Iron in PDB 1r27: Crystal Structure of Nargh Complex

All present enzymatic activity of Crystal Structure of Nargh Complex:
1.7.99.4;

The structure of Crystal Structure of Nargh Complex, PDB code: 1r27 was solved by M.Jormakka, D.Richardson, B.Byrne, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.86 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	127.401, 298.300, 296.853, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23

The structure of Crystal Structure of Nargh Complex also contains other interesting chemical elements:

Molybdenum

(Mo)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Nargh Complex (pdb code 1r27). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 38 binding sites of Iron where determined in the Crystal Structure of Nargh Complex, PDB code: 1r27:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe5807 b:27.0 occ:1.00 FE1 A:SF45807 0.0 27.0 1.0 SG A:CYS53 2.2 24.7 1.0 S4 A:SF45807 2.3 22.8 1.0 S3 A:SF45807 2.3 24.0 1.0 S2 A:SF45807 2.3 21.6 1.0 FE3 A:SF45807 2.7 22.4 1.0 FE2 A:SF45807 2.7 24.8 1.0 FE4 A:SF45807 2.7 25.4 1.0 CB A:CYS53 3.3 25.2 1.0 S1 A:SF45807 3.9 23.2 1.0 CA A:GLY55 4.0 23.5 1.0 CG1 A:VAL51 4.1 24.5 1.0 N A:GLY55 4.2 24.4 1.0 O A:HOH5924 4.3 28.5 1.0 N A:SER56 4.5 21.8 1.0 C A:GLY55 4.6 22.3 1.0 SG A:CYS57 4.7 18.3 1.0 CA A:CYS53 4.7 25.3 1.0 SG A:CYS92 4.7 18.3 1.0 ND1 A:HIS49 4.7 20.7 1.0 O A:HOH6307 4.7 55.5 1.0 O A:HOH5974 4.8 35.0 1.0 CB A:HIS49 4.8 19.8 1.0

Iron binding site 2 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe5807 b:24.8 occ:1.00 FE2 A:SF45807 0.0 24.8 1.0 S3 A:SF45807 2.2 24.0 1.0 ND1 A:HIS49 2.2 20.7 1.0 S1 A:SF45807 2.3 23.2 1.0 S4 A:SF45807 2.3 22.8 1.0 FE4 A:SF45807 2.6 25.4 1.0 FE1 A:SF45807 2.7 27.0 1.0 FE3 A:SF45807 2.7 22.4 1.0 CE1 A:HIS49 3.2 20.6 1.0 CG A:HIS49 3.2 22.0 1.0 CB A:HIS49 3.5 19.8 1.0 CA A:GLY95 3.7 17.3 1.0 S2 A:SF45807 3.8 21.6 1.0 NE1 A:TRP59 4.1 18.6 1.0 OH A:TYR1101 4.3 25.7 1.0 NE2 A:HIS49 4.3 21.7 1.0 CD2 A:HIS49 4.4 21.1 1.0 N A:GLY95 4.4 17.2 1.0 SG A:CYS92 4.7 18.3 1.0 SG A:CYS53 4.7 24.7 1.0 SG A:CYS57 4.7 18.3 1.0 CB A:CYS57 4.8 18.4 1.0 CG1 A:VAL51 4.8 24.5 1.0 CA A:HIS49 4.9 21.6 1.0 CE2 A:TRP59 4.9 18.5 1.0 CD1 A:TRP59 4.9 18.2 1.0 C A:GLY95 4.9 18.0 1.0

Iron binding site 3 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe5807 b:22.4 occ:1.00 FE3 A:SF45807 0.0 22.4 1.0 S2 A:SF45807 2.3 21.6 1.0 S4 A:SF45807 2.3 22.8 1.0 SG A:CYS57 2.3 18.3 1.0 S1 A:SF45807 2.3 23.2 1.0 FE1 A:SF45807 2.7 27.0 1.0 FE4 A:SF45807 2.7 25.4 1.0 FE2 A:SF45807 2.7 24.8 1.0 CB A:CYS57 3.2 18.4 1.0 S3 A:SF45807 3.9 24.0 1.0 CA A:GLY55 3.9 23.5 1.0 N A:CYS57 4.0 18.0 1.0 CA A:GLY91 4.2 15.8 1.0 C A:GLY55 4.2 22.3 1.0 CA A:CYS57 4.2 18.9 1.0 C A:GLY91 4.4 18.1 1.0 N A:SER56 4.4 21.8 1.0 N A:GLY91 4.4 18.0 1.0 NE1 A:TRP59 4.5 18.6 1.0 SG A:CYS53 4.6 24.7 1.0 CG A:PRO262 4.6 20.3 1.0 N A:CYS92 4.7 17.4 1.0 SG A:CYS92 4.7 18.3 1.0 ND1 A:HIS49 4.7 20.7 1.0 O A:GLY55 4.7 24.2 1.0 O A:GLY91 4.8 18.4 1.0 CB A:PRO262 4.9 19.9 1.0 N A:GLY55 4.9 24.4 1.0 C A:SER56 5.0 20.0 1.0 CB A:CYS92 5.0 16.1 1.0

