Iron in PDB 4q0t: Free Form of Tvnir, Low Dose Data Set

The structure of Free Form of Tvnir, Low Dose Data Set, PDB code: 4q0t was solved by V.A.Lazarenko, K.M.Polyakov, A.A.Trofimov, A.N.Popov, T.V.Tikhonova, A.V.Tikhonov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.01 / 1.70
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	195.480, 195.480, 195.480, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17

The structure of Free Form of Tvnir, Low Dose Data Set also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Free Form of Tvnir, Low Dose Data Set (pdb code 4q0t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Free Form of Tvnir, Low Dose Data Set, PDB code: 4q0t:
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 Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:13.7 occ:1.00 FE A:HEC601 0.0 13.7 1.0 NZ A:LYS188 1.9 14.7 1.0 O A:HOH701 2.0 15.8 1.0 NC A:HEC601 2.0 13.5 1.0 NA A:HEC601 2.0 14.0 1.0 ND A:HEC601 2.0 12.5 1.0 NB A:HEC601 2.0 13.6 1.0 CE A:LYS188 3.0 16.7 1.0 C1A A:HEC601 3.0 13.8 1.0 C4B A:HEC601 3.1 14.7 1.0 C4C A:HEC601 3.1 13.7 1.0 C1C A:HEC601 3.1 13.9 1.0 C4D A:HEC601 3.1 12.7 1.0 C4A A:HEC601 3.1 13.7 1.0 C1D A:HEC601 3.1 12.7 1.0 C1B A:HEC601 3.1 14.1 1.0 CHA A:HEC601 3.4 12.7 1.0 CHC A:HEC601 3.4 13.9 1.0 CHD A:HEC601 3.5 12.9 1.0 CHB A:HEC601 3.5 14.1 1.0 O A:HOH1081 4.2 25.0 1.0 NE2 A:HIS361 4.3 15.1 1.0 C2A A:HEC601 4.3 12.7 1.0 C3A A:HEC601 4.3 13.4 1.0 C3B A:HEC601 4.3 14.1 1.0 C3D A:HEC601 4.4 12.1 1.0 C3C A:HEC601 4.4 13.5 1.0 C2C A:HEC601 4.4 14.2 1.0 C2D A:HEC601 4.4 12.2 1.0 C2B A:HEC601 4.4 14.4 1.0 CD A:LYS188 4.4 14.9 1.0 O A:HOH832 4.5 21.2 1.0 O A:HOH823 4.6 15.4 1.0 CMD A:HEC603 4.8 12.2 1.0 OH A:TYR303 4.9 19.2 1.0

Iron binding site 2 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:12.6 occ:1.00 FE A:HEC602 0.0 12.6 1.0 NE2 A:HIS398 2.0 12.1 1.0 NE2 A:HIS231 2.0 12.0 1.0 NA A:HEC602 2.0 12.1 1.0 NB A:HEC602 2.0 11.8 1.0 NC A:HEC602 2.0 12.5 1.0 ND A:HEC602 2.0 12.9 1.0 CD2 A:HIS398 3.0 13.1 1.0 CE1 A:HIS231 3.0 13.1 1.0 CE1 A:HIS398 3.0 13.0 1.0 CD2 A:HIS231 3.0 12.7 1.0 C4B A:HEC602 3.0 11.5 1.0 C4D A:HEC602 3.0 12.4 1.0 C1D A:HEC602 3.0 12.6 1.0 C4A A:HEC602 3.0 11.7 1.0 C4C A:HEC602 3.0 11.7 1.0 C1C A:HEC602 3.1 11.9 1.0 C1B A:HEC602 3.1 10.9 1.0 C1A A:HEC602 3.1 12.1 1.0 CHD A:HEC602 3.4 11.9 1.0 CHA A:HEC602 3.4 11.9 1.0 CHC A:HEC602 3.4 11.3 1.0 CHB A:HEC602 3.4 10.7 1.0 ND1 A:HIS398 4.1 13.6 1.0 ND1 A:HIS231 4.1 12.9 1.0 CG A:HIS398 4.1 13.5 1.0 CG A:HIS231 4.1 12.9 1.0 C3B A:HEC602 4.3 11.7 1.0 C3D A:HEC602 4.3 13.1 1.0 C3A A:HEC602 4.3 11.7 1.0 C2D A:HEC602 4.3 12.7 1.0 C2B A:HEC602 4.3 11.2 1.0 C3C A:HEC602 4.3 12.2 1.0 C2C A:HEC602 4.4 12.4 1.0 C2A A:HEC602 4.4 12.4 1.0

