Iron in PDB 7cnr: Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form)

The structure of Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form), PDB code: 7cnr 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)	23.29 / 3.39
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.72, 141.72, 278.108, 90, 90, 90
R / Rfree (%)	18.2 / 22.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form) (pdb code 7cnr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form), PDB code: 7cnr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis 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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:94.8 occ:1.00 FE1 A:F3S401 0.0 94.8 1.0 S1 A:F3S401 2.2 106.3 1.0 S2 A:F3S401 2.3 87.7 1.0 S3 A:F3S401 2.3 162.6 1.0 FE4 A:F3S401 2.6 86.2 1.0 SG A:CYS110 2.7 64.9 1.0 FE3 A:F3S401 2.7 98.1 1.0 CB A:CYS110 3.7 72.7 1.0 S4 A:F3S401 3.9 95.5 1.0 CA A:PRO284 4.2 91.1 1.0 N A:HIS285 4.5 78.5 1.0 CG A:PRO80 4.5 78.2 1.0 CD2 A:HIS285 4.5 81.2 1.0 CB A:PRO284 4.6 81.7 1.0 NE2 A:HIS285 4.8 81.3 1.0 C A:PRO284 4.8 87.0 1.0 OE2 A:GLU129 4.9 88.8 1.0 CB A:CYS342 5.0 75.7 1.0 OG A:SER131 5.0 85.9 1.0

Iron binding site 2 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis 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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:98.1 occ:1.00 FE3 A:F3S401 0.0 98.1 1.0 S1 A:F3S401 2.2 106.3 1.0 S4 A:F3S401 2.3 95.5 1.0 S3 A:F3S401 2.3 162.6 1.0 FE1 A:F3S401 2.7 94.8 1.0 FE4 A:F3S401 2.7 86.2 1.0 SG A:CYS283 2.8 94.3 1.0 CB A:CYS283 3.4 91.8 1.0 CA A:CYS283 3.6 87.0 1.0 C A:CYS283 4.0 87.2 1.0 CD A:LYS361 4.0 82.8 1.0 S2 A:F3S401 4.0 87.7 1.0 CA A:PRO284 4.1 91.1 1.0 N A:PRO284 4.2 89.4 1.0 CE A:LYS361 4.4 85.5 1.0 NZ A:LYS361 4.5 86.3 1.0 CG A:LYS361 4.7 75.6 1.0 O A:CYS283 4.7 86.7 1.0 CB A:PRO284 4.9 81.7 1.0 OG A:SER362 4.9 91.0 1.0 CB A:LYS361 5.0 74.0 1.0 N A:CYS283 5.0 83.3 1.0

Iron binding site 3 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis 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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:86.2 occ:1.00 FE4 A:F3S401 0.0 86.2 1.0 S4 A:F3S401 2.3 95.5 1.0 S2 A:F3S401 2.3 87.7 1.0 S3 A:F3S401 2.3 162.6 1.0 FE1 A:F3S401 2.6 94.8 1.0 FE3 A:F3S401 2.7 98.1 1.0 SG A:CYS342 2.8 94.5 1.0 CB A:CYS342 3.6 75.7 1.0 S1 A:F3S401 3.8 106.3 1.0 CG2 A:VAL344 3.9 69.6 1.0 CA A:CYS342 4.6 77.0 1.0 CG1 A:VAL344 4.7 78.8 1.0 CB A:VAL344 4.9 77.0 1.0

