Iron in PDB 2y0f: Structure of Gcpe (Ispg) From Thermus Thermophilus HB27

All present enzymatic activity of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27:
1.17.7.1;

The structure of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27, PDB code: 2y0f was solved by I.Rekittke, T.Nonaka, J.Wiesner, U.Demmer, E.Warkentin, H.Jomaa, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.500, 130.970, 101.260, 90.00, 102.10, 90.00
R / Rfree (%)	19.9 / 26.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 (pdb code 2y0f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27, PDB code: 2y0f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:77.3 occ:1.00 FE1 A:SF4501 0.0 77.3 1.0 SG A:CYS343 2.2 82.0 1.0 S3 A:SF4501 2.3 72.7 1.0 S2 A:SF4501 2.3 82.3 1.0 S4 A:SF4501 2.3 80.2 1.0 FE4 A:SF4501 2.7 75.6 1.0 FE3 A:SF4501 2.7 81.3 1.0 FE2 A:SF4501 2.8 75.8 1.0 CB A:CYS343 3.4 79.7 1.0 N A:CYS343 3.7 78.5 1.0 S1 A:SF4501 3.9 79.0 1.0 CB A:ASN346 4.0 77.1 1.0 CA A:CYS343 4.0 79.9 1.0 C A:GLY342 4.2 84.0 1.0 CB A:ARG302 4.5 92.3 1.0 OE1 A:GLU350 4.5 74.1 1.0 CD A:ARG302 4.6 89.5 1.0 N A:GLY347 4.6 76.5 1.0 SG A:CYS300 4.6 83.9 1.0 C A:CYS343 4.7 83.2 1.0 O A:CYS343 4.7 90.6 1.0 CA A:GLY342 4.7 86.9 1.0 O A:GLY342 4.7 85.2 1.0 SG A:CYS297 4.7 74.4 1.0 CG A:ARG302 4.8 91.8 1.0 CA A:ASN346 4.8 72.2 1.0 N A:GLY342 4.9 86.1 1.0 C A:ASN346 4.9 74.2 1.0 OE2 A:GLU350 4.9 79.9 1.0 CG A:ASN346 4.9 76.0 1.0 OD1 A:ASN346 5.0 82.8 1.0 N A:ASN346 5.0 70.9 1.0

Iron binding site 2 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:75.8 occ:1.00 FE2 A:SF4501 0.0 75.8 1.0 OE1 A:GLU350 2.1 74.1 1.0 S3 A:SF4501 2.3 72.7 1.0 S4 A:SF4501 2.3 80.2 1.0 S1 A:SF4501 2.3 79.0 1.0 FE3 A:SF4501 2.7 81.3 1.0 FE1 A:SF4501 2.8 77.3 1.0 FE4 A:SF4501 2.8 75.6 1.0 CD A:GLU350 2.9 73.3 1.0 OE2 A:GLU350 3.1 79.9 1.0 SD B:MET158 3.3 79.3 1.0 CG B:MET158 3.8 80.7 1.0 S2 A:SF4501 3.9 82.3 1.0 CE B:MET158 4.1 77.9 1.0 CB B:MET158 4.3 76.5 1.0 CG A:GLU350 4.4 67.9 1.0 CB A:ASN346 4.4 77.1 1.0 CB A:CYS297 4.4 74.3 1.0 SG A:CYS297 4.5 74.4 1.0 SG A:CYS300 4.7 83.9 1.0 SG A:CYS343 4.7 82.0 1.0 CB A:GLU350 4.8 65.2 1.0 CB B:ALA170 4.9 60.4 1.0