Iron binding site 3 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:12.0 occ:1.00 FE A:HEC603 0.0 12.0 1.0 NE2 A:HIS300 1.9 11.6 1.0 NE2 A:HIS119 1.9 11.6 1.0 NA A:HEC603 2.0 11.6 1.0 ND A:HEC603 2.0 12.1 1.0 NB A:HEC603 2.0 12.1 1.0 NC A:HEC603 2.1 11.6 1.0 CE1 A:HIS300 2.9 11.7 1.0 CE1 A:HIS119 2.9 11.8 1.0 CD2 A:HIS300 3.0 12.5 1.0 CD2 A:HIS119 3.0 12.3 1.0 C4A A:HEC603 3.0 12.5 1.0 C1A A:HEC603 3.0 11.9 1.0 C4C A:HEC603 3.0 12.3 1.0 C1D A:HEC603 3.1 11.8 1.0 C1C A:HEC603 3.1 12.0 1.0 C4D A:HEC603 3.1 11.6 1.0 C1B A:HEC603 3.1 12.0 1.0 C4B A:HEC603 3.1 12.0 1.0 CHD A:HEC603 3.4 12.2 1.0 CHA A:HEC603 3.4 11.6 1.0 CHB A:HEC603 3.4 11.4 1.0 CHC A:HEC603 3.4 11.9 1.0 ND1 A:HIS300 4.0 12.3 1.0 ND1 A:HIS119 4.1 11.7 1.0 CG A:HIS300 4.1 11.7 1.0 CG A:HIS119 4.1 12.1 1.0 C2A A:HEC603 4.3 11.5 1.0 C3A A:HEC603 4.3 11.7 1.0 C3C A:HEC603 4.4 12.0 1.0 C2D A:HEC603 4.4 11.7 1.0 C2C A:HEC603 4.4 11.6 1.0 C3B A:HEC603 4.4 12.0 1.0 C3D A:HEC603 4.4 11.6 1.0 C2B A:HEC603 4.4 12.1 1.0 CMD A:HEC601 4.9 12.0 1.0

Iron binding site 4 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe604 b:12.2 occ:1.00 FE A:HEC604 0.0 12.2 1.0 NE2 A:HIS491 1.9 11.7 1.0 NE2 A:HIS383 1.9 12.4 1.0 NA A:HEC604 2.0 11.9 1.0 NC A:HEC604 2.0 12.3 1.0 NB A:HEC604 2.0 11.5 1.0 ND A:HEC604 2.1 11.8 1.0 CE1 A:HIS491 2.9 12.0 1.0 CE1 A:HIS383 2.9 12.8 1.0 CD2 A:HIS383 3.0 11.7 1.0 C4C A:HEC604 3.0 12.6 1.0 CD2 A:HIS491 3.0 12.0 1.0 C1A A:HEC604 3.0 12.0 1.0 C4B A:HEC604 3.0 12.0 1.0 C4A A:HEC604 3.0 11.8 1.0 C4D A:HEC604 3.0 12.0 1.0 C1B A:HEC604 3.0 12.1 1.0 C1D A:HEC604 3.1 12.6 1.0 C1C A:HEC604 3.1 12.2 1.0 CHD A:HEC604 3.4 12.7 1.0 CHA A:HEC604 3.4 11.8 1.0 CHB A:HEC604 3.4 12.2 1.0 CHC A:HEC604 3.4 11.6 1.0 ND1 A:HIS491 4.0 12.0 1.0 ND1 A:HIS383 4.0 12.7 1.0 CG A:HIS383 4.1 12.3 1.0 CG A:HIS491 4.1 12.0 1.0 C3B A:HEC604 4.3 11.8 1.0 C2A A:HEC604 4.3 12.2 1.0 C3A A:HEC604 4.3 12.1 1.0 C3C A:HEC604 4.3 12.4 1.0 C2B A:HEC604 4.3 12.1 1.0 C3D A:HEC604 4.3 12.2 1.0 C2D A:HEC604 4.4 12.3 1.0 C2C A:HEC604 4.4 12.2 1.0

