 B:SF4501 2.3 12.3 1.0 FE4 B:SF4501 3.2 14.2 1.0 FE3 B:SF4501 3.2 20.7 1.0 FE1 B:SF4501 3.2 14.3 1.0 CB B:CYS65 3.3 7.3 1.0 N B:CYS65 3.4 7.6 1.0 CA B:CYS65 3.8 8.7 1.0 S2 B:SF4501 3.9 5.8 1.0 O B:HOH678 4.0 16.6 1.0 N B:GLY66 4.0 10.6 1.0 CB B:LEU67 4.1 9.9 1.0 N B:LEU67 4.2 11.4 1.0 C B:CYS65 4.3 9.3 1.0 C B:GLN64 4.6 8.5 1.0 N B:GLN64 4.7 7.6 1.0 OG B:SER63 4.8 5.1 1.0 CA B:LEU67 4.8 10.2 1.0 CA B:GLN64 4.8 9.0 1.0

X.Wang, L.Liu. Crystal Structure and Catalytic Mechanism of 7-Hydroxymethyl Chlorophyll A Reductase J.Biol.Chem. V. 291 13349 2016.
ISSN: ESSN 1083-351X
PubMed: 27072131
DOI: 10.1074/JBC.M116.720342