Iron binding site 3 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:81.3 occ:1.00 FE3 A:SF4501 0.0 81.3 1.0 SG A:CYS300 2.3 83.9 1.0 S4 A:SF4501 2.3 80.2 1.0 S1 A:SF4501 2.3 79.0 1.0 S2 A:SF4501 2.3 82.3 1.0 FE1 A:SF4501 2.7 77.3 1.0 FE2 A:SF4501 2.7 75.8 1.0 FE4 A:SF4501 2.8 75.6 1.0 CB A:CYS300 3.2 85.7 1.0 N A:CYS300 3.5 86.6 1.0 S3 A:SF4501 3.9 72.7 1.0 CA A:CYS300 3.9 89.2 1.0 C A:GLY299 4.1 83.6 1.0 CG B:MET158 4.1 80.7 1.0 CA A:GLY299 4.3 82.7 1.0 CB A:ARG302 4.5 92.3 1.0 SG A:CYS343 4.6 82.0 1.0 CG A:ARG302 4.6 91.8 1.0 C A:CYS300 4.6 97.6 1.0 SD B:MET158 4.6 79.3 1.0 CB B:MET158 4.7 76.5 1.0 SG A:CYS297 4.8 74.4 1.0 N A:GLY299 4.8 78.8 1.0 OE1 A:GLU350 4.8 74.1 1.0 O A:GLY299 4.8 90.2 1.0 N A:ARG302 5.0 0.7 1.0 N A:GLY301 5.0 96.2 1.0

Iron binding site 4 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:75.6 occ:1.00 FE4 A:SF4501 0.0 75.6 1.0 SG A:CYS297 2.2 74.4 1.0 S2 A:SF4501 2.3 82.3 1.0 S3 A:SF4501 2.3 72.7 1.0 S1 A:SF4501 2.3 79.0 1.0 FE1 A:SF4501 2.7 77.3 1.0 FE2 A:SF4501 2.8 75.8 1.0 FE3 A:SF4501 2.8 81.3 1.0 CB A:CYS297 3.1 74.3 1.0 N A:GLY342 3.7 86.1 1.0 CA A:GLY342 3.8 86.9 1.0 S4 A:SF4501 3.9 80.2 1.0 N A:GLY299 4.0 78.8 1.0 CA A:GLY299 4.0 82.7 1.0 C A:GLY342 4.3 84.0 1.0 OE1 A:GLU350 4.3 74.1 1.0 N A:CYS343 4.4 78.5 1.0 CA A:CYS297 4.5 71.9 1.0 C A:GLY299 4.7 83.6 1.0 SG A:CYS343 4.7 82.0 1.0 N A:CYS300 4.8 86.6 1.0 C A:CYS297 4.8 78.7 1.0 CD A:PRO298 4.8 71.7 1.0 N A:PRO298 4.9 76.2 1.0 C A:MET341 5.0 80.7 1.0 O A:GLY342 5.0 85.2 1.0

Iron binding site 5 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:69.2 occ:1.00 FE1 B:SF4501 0.0 69.2 1.0 S2 B:SF4501 2.3 62.4 1.0 SG B:CYS343 2.3 80.8 1.0 S3 B:SF4501 2.3 68.8 1.0 S4 B:SF4501 2.3 66.0 1.0 FE3 B:SF4501 2.6 67.0 1.0 FE2 B:SF4501 2.7 66.0 1.0 FE4 B:SF4501 2.7 68.6 1.0 CB B:CYS343 3.4 72.7 1.0 N B:CYS343 3.8 69.4 1.0 S1 B:SF4501 3.8 64.8 1.0 CA B:CYS343 4.1 72.7 1.0 CB B:ARG302 4.2 76.2 1.0 C B:GLY342 4.3 72.9 1.0 CB B:ASN346 4.3 66.2 1.0 CG B:ARG302 4.4 75.9 1.0 OE2 B:GLU350 4.4 73.9 1.0 OE1 B:GLU350 4.5 65.3 1.0 SG B:CYS300 4.6 67.1 1.0 O B:CYS343 4.6 78.1 1.0 C B:CYS343 4.6 73.8 1.0 O B:GLY342 4.7 75.4 1.0 SG B:CYS297 4.7 64.7 1.0 N B:GLY347 4.8 70.6 1.0 OD1 B:ASN346 4.8 66.9 1.0 CA B:GLY342 4.9 70.8 1.0 CD B:GLU350 4.9 70.3 1.0 N B:GLY342 4.9 74.0 1.0