Iron binding site 5 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe605 b:23.7 occ:1.00 FE A:HEC605 0.0 23.7 1.0 NE2 A:HIS372 1.9 20.4 1.0 NE2 A:HIS415 1.9 24.6 1.0 NB A:HEC605 2.1 22.6 1.0 NC A:HEC605 2.1 25.4 1.0 ND A:HEC605 2.1 31.9 1.0 NA A:HEC605 2.1 28.4 1.0 CE1 A:HIS415 2.9 26.8 1.0 CE1 A:HIS372 2.9 22.0 1.0 CD2 A:HIS372 3.0 19.4 1.0 CD2 A:HIS415 3.0 24.7 1.0 C4B A:HEC605 3.1 23.1 1.0 C1B A:HEC605 3.1 23.5 1.0 C1C A:HEC605 3.1 24.3 1.0 C1D A:HEC605 3.1 35.1 1.0 C4D A:HEC605 3.1 36.7 1.0 C1A A:HEC605 3.1 34.0 1.0 C4C A:HEC605 3.1 28.8 1.0 C4A A:HEC605 3.2 29.8 1.0 CHC A:HEC605 3.4 21.5 1.0 CHA A:HEC605 3.4 35.5 1.0 CHD A:HEC605 3.5 32.0 1.0 CHB A:HEC605 3.5 25.7 1.0 ND1 A:HIS415 4.0 24.4 1.0 ND1 A:HIS372 4.0 21.2 1.0 CG A:HIS372 4.1 19.1 1.0 CG A:HIS415 4.1 24.3 1.0 C3B A:HEC605 4.3 21.7 1.0 C2B A:HEC605 4.4 23.4 1.0 C2C A:HEC605 4.4 26.1 1.0 C2D A:HEC605 4.4 40.3 1.0 C3C A:HEC605 4.4 27.6 1.0 C3D A:HEC605 4.4 40.4 1.0 C2A A:HEC605 4.4 35.2 1.0 C3A A:HEC605 4.5 33.7 1.0 CBC A:HEC604 5.0 12.6 1.0

Iron binding site 6 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe606 b:14.7 occ:1.00 FE A:HEC606 0.0 14.7 1.0 NE2 A:HIS39 1.9 13.1 1.0 NE2 A:HIS234 1.9 13.2 1.0 ND A:HEC606 2.0 14.2 1.0 NA A:HEC606 2.1 14.5 1.0 NB A:HEC606 2.1 14.5 1.0 NC A:HEC606 2.1 13.8 1.0 CE1 A:HIS39 2.9 13.0 1.0 CD2 A:HIS234 2.9 12.8 1.0 CE1 A:HIS234 3.0 12.9 1.0 CD2 A:HIS39 3.0 13.3 1.0 C4A A:HEC606 3.1 14.3 1.0 C1A A:HEC606 3.1 14.3 1.0 C1D A:HEC606 3.1 14.1 1.0 C1B A:HEC606 3.1 14.8 1.0 C4C A:HEC606 3.1 13.8 1.0 C4D A:HEC606 3.1 13.6 1.0 C4B A:HEC606 3.1 14.2 1.0 C1C A:HEC606 3.1 13.4 1.0 CHB A:HEC606 3.4 14.4 1.0 CHD A:HEC606 3.4 13.3 1.0 CHA A:HEC606 3.5 13.7 1.0 CHC A:HEC606 3.5 13.2 1.0 ND1 A:HIS39 4.0 13.9 1.0 ND1 A:HIS234 4.1 13.4 1.0 CG A:HIS234 4.1 13.4 1.0 CG A:HIS39 4.1 13.8 1.0 C3A A:HEC606 4.3 14.4 1.0 C2A A:HEC606 4.3 14.5 1.0 C2D A:HEC606 4.3 13.8 1.0 C2B A:HEC606 4.4 14.7 1.0 C3C A:HEC606 4.4 13.1 1.0 C3D A:HEC606 4.4 13.6 1.0 C3B A:HEC606 4.4 13.9 1.0 C2C A:HEC606 4.4 13.3 1.0