Iron binding site 4 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis 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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:91.8 occ:1.00 FE1 C:F3S401 0.0 91.8 1.0 S1 C:F3S401 2.2 138.9 1.0 S2 C:F3S401 2.3 109.5 1.0 S3 C:F3S401 2.3 132.7 1.0 FE4 C:F3S401 2.7 98.4 1.0 FE3 C:F3S401 2.7 107.2 1.0 SG C:CYS110 2.8 70.4 1.0 CB C:CYS110 3.4 73.9 1.0 OE1 C:GLU129 3.9 98.0 1.0 S4 C:F3S401 4.0 117.8 1.0 CG C:PRO80 4.2 79.2 1.0 NE2 C:HIS285 4.4 77.7 1.0 CD2 C:HIS285 4.5 77.8 1.0 CA C:PRO284 4.5 81.7 1.0 N C:HIS285 4.8 74.4 1.0 CB C:CYS342 4.8 82.2 1.0 SG C:CYS342 4.8 106.3 1.0 CA C:CYS110 4.8 72.3 1.0 CE1 C:HIS285 4.9 77.6 1.0 CD C:GLU129 4.9 89.6 1.0 OG C:SER131 4.9 88.1 1.0 CG C:HIS285 5.0 81.6 1.0

Iron binding site 5 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis 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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:107.2 occ:1.00 FE3 C:F3S401 0.0 107.2 1.0 S1 C:F3S401 2.2 138.9 1.0 S4 C:F3S401 2.3 117.8 1.0 S3 C:F3S401 2.3 132.7 1.0 FE4 C:F3S401 2.7 98.4 1.0 FE1 C:F3S401 2.7 91.8 1.0 SG C:CYS283 2.8 84.2 1.0 CA C:CYS283 3.5 78.9 1.0 CB C:CYS283 3.6 83.3 1.0 C C:CYS283 3.7 77.7 1.0 CA C:PRO284 3.8 81.7 1.0 N C:PRO284 3.8 79.4 1.0 S2 C:F3S401 4.0 109.5 1.0 CD C:LYS361 4.3 87.0 1.0 O C:CYS283 4.4 77.2 1.0 CB C:PRO284 4.6 78.0 1.0 CD C:PRO284 4.8 76.6 1.0 SG C:CYS110 4.8 70.4 1.0 CG C:PRO284 4.8 75.1 1.0 C C:PRO284 4.8 77.1 1.0 CE C:LYS361 4.8 92.0 1.0 CG C:LYS361 4.8 79.7 1.0 OE1 C:GLU129 4.9 98.0 1.0 N C:CYS283 4.9 80.1 1.0

Iron binding site 6 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis 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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:98.4 occ:1.00 FE4 C:F3S401 0.0 98.4 1.0 S4 C:F3S401 2.3 117.8 1.0 S2 C:F3S401 2.3 109.5 1.0 S3 C:F3S401 2.3 132.7 1.0 FE1 C:F3S401 2.7 91.8 1.0 FE3 C:F3S401 2.7 107.2 1.0 SG C:CYS342 2.8 106.3 1.0 CB C:CYS342 3.7 82.2 1.0 S1 C:F3S401 3.8 138.9 1.0 CG2 C:VAL344 3.9 72.9 1.0 SG C:CYS283 4.5 84.2 1.0 CG1 C:VAL344 4.7 87.8 1.0 CA C:CYS342 4.7 78.5 1.0 CB C:VAL344 4.9 86.0 1.0

Iron binding site 7 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form)


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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:89.9 occ:1.00 FE1 E:F3S401 0.0 89.9 1.0 S1 E:F3S401 2.2 198.0 1.0 S2 E:F3S401 2.3 131.6 1.0 S3 E:F3S401 2.3 142.8 1.0 FE4 E:F3S401 2.7 106.7 1.0 FE3 E:F3S401 2.7 98.5 1.0 SG E:CYS110 2.8 92.6 1.0 CB E:CYS110 3.5 82.9 1.0 S4 E:F3S401 3.9 178.0 1.0 CA E:PRO284 4.3 92.7 1.0 CD2 E:HIS285 4.3 83.4 1.0 NE2 E:HIS285 4.4 83.3 1.0 OE1 E:GLU129 4.5 94.8 1.0 CG E:PRO80 4.6 91.6 1.0 N E:HIS285 4.6 85.3 1.0 SG E:CYS342 4.7 96.0 1.0 CB E:CYS342 4.8 81.8 1.0 CD E:GLU129 4.9 95.2 1.0 CB E:PRO284 4.9 88.3 1.0 CA E:CYS110 4.9 82.5 1.0 CG E:HIS285 5.0 84.4 1.0

