Iron in PDB 7cnp: Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)

The structure of Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form), PDB code: 7cnp was solved by Y.Murase, Y.Watanabe, S.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.06 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.131, 73.15, 133.603, 90, 101.39, 90
R / Rfree (%)	17.6 / 20.5

The structure of Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Iron atom in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form) (pdb code 7cnp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form), PDB code: 7cnp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


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 Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:10.5 occ:1.00 FE1 A:FES601 0.0 10.5 1.0 S1 A:FES601 2.2 10.2 1.0 S2 A:FES601 2.2 10.5 1.0 O A:HOH720 2.3 11.7 1.0 SG A:CYS510 2.4 10.2 1.0 FE2 A:FES601 2.6 9.1 1.0 CB A:CYS510 3.3 10.5 1.0 NZ A:LYS530 3.6 11.2 1.0 OE1 A:GLU292 3.8 11.7 1.0 CE A:LYS530 3.8 12.1 1.0 O A:HOH1088 4.2 12.8 1.0 SG A:CYS508 4.2 11.2 1.0 OE2 A:GLU292 4.3 10.3 1.0 CD A:GLU292 4.4 9.4 1.0 CA A:CYS510 4.6 11.0 1.0 CD A:LYS530 4.6 9.8 1.0 N A:CYS510 4.7 10.2 1.0 CB A:CYS273 4.7 9.6 1.0 OG A:SER449 4.7 10.3 1.0 SG A:CYS273 4.8 9.8 1.0 CB A:CYS508 4.8 9.1 1.0 O A:HOH1109 4.9 10.7 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


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 Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:9.1 occ:1.00 FE2 A:FES601 0.0 9.1 1.0 S2 A:FES601 2.2 10.5 1.0 S1 A:FES601 2.2 10.2 1.0 SG A:CYS273 2.4 9.8 1.0 SG A:CYS508 2.4 11.2 1.0 FE1 A:FES601 2.6 10.5 1.0 CB A:CYS508 3.1 9.1 1.0 CB A:CYS273 3.2 9.6 1.0 CA A:PRO450 4.1 10.2 1.0 SG A:CYS510 4.3 10.2 1.0 N A:HIS451 4.5 10.1 1.0 OG A:SER449 4.6 10.3 1.0 O A:HOH720 4.6 11.7 1.0 CB A:ALA234 4.6 9.3 1.0 CA A:CYS508 4.6 9.9 1.0 CB A:PRO450 4.6 13.0 1.0 CA A:CYS273 4.6 10.7 1.0 CA A:SER449 4.7 8.3 1.0 CB A:CYS510 4.7 10.5 1.0 CB A:SER449 4.8 9.5 1.0 C A:PRO450 4.8 9.8 1.0 CD2 A:HIS451 5.0 9.7 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


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 Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:10.7 occ:1.00 FE1 B:FES601 0.0 10.7 1.0 S1 B:FES601 2.2 10.3 1.0 S2 B:FES601 2.2 10.4 1.0 O B:HOH733 2.3 12.0 1.0 SG B:CYS510 2.5 10.2 1.0 FE2 B:FES601 2.6 9.0 1.0 CB B:CYS510 3.3 9.5 1.0 NZ B:LYS530 3.6 9.7 1.0 OE1 B:GLU292 3.8 11.8 1.0 CE B:LYS530 3.9 9.8 1.0 O B:HOH1040 4.2 12.9 1.0 SG B:CYS508 4.2 11.2 1.0 OE2 B:GLU292 4.2 9.4 1.0 CD B:GLU292 4.4 10.0 1.0 CA B:CYS510 4.6 9.1 1.0 CD B:LYS530 4.7 6.5 1.0 CB B:CYS273 4.7 9.4 1.0 N B:CYS510 4.7 8.4 1.0 OG B:SER449 4.7 12.7 1.0 SG B:CYS273 4.8 9.7 1.0 CB B:CYS508 4.8 9.7 1.0 O B:HOH1093 4.9 11.7 1.0 O B:HOH1155 5.0 7.5 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