Iron binding site 4 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe5807 b:25.4 occ:1.00 FE4 A:SF45807 0.0 25.4 1.0 SG A:CYS92 2.2 18.3 1.0 S3 A:SF45807 2.2 24.0 1.0 S1 A:SF45807 2.3 23.2 1.0 S2 A:SF45807 2.3 21.6 1.0 FE2 A:SF45807 2.6 24.8 1.0 FE3 A:SF45807 2.7 22.4 1.0 FE1 A:SF45807 2.7 27.0 1.0 CB A:CYS92 3.3 16.1 1.0 N A:GLY95 3.8 17.2 1.0 S4 A:SF45807 3.9 22.8 1.0 O A:HOH5974 3.9 35.0 1.0 N A:CYS92 3.9 17.4 1.0 CA A:GLY95 4.0 17.3 1.0 CA A:CYS92 4.1 16.7 1.0 C A:GLY91 4.4 18.1 1.0 C A:CYS92 4.6 18.4 1.0 O A:CYS92 4.6 15.8 1.0 ND1 A:HIS49 4.7 20.7 1.0 SG A:CYS53 4.8 24.7 1.0 SG A:CYS57 4.8 18.3 1.0 O A:GLY91 4.9 18.4 1.0 CA A:GLY91 4.9 15.8 1.0 CB A:ARG94 4.9 20.0 1.0 C A:ARG94 4.9 19.3 1.0

Iron binding site 5 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe5808 b:24.7 occ:1.00 FE1 B:F3S5808 0.0 24.7 1.0 S1 B:F3S5808 2.2 23.3 1.0 SG B:CYS196 2.3 25.6 1.0 S2 B:F3S5808 2.3 17.9 1.0 S3 B:F3S5808 2.3 22.2 1.0 FE3 B:F3S5808 2.7 24.2 1.0 FE4 B:F3S5808 2.8 24.5 1.0 CB B:CYS196 3.2 26.5 1.0 S4 B:F3S5808 3.9 20.6 1.0 CA B:CYS196 4.1 27.8 1.0 CB B:ALA200 4.3 20.6 1.0 OG B:SER198 4.5 34.7 1.0 CE3 B:TRP220 4.5 28.9 1.0 O B:HOH5898 4.7 34.3 1.0 CG1 B:ILE201 4.8 19.8 1.0 SG B:CYS223 4.8 23.6 1.0 CB B:TRP220 4.9 24.0 1.0 SG B:CYS217 4.9 22.4 1.0 C B:CYS196 4.9 29.7 1.0 CD1 B:ILE201 4.9 19.7 1.0

Iron binding site 6 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe5808 b:24.2 occ:1.00 FE3 B:F3S5808 0.0 24.2 1.0 SG B:CYS217 2.2 22.4 1.0 S4 B:F3S5808 2.3 20.6 1.0 S1 B:F3S5808 2.3 23.3 1.0 S3 B:F3S5808 2.3 22.2 1.0 FE1 B:F3S5808 2.7 24.7 1.0 FE4 B:F3S5808 2.8 24.5 1.0 CB B:CYS217 3.3 24.3 1.0 CA B:CYS217 3.7 24.4 1.0 N B:GLY219 3.8 23.2 1.0 N B:ARG218 3.8 23.7 1.0 S2 B:F3S5808 3.9 17.9 1.0 C B:CYS217 4.2 24.1 1.0 CA B:GLY219 4.3 23.4 1.0 N B:TRP220 4.3 22.8 1.0 CB B:SER241 4.7 20.6 1.0 C B:GLY219 4.8 23.8 1.0 C B:ARG218 4.8 24.5 1.0 N B:ARG221 4.8 22.4 1.0 SG B:CYS196 4.8 25.6 1.0 SG B:CYS223 4.8 23.6 1.0 OG B:SER241 4.8 22.3 1.0 CG2 B:ILE212 4.8 19.6 1.0 CA B:ARG218 4.9 24.7 1.0 N B:SER241 4.9 22.2 1.0 CB B:ALA200 4.9 20.6 1.0 N B:CYS217 5.0 25.5 1.0

Iron binding site 7 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe5808 b:24.5 occ:1.00 FE4 B:F3S5808 0.0 24.5 1.0 S4 B:F3S5808 2.2 20.6 1.0 SG B:CYS223 2.3 23.6 1.0 S2 B:F3S5808 2.3 17.9 1.0 S3 B:F3S5808 2.3 22.2 1.0 FE1 B:F3S5808 2.8 24.7 1.0 FE3 B:F3S5808 2.8 24.2 1.0 CB B:CYS223 3.3 22.0 1.0 S1 B:F3S5808 3.9 23.3 1.0 N B:ARG221 3.9 22.4 1.0 N B:CYS223 4.0 21.1 1.0 CA B:ARG221 4.1 22.2 1.0 CA B:CYS223 4.3 21.5 1.0 OG B:SER241 4.3 22.3 1.0 CD1 B:ILE201 4.4 19.7 1.0 C B:ARG221 4.5 21.0 1.0 CB B:SER241 4.5 20.6 1.0 N B:MET222 4.5 21.3 1.0 SG B:CYS196 4.7 25.6 1.0 SG B:CYS217 4.7 22.4 1.0 CB B:CYS196 4.7 26.5 1.0 CG1 B:ILE201 5.0 19.8 1.0