Iron binding site 8 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form)


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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:98.5 occ:1.00 FE3 E:F3S401 0.0 98.5 1.0 S1 E:F3S401 2.2 198.0 1.0 S4 E:F3S401 2.3 178.0 1.0 S3 E:F3S401 2.3 142.8 1.0 FE4 E:F3S401 2.7 106.7 1.0 FE1 E:F3S401 2.7 89.9 1.0 SG E:CYS283 2.8 95.2 1.0 CA E:CYS283 3.6 88.8 1.0 CB E:CYS283 3.6 91.0 1.0 C E:CYS283 3.8 90.1 1.0 N E:PRO284 4.0 93.0 1.0 S2 E:F3S401 4.0 131.6 1.0 CA E:PRO284 4.0 92.7 1.0 CD E:LYS361 4.2 90.2 1.0 CE E:LYS361 4.4 100.7 1.0 O E:CYS283 4.4 84.3 1.0 NZ E:LYS361 4.5 100.7 1.0 CG E:LYS361 4.8 79.5 1.0 CD E:PRO284 4.8 90.9 1.0 SG E:CYS110 4.9 92.6 1.0 CG E:PRO284 4.9 86.8 1.0 CB E:PRO284 4.9 88.3 1.0 N E:CYS283 4.9 86.9 1.0

Iron binding site 9 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form)


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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:106.7 occ:1.00 FE4 E:F3S401 0.0 106.7 1.0 S4 E:F3S401 2.3 178.0 1.0 S2 E:F3S401 2.3 131.6 1.0 S3 E:F3S401 2.3 142.8 1.0 FE1 E:F3S401 2.7 89.9 1.0 FE3 E:F3S401 2.7 98.5 1.0 SG E:CYS342 2.7 96.0 1.0 CB E:CYS342 3.7 81.8 1.0 S1 E:F3S401 3.8 198.0 1.0 CG2 E:VAL344 3.9 76.4 1.0 CG2 E:VAL345 4.7 91.2 1.0 SG E:CYS283 4.7 95.2 1.0 CA E:CYS342 4.8 78.1 1.0 CG1 E:VAL344 4.9 95.6 1.0 CB E:VAL344 5.0 91.3 1.0

Iron binding site 10 out of 12 in the Crystal Structure of Thermococcus Kodakaraensis Aconitase X (Apo-Form)


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 Thermococcus Kodakaraensis Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe401 b:108.1 occ:1.00 FE1 G:F3S401 0.0 108.1 1.0 S1 G:F3S401 2.2 137.8 1.0 S2 G:F3S401 2.3 131.2 1.0 S3 G:F3S401 2.3 141.5 1.0 FE4 G:F3S401 2.7 122.1 1.0 FE3 G:F3S401 2.7 121.3 1.0 SG G:CYS110 2.8 85.1 1.0 CB G:CYS110 3.2 85.3 1.0 S4 G:F3S401 4.0 119.9 1.0 CG G:PRO80 4.2 86.7 1.0 CD2 G:HIS285 4.3 87.3 1.0 NE2 G:HIS285 4.5 84.8 1.0 CA G:PRO284 4.5 95.3 1.0 N G:HIS285 4.6 81.9 1.0 OE2 G:GLU129 4.7 108.4 1.0 CA G:CYS110 4.7 82.9 1.0 CB G:CYS342 4.7 95.7 1.0 CD G:GLU129 4.7 102.8 1.0 SG G:CYS342 4.8 98.8 1.0 OE1 G:GLU129 4.8 105.0 1.0 CG G:HIS285 4.9 87.5 1.0 CD G:PRO80 5.0 86.3 1.0

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