Iron binding site 6 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:66.0 occ:1.00 FE2 B:SF4501 0.0 66.0 1.0 S3 B:SF4501 2.3 68.8 1.0 S1 B:SF4501 2.3 64.8 1.0 S4 B:SF4501 2.3 66.0 1.0 SG B:CYS300 2.4 67.1 1.0 FE1 B:SF4501 2.7 69.2 1.0 FE4 B:SF4501 2.7 68.6 1.0 FE3 B:SF4501 2.7 67.0 1.0 CB B:CYS300 3.1 69.6 1.0 N B:CYS300 3.4 73.6 1.0 CA B:CYS300 3.8 77.6 1.0 S2 B:SF4501 3.9 62.4 1.0 C B:GLY299 4.0 65.2 1.0 CG A:MET158 4.1 66.2 1.0 CB B:ARG302 4.1 76.2 1.0 CA B:GLY299 4.3 65.0 1.0 SD A:MET158 4.5 65.8 1.0 CB A:MET158 4.6 62.4 1.0 C B:CYS300 4.6 86.5 1.0 SG B:CYS343 4.7 80.8 1.0 O B:GLY299 4.7 69.9 1.0 SG B:CYS297 4.7 64.7 1.0 OE1 B:GLU350 4.8 65.3 1.0 N B:GLY299 4.8 62.7 1.0 CE A:MET158 4.9 59.8 1.0 N B:ARG302 5.0 81.1 1.0 CG B:ARG302 5.0 75.9 1.0

Iron binding site 7 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:67.0 occ:1.00 FE3 B:SF4501 0.0 67.0 1.0 SG B:CYS297 2.2 64.7 1.0 S2 B:SF4501 2.2 62.4 1.0 S1 B:SF4501 2.3 64.8 1.0 S4 B:SF4501 2.3 66.0 1.0 FE1 B:SF4501 2.6 69.2 1.0 FE2 B:SF4501 2.7 66.0 1.0 FE4 B:SF4501 2.8 68.6 1.0 CB B:CYS297 3.2 67.8 1.0 S3 B:SF4501 3.9 68.8 1.0 N B:GLY342 3.9 74.0 1.0 N B:GLY299 4.0 62.7 1.0 CA B:GLY299 4.0 65.0 1.0 CA B:GLY342 4.2 70.8 1.0 OE1 B:GLU350 4.2 65.3 1.0 C B:GLY342 4.5 72.9 1.0 N B:CYS343 4.5 69.4 1.0 CA B:CYS297 4.6 58.2 1.0 C B:GLY299 4.6 65.2 1.0 N B:CYS300 4.7 73.6 1.0 SG B:CYS343 4.8 80.8 1.0 C B:CYS297 4.8 61.2 1.0 N B:PRO298 4.8 57.4 1.0 CD B:PRO298 5.0 57.7 1.0

Iron binding site 8 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:68.6 occ:1.00 FE4 B:SF4501 0.0 68.6 1.0 OE1 B:GLU350 2.1 65.3 1.0 S1 B:SF4501 2.3 64.8 1.0 S3 B:SF4501 2.3 68.8 1.0 S2 B:SF4501 2.3 62.4 1.0 OE2 B:GLU350 2.7 73.9 1.0 FE1 B:SF4501 2.7 69.2 1.0 CD B:GLU350 2.7 70.3 1.0 FE2 B:SF4501 2.7 66.0 1.0 FE3 B:SF4501 2.8 67.0 1.0 SD A:MET158 3.2 65.8 1.0 CG A:MET158 3.9 66.2 1.0 S4 B:SF4501 4.0 66.0 1.0 CE A:MET158 4.0 59.8 1.0 CG B:GLU350 4.2 57.1 1.0 CB A:MET158 4.4 62.4 1.0 CB B:ASN346 4.5 66.2 1.0 SG B:CYS297 4.6 64.7 1.0 CB B:CYS297 4.6 67.8 1.0 SG B:CYS300 4.7 67.1 1.0 SG B:CYS343 4.7 80.8 1.0 CB B:GLU350 4.8 57.2 1.0 CB A:ALA170 5.0 58.3 1.0 OD1 B:ASN346 5.0 66.9 1.0