Iron binding site 8 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe5800 b:19.0 occ:1.00 FE1 B:SF45800 0.0 19.0 1.0 S4 B:SF45800 2.3 16.7 1.0 SG B:CYS26 2.3 17.1 1.0 S2 B:SF45800 2.3 18.3 1.0 S3 B:SF45800 2.3 16.9 1.0 FE3 B:SF45800 2.7 20.7 1.0 FE2 B:SF45800 2.7 18.4 1.0 FE4 B:SF45800 2.7 19.1 1.0 CB B:CYS26 3.3 16.3 1.0 S1 B:SF45800 3.9 16.0 1.0 CD1 B:TRP30 4.0 18.8 1.0 CB B:PHE41 4.2 16.9 1.0 CA B:CYS26 4.3 18.4 1.0 NE1 B:TRP30 4.5 17.2 1.0 SG B:CYS247 4.6 16.7 1.0 CD1 B:PHE41 4.7 16.3 1.0 CB B:ASN42 4.7 20.0 1.0 SG B:CYS244 4.7 16.7 1.0 SG B:CYS259 4.8 19.1 1.0 N B:ASN42 4.9 18.1 1.0 CG B:PHE41 5.0 16.8 1.0

Iron binding site 9 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe5800 b:18.4 occ:1.00 FE2 B:SF45800 0.0 18.4 1.0 S3 B:SF45800 2.2 16.9 1.0 SG B:CYS247 2.3 16.7 1.0 S1 B:SF45800 2.3 16.0 1.0 S4 B:SF45800 2.3 16.7 1.0 FE4 B:SF45800 2.6 19.1 1.0 FE3 B:SF45800 2.7 20.7 1.0 FE1 B:SF45800 2.7 19.0 1.0 N B:CYS247 3.4 17.5 1.0 CB B:CYS247 3.5 17.0 1.0 S2 B:SF45800 3.8 18.3 1.0 CA B:CYS247 3.9 19.4 1.0 C B:PHE246 4.0 19.4 1.0 NE1 B:TRP30 4.0 17.2 1.0 CB B:THR257 4.2 18.4 1.0 CA B:PHE246 4.2 18.7 1.0 N B:PHE246 4.4 18.1 1.0 CD1 B:TRP30 4.4 18.8 1.0 SG B:CYS259 4.5 19.1 1.0 N B:VAL258 4.6 16.9 1.0 SG B:CYS244 4.7 16.7 1.0 CG2 B:THR257 4.8 19.4 1.0 SG B:CYS26 4.8 17.1 1.0 OG1 B:THR257 4.9 18.9 1.0 O B:PHE246 4.9 18.3 1.0 N B:CYS259 5.0 18.9 1.0

Iron binding site 10 out of 38 in the Crystal Structure of Nargh Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Nargh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe5800 b:20.7 occ:1.00 FE3 B:SF45800 0.0 20.7 1.0 S2 B:SF45800 2.3 18.3 1.0 SG B:CYS259 2.3 19.1 1.0 S4 B:SF45800 2.3 16.7 1.0 S1 B:SF45800 2.3 16.0 1.0 FE2 B:SF45800 2.7 18.4 1.0 FE1 B:SF45800 2.7 19.0 1.0 FE4 B:SF45800 2.7 19.1 1.0 CB B:CYS259 3.2 18.7 1.0 S3 B:SF45800 3.9 16.9 1.0 N B:CYS259 4.1 18.9 1.0 CA B:CYS259 4.3 18.7 1.0 OG1 B:THR257 4.3 18.9 1.0 CB B:THR257 4.5 18.4 1.0 SG B:CYS247 4.5 16.7 1.0 CD1 B:LEU183 4.5 17.9 1.0 SG B:CYS26 4.7 17.1 1.0 CB B:ASN42 4.7 20.0 1.0 SG B:CYS244 4.7 16.7 1.0 NH1 B:ARG268 4.9 25.6 1.0 OD1 B:ASN42 4.9 23.5 1.0 CB B:CYS26 4.9 16.3 1.0

M.Jormakka, D.Richardson, B.Byrne, S.Iwata. Architecture of Nargh Reveals A Structural Classification of Mo-Bismgd Enzymes Structure V. 12 95 2004.
ISSN: ISSN 0969-2126
PubMed: 14725769
DOI: 10.1016/J.STR.2003.11.020