Iron in PDB 1qdb: Cytochrome C Nitrite Reductase

The structure of Cytochrome C Nitrite Reductase, PDB code: 1qdb was solved by O.Einsle, A.Messerschmidt, P.Stach, R.Huber, P.M.H.Kroneck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.484, 185.344, 92.192, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22

The structure of Cytochrome C Nitrite Reductase also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iron atom in the Cytochrome C Nitrite Reductase (pdb code 1qdb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Cytochrome C Nitrite Reductase, PDB code: 1qdb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe515 b:26.5 occ:1.00 FE A:HEM515 0.0 26.5 1.0 NZ A:LYS133 1.9 25.4 1.0 NA A:HEM515 1.9 23.1 1.0 ND A:HEM515 1.9 22.2 1.0 NC A:HEM515 2.0 22.6 1.0 NB A:HEM515 2.0 26.2 1.0 O1 A:SO41501 2.1 46.6 1.0 C1D A:HEM515 3.0 21.0 1.0 C4C A:HEM515 3.0 23.9 1.0 C4A A:HEM515 3.0 24.5 1.0 C1B A:HEM515 3.0 25.7 1.0 C1A A:HEM515 3.0 24.5 1.0 C4D A:HEM515 3.0 23.6 1.0 C1C A:HEM515 3.0 23.9 1.0 CE A:LYS133 3.1 28.3 1.0 C4B A:HEM515 3.1 24.7 1.0 CHD A:HEM515 3.3 21.5 1.0 S A:SO41501 3.3 53.9 1.0 CHB A:HEM515 3.3 24.7 1.0 CHA A:HEM515 3.4 21.9 1.0 CHC A:HEM515 3.5 25.9 1.0 O2 A:SO41501 3.7 54.1 1.0 O3 A:SO41501 3.9 54.3 1.0 C2D A:HEM515 4.2 22.2 1.0 C3A A:HEM515 4.2 21.8 1.0 C3D A:HEM515 4.2 20.4 1.0 C2A A:HEM515 4.3 22.2 1.0 O A:HOH1553 4.3 24.5 1.0 C3C A:HEM515 4.3 22.0 1.0 C2C A:HEM515 4.3 22.6 1.0 C2B A:HEM515 4.3 25.8 1.0 C3B A:HEM515 4.3 25.0 1.0 NE2 A:HIS282 4.3 23.4 1.0 O4 A:SO41501 4.4 50.6 1.0 CD A:LYS133 4.4 28.0 1.0 O A:HOH1607 4.7 29.0 1.0 CMD A:HEM517 4.9 20.1 1.0 CD2 A:HIS282 4.9 23.1 1.0

Iron binding site 2 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe516 b:28.4 occ:1.00 FE A:HEM516 0.0 28.4 1.0 NE2 A:HIS171 1.9 25.4 1.0 NA A:HEM516 2.0 30.0 1.0 NE2 A:HIS318 2.0 22.9 1.0 ND A:HEM516 2.0 27.8 1.0 NC A:HEM516 2.0 28.3 1.0 NB A:HEM516 2.0 29.5 1.0 CE1 A:HIS171 2.8 27.6 1.0 CD2 A:HIS318 2.9 24.0 1.0 C4A A:HEM516 3.0 32.5 1.0 C1D A:HEM516 3.0 27.3 1.0 C1A A:HEM516 3.0 30.9 1.0 C4D A:HEM516 3.0 26.4 1.0 C4C A:HEM516 3.0 27.7 1.0 C1B A:HEM516 3.0 31.1 1.0 CE1 A:HIS318 3.0 24.8 1.0 CD2 A:HIS171 3.0 26.2 1.0 C1C A:HEM516 3.0 28.6 1.0 C4B A:HEM516 3.1 29.9 1.0 CHB A:HEM516 3.3 32.2 1.0 CHD A:HEM516 3.4 26.7 1.0 CHA A:HEM516 3.4 29.6 1.0 CHC A:HEM516 3.4 30.2 1.0 ND1 A:HIS171 4.0 25.8 1.0 CG A:HIS171 4.1 25.4 1.0 CG A:HIS318 4.1 23.1 1.0 ND1 A:HIS318 4.1 22.6 1.0 C3A A:HEM516 4.2 33.8 1.0 C2A A:HEM516 4.2 32.4 1.0 C2C A:HEM516 4.3 28.4 1.0 C3C A:HEM516 4.3 26.7 1.0 C3D A:HEM516 4.3 26.4 1.0 C2D A:HEM516 4.3 27.0 1.0 C2B A:HEM516 4.3 31.1 1.0 C3B A:HEM516 4.3 29.3 1.0 CE A:MET305 4.7 23.5 1.0 CG A:GLN59 5.0 33.0 1.0