Iron binding site 9 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:65.5 occ:1.00 FE1 C:SF4501 0.0 65.5 1.0 SG C:CYS343 2.2 74.5 1.0 S2 C:SF4501 2.2 68.0 1.0 S3 C:SF4501 2.3 70.7 1.0 S4 C:SF4501 2.3 77.5 1.0 FE2 C:SF4501 2.7 69.9 1.0 FE3 C:SF4501 2.7 67.0 1.0 FE4 C:SF4501 2.7 66.4 1.0 CB C:CYS343 3.3 78.8 1.0 N C:CYS343 3.7 72.6 1.0 S1 C:SF4501 3.9 69.8 1.0 CB C:ASN346 4.0 69.7 1.0 CA C:CYS343 4.0 78.6 1.0 OE1 C:GLU350 4.2 60.1 1.0 C C:GLY342 4.3 73.7 1.0 OE2 C:GLU350 4.4 71.8 1.0 O C:CYS343 4.5 64.2 1.0 CB C:ARG302 4.5 75.4 1.0 N C:GLY347 4.5 58.0 1.0 SG C:CYS300 4.6 69.7 1.0 C C:CYS343 4.6 71.9 1.0 SG C:CYS297 4.7 71.4 1.0 CD C:GLU350 4.7 64.3 1.0 OD1 C:ASN346 4.7 66.7 1.0 N C:GLY342 4.8 72.0 1.0 O C:GLY342 4.8 70.7 1.0 CA C:GLY342 4.8 77.7 1.0 CA C:ASN346 4.8 67.7 1.0 CG C:ASN346 4.8 73.4 1.0 C C:ASN346 4.8 68.6 1.0 CD C:ARG302 4.9 84.1 1.0 N C:ASN346 5.0 72.2 1.0

Iron binding site 10 out of 16 in the Structure of Gcpe (Ispg) From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Gcpe (Ispg) From Thermus Thermophilus HB27 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:69.9 occ:1.00 FE2 C:SF4501 0.0 69.9 1.0 S3 C:SF4501 2.3 70.7 1.0 S4 C:SF4501 2.3 77.5 1.0 S1 C:SF4501 2.3 69.8 1.0 SG C:CYS300 2.4 69.7 1.0 FE4 C:SF4501 2.6 66.4 1.0 FE1 C:SF4501 2.7 65.5 1.0 FE3 C:SF4501 2.7 67.0 1.0 CB C:CYS300 3.4 73.3 1.0 N C:CYS300 3.7 83.0 1.0 S2 C:SF4501 3.9 68.0 1.0 CA C:CYS300 4.1 82.2 1.0 C C:GLY299 4.2 74.3 1.0 SD D:MET158 4.3 70.7 1.0 OE1 C:GLU350 4.5 60.1 1.0 CA C:GLY299 4.5 69.4 1.0 CG D:MET158 4.6 73.2 1.0 SG C:CYS343 4.6 74.5 1.0 C C:CYS300 4.6 86.8 1.0 CB C:ARG302 4.7 75.4 1.0 SG C:CYS297 4.7 71.4 1.0 CE D:MET158 4.8 66.3 1.0 O C:GLY299 4.8 83.5 1.0 OE2 C:GLU350 4.9 71.8 1.0 N C:ARG302 4.9 77.1 1.0 CG C:ARG302 4.9 77.5 1.0 CB D:MET158 4.9 70.6 1.0

I.Rekittke, T.Nonaka, J.Wiesner, U.Demmer, E.Warkentin, H.Jomaa, U.Ermler. Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Synthase (Gcpe) From Thermus Thermophilus. Febs Lett. V. 585 447 2011.
ISSN: ISSN 0014-5793
PubMed: 21167158
DOI: 10.1016/J.FEBSLET.2010.12.012