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 Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:9.0 occ:1.00 FE2 B:FES601 0.0 9.0 1.0 S2 B:FES601 2.2 10.4 1.0 S1 B:FES601 2.2 10.3 1.0 SG B:CYS273 2.4 9.7 1.0 SG B:CYS508 2.5 11.2 1.0 FE1 B:FES601 2.6 10.7 1.0 CB B:CYS508 3.2 9.7 1.0 CB B:CYS273 3.2 9.4 1.0 CA B:PRO450 4.2 9.4 1.0 SG B:CYS510 4.3 10.2 1.0 N B:HIS451 4.5 7.7 1.0 OG B:SER449 4.6 12.7 1.0 O B:HOH733 4.6 12.0 1.0 CA B:SER449 4.6 8.6 1.0 CA B:CYS273 4.6 8.8 1.0 CA B:CYS508 4.7 9.5 1.0 CB B:CYS510 4.7 9.5 1.0 CB B:ALA234 4.7 10.4 1.0 CB B:SER449 4.7 9.1 1.0 CB B:PRO450 4.8 10.2 1.0 C B:PRO450 4.9 9.0 1.0 CD2 B:HIS451 4.9 8.2 1.0 O B:GLY448 4.9 8.4 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


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 Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:12.1 occ:1.00 FE1 C:FES601 0.0 12.1 1.0 S1 C:FES601 2.2 13.1 1.0 S2 C:FES601 2.2 11.1 1.0 O C:HOH729 2.4 16.1 1.0 SG C:CYS510 2.5 11.5 1.0 FE2 C:FES601 2.7 10.2 1.0 CB C:CYS510 3.3 11.9 1.0 NZ C:LYS530 3.6 11.3 1.0 OE1 C:GLU292 3.8 13.2 1.0 CE C:LYS530 3.8 12.5 1.0 O C:HOH1101 4.1 15.0 1.0 SG C:CYS508 4.3 12.5 1.0 OE2 C:GLU292 4.3 10.7 1.0 CD C:GLU292 4.4 11.3 1.0 CA C:CYS510 4.6 10.5 1.0 OG C:SER449 4.7 12.4 1.0 CD C:LYS530 4.7 11.5 1.0 CB C:CYS273 4.7 9.4 1.0 N C:CYS510 4.7 12.7 1.0 CB C:CYS508 4.8 10.8 1.0 SG C:CYS273 4.8 10.9 1.0 O C:HOH1029 4.9 14.1 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


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 Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:10.2 occ:1.00 FE2 C:FES601 0.0 10.2 1.0 S2 C:FES601 2.2 11.1 1.0 S1 C:FES601 2.2 13.1 1.0 SG C:CYS273 2.5 10.9 1.0 SG C:CYS508 2.5 12.5 1.0 FE1 C:FES601 2.7 12.1 1.0 CB C:CYS508 3.1 10.8 1.0 CB C:CYS273 3.2 9.4 1.0 CA C:PRO450 4.2 10.4 1.0 SG C:CYS510 4.4 11.5 1.0 N C:HIS451 4.5 9.8 1.0 OG C:SER449 4.5 12.4 1.0 CA C:CYS508 4.6 13.2 1.0 CA C:CYS273 4.6 10.0 1.0 CB C:ALA234 4.6 10.9 1.0 O C:HOH729 4.7 16.1 1.0 CA C:SER449 4.7 9.8 1.0 CB C:PRO450 4.8 12.8 1.0 CB C:CYS510 4.8 11.9 1.0 C C:PRO450 4.8 12.9 1.0 O C:GLY448 4.9 10.4 1.0 CD2 C:HIS451 4.9 11.4 1.0 CB C:SER449 4.9 11.6 1.0

Y.Murase, S.Watanabe, Y.Watanabe. Crystal Structure of Aconitase X To Be Published.