Iron binding site 7 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe607 b:13.2 occ:1.00 FE A:HEC607 0.0 13.2 1.0 NE2 A:HIS70 2.0 12.7 1.0 NE2 A:HIS30 2.0 12.9 1.0 ND A:HEC607 2.0 13.1 1.0 NB A:HEC607 2.0 12.7 1.0 NC A:HEC607 2.0 13.0 1.0 NA A:HEC607 2.1 13.7 1.0 CE1 A:HIS30 2.9 14.0 1.0 CD2 A:HIS70 3.0 13.0 1.0 CE1 A:HIS70 3.0 13.2 1.0 CD2 A:HIS30 3.0 14.1 1.0 C1B A:HEC607 3.0 12.8 1.0 C4D A:HEC607 3.0 13.3 1.0 C4C A:HEC607 3.0 12.2 1.0 C1D A:HEC607 3.0 13.0 1.0 C4A A:HEC607 3.1 13.0 1.0 C4B A:HEC607 3.1 12.4 1.0 C1C A:HEC607 3.1 12.2 1.0 C1A A:HEC607 3.1 13.0 1.0 CHD A:HEC607 3.4 12.0 1.0 CHB A:HEC607 3.4 12.3 1.0 CHC A:HEC607 3.4 12.1 1.0 CHA A:HEC607 3.5 13.3 1.0 ND1 A:HIS30 4.0 15.0 1.0 ND1 A:HIS70 4.1 12.0 1.0 CG A:HIS70 4.1 12.3 1.0 CG A:HIS30 4.1 14.0 1.0 C3D A:HEC607 4.3 15.1 1.0 C3B A:HEC607 4.3 12.5 1.0 C2D A:HEC607 4.3 13.4 1.0 C2B A:HEC607 4.3 12.2 1.0 C3C A:HEC607 4.4 12.3 1.0 C3A A:HEC607 4.4 13.2 1.0 C2A A:HEC607 4.4 13.9 1.0 C2C A:HEC607 4.4 12.4 1.0

Iron binding site 8 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe608 b:15.6 occ:1.00 FE A:HEC608 0.0 15.6 1.0 NE2 A:HIS18 1.9 15.3 1.0 NE2 A:HIS44 1.9 15.4 1.0 ND A:HEC608 2.1 16.5 1.0 NA A:HEC608 2.1 15.3 1.0 NC A:HEC608 2.1 15.6 1.0 NB A:HEC608 2.1 15.9 1.0 CE1 A:HIS18 2.8 15.6 1.0 CD2 A:HIS44 2.9 15.4 1.0 CE1 A:HIS44 2.9 15.0 1.0 CD2 A:HIS18 3.0 15.0 1.0 C4A A:HEC608 3.1 15.4 1.0 C4C A:HEC608 3.1 16.6 1.0 C1D A:HEC608 3.1 16.7 1.0 C1C A:HEC608 3.1 16.1 1.0 C1B A:HEC608 3.1 16.3 1.0 C1A A:HEC608 3.1 15.9 1.0 C4D A:HEC608 3.1 16.7 1.0 C4B A:HEC608 3.1 16.0 1.0 CHD A:HEC608 3.4 17.2 1.0 CHB A:HEC608 3.4 15.1 1.0 CHA A:HEC608 3.5 16.2 1.0 CHC A:HEC608 3.5 16.3 1.0 ND1 A:HIS18 4.0 15.2 1.0 ND1 A:HIS44 4.0 16.0 1.0 CG A:HIS18 4.1 15.6 1.0 CG A:HIS44 4.1 15.8 1.0 C3A A:HEC608 4.4 14.9 1.0 C3C A:HEC608 4.4 16.3 1.0 C2D A:HEC608 4.4 17.2 1.0 C2A A:HEC608 4.4 15.0 1.0 C3D A:HEC608 4.4 16.7 1.0 C2C A:HEC608 4.4 16.3 1.0 C2B A:HEC608 4.4 16.3 1.0 C3B A:HEC608 4.4 16.5 1.0 CMA A:HEC606 4.9 14.1 1.0

Iron binding site 9 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:12.1 occ:1.00 FE B:HEC601 0.0 12.1 1.0 NZ B:LYS188 1.9 14.7 1.0 O B:HOH701 2.0 14.0 1.0 ND B:HEC601 2.0 10.7 1.0 NA B:HEC601 2.0 11.3 1.0 NC B:HEC601 2.0 11.6 1.0 NB B:HEC601 2.1 11.9 1.0 C1A B:HEC601 3.0 11.3 1.0 C1C B:HEC601 3.0 12.0 1.0 C4D B:HEC601 3.0 10.4 1.0 C1D B:HEC601 3.0 10.4 1.0 CE B:LYS188 3.0 15.9 1.0 C4A B:HEC601 3.1 11.2 1.0 C4B B:HEC601 3.1 12.1 1.0 C4C B:HEC601 3.1 11.1 1.0 C1B B:HEC601 3.1 11.6 1.0 CHA B:HEC601 3.4 10.8 1.0 CHC B:HEC601 3.4 11.9 1.0 CHB B:HEC601 3.5 11.9 1.0 CHD B:HEC601 3.5 10.6 1.0 O B:HOH1106 4.2 15.0 0.5 NE2 B:HIS361 4.2 11.8 1.0 O B:HOH1278 4.3 16.5 0.5 C3D B:HEC601 4.3 10.3 1.0 C2A B:HEC601 4.3 11.1 1.0 C3A B:HEC601 4.3 11.1 1.0 C2D B:HEC601 4.3 10.2 1.0 C2C B:HEC601 4.3 11.3 1.0 C3C B:HEC601 4.4 11.4 1.0 CD B:LYS188 4.4 14.3 1.0 C3B B:HEC601 4.4 12.2 1.0 C2B B:HEC601 4.4 11.8 1.0 O B:HOH849 4.5 14.7 1.0 O B:HOH858 4.6 21.6 1.0 CMD B:HEC603 4.8 8.6 1.0 OH B:TYR303 4.9 21.0 1.0

Iron binding site 10 out of 16 in the Free Form of Tvnir, Low Dose Data Set


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:12.4 occ:1.00 FE B:HEC602 0.0 12.4 1.0 NE2 B:HIS398 2.0 11.9 1.0 NE2 B:HIS231 2.0 11.6 1.0 ND B:HEC602 2.0 11.8 1.0 NC B:HEC602 2.0 11.3 1.0 NB B:HEC602 2.0 11.3 1.0 NA B:HEC602 2.0 11.6 1.0 CE1 B:HIS398 2.9 13.8 1.0 CD2 B:HIS231 3.0 11.8 1.0 CE1 B:HIS231 3.0 12.7 1.0 CD2 B:HIS398 3.0 13.2 1.0 C4B B:HEC602 3.0 10.8 1.0 C1D B:HEC602 3.0 11.3 1.0 C4A B:HEC602 3.0 11.5 1.0 C4C B:HEC602 3.0 10.8 1.0 C4D B:HEC602 3.0 11.6 1.0 C1C B:HEC602 3.1 10.6 1.0 C1B B:HEC602 3.1 10.9 1.0 C1A B:HEC602 3.1 11.6 1.0 CHD B:HEC602 3.4 10.4 1.0 CHC B:HEC602 3.4 10.4 1.0 CHB B:HEC602 3.4 10.8 1.0 CHA B:HEC602 3.4 11.1 1.0 ND1 B:HIS398 4.1 13.6 1.0 ND1 B:HIS231 4.1 11.9 1.0 CG B:HIS231 4.1 11.7 1.0 CG B:HIS398 4.1 13.1 1.0 C3B B:HEC602 4.3 10.7 1.0 C3D B:HEC602 4.3 12.3 1.0 C2D B:HEC602 4.3 12.3 1.0 C3C B:HEC602 4.3 10.7 1.0 C2B B:HEC602 4.3 10.9 1.0 C3A B:HEC602 4.4 11.4 1.0 C2A B:HEC602 4.4 12.0 1.0 C2C B:HEC602 4.4 11.1 1.0

V.A.Lazarenko, K.M.Polyakov, A.A.Trofimov, A.N.Popov, T.V.Tikhonova, A.V.Tikhonov, V.O.Popov. X-Ray-Induced Changes in the Active Site Structure of Octaheme Cytochrome C Nitrite Reductase and Its Substrate Complexes To Be Published.