Iron binding site 3 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe517 b:20.7 occ:1.00 FE A:HEM517 0.0 20.7 1.0 NA A:HEM517 1.9 21.6 1.0 NC A:HEM517 1.9 25.6 1.0 NE2 A:HIS214 2.0 23.7 1.0 NE2 A:HIS101 2.0 25.5 1.0 NB A:HEM517 2.0 23.8 1.0 ND A:HEM517 2.0 22.4 1.0 CE1 A:HIS214 2.9 23.1 1.0 C1C A:HEM517 3.0 23.7 1.0 CE1 A:HIS101 3.0 26.5 1.0 C1A A:HEM517 3.0 22.0 1.0 C4A A:HEM517 3.0 21.8 1.0 C4D A:HEM517 3.0 20.8 1.0 C4B A:HEM517 3.0 23.8 1.0 C4C A:HEM517 3.0 23.2 1.0 C1B A:HEM517 3.0 22.1 1.0 C1D A:HEM517 3.1 22.1 1.0 CD2 A:HIS101 3.1 25.0 1.0 CD2 A:HIS214 3.1 21.6 1.0 CHC A:HEM517 3.3 22.8 1.0 CHA A:HEM517 3.3 21.4 1.0 CHB A:HEM517 3.4 23.4 1.0 CHD A:HEM517 3.5 21.6 1.0 ND1 A:HIS214 4.1 20.8 1.0 ND1 A:HIS101 4.1 26.6 1.0 C2C A:HEM517 4.2 25.0 1.0 C2A A:HEM517 4.2 21.4 1.0 C3A A:HEM517 4.2 20.9 1.0 CG A:HIS214 4.2 22.0 1.0 CG A:HIS101 4.2 25.1 1.0 C3C A:HEM517 4.2 24.3 1.0 C2B A:HEM517 4.3 23.8 1.0 C3D A:HEM517 4.3 21.5 1.0 C3B A:HEM517 4.3 20.8 1.0 C2D A:HEM517 4.3 21.7 1.0

Iron binding site 4 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe518 b:20.6 occ:1.00 FE A:HEM518 0.0 20.6 1.0 NB A:HEM518 1.9 16.9 1.0 ND A:HEM518 1.9 15.8 1.0 NC A:HEM518 2.0 16.2 1.0 NA A:HEM518 2.0 19.4 1.0 NE2 A:HIS411 2.0 17.3 1.0 NE2 A:HIS304 2.0 20.5 1.0 CE1 A:HIS411 2.8 15.2 1.0 C1C A:HEM518 3.0 15.9 1.0 C4B A:HEM518 3.0 16.3 1.0 C4D A:HEM518 3.0 20.6 1.0 C1B A:HEM518 3.0 16.3 1.0 CE1 A:HIS304 3.0 22.6 1.0 C1A A:HEM518 3.0 18.4 1.0 C4A A:HEM518 3.0 18.4 1.0 C1D A:HEM518 3.0 16.6 1.0 C4C A:HEM518 3.0 14.3 1.0 CD2 A:HIS304 3.1 23.2 1.0 CD2 A:HIS411 3.2 17.1 1.0 CHC A:HEM518 3.3 16.1 1.0 CHA A:HEM518 3.3 19.6 1.0 CHB A:HEM518 3.4 17.6 1.0 CHD A:HEM518 3.5 15.8 1.0 ND1 A:HIS411 4.0 17.1 1.0 ND1 A:HIS304 4.2 20.9 1.0 C2B A:HEM518 4.2 15.1 1.0 C3B A:HEM518 4.2 17.9 1.0 C2C A:HEM518 4.2 13.7 1.0 CG A:HIS411 4.2 17.2 1.0 C3D A:HEM518 4.2 19.6 1.0 C2D A:HEM518 4.2 18.8 1.0 CG A:HIS304 4.2 23.0 1.0 C3C A:HEM518 4.3 14.0 1.0 C3A A:HEM518 4.3 20.6 1.0 C2A A:HEM518 4.3 21.2 1.0

Iron binding site 5 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe519 b:17.8 occ:1.00 FE A:HEM519 0.0 17.8 1.0 NE2 A:HIS336 2.0 21.8 1.0 NE2 A:HIS293 2.0 16.5 1.0 NB A:HEM519 2.0 19.5 1.0 NA A:HEM519 2.0 17.3 1.0 ND A:HEM519 2.0 20.3 1.0 NC A:HEM519 2.0 19.3 1.0 CE1 A:HIS336 2.9 24.0 1.0 CE1 A:HIS293 2.9 15.2 1.0 C1A A:HEM519 3.0 16.7 1.0 C4C A:HEM519 3.0 20.7 1.0 C1C A:HEM519 3.0 21.0 1.0 C1D A:HEM519 3.0 20.4 1.0 C4A A:HEM519 3.0 16.5 1.0 C4D A:HEM519 3.0 20.3 1.0 C1B A:HEM519 3.0 22.4 1.0 C4B A:HEM519 3.0 20.7 1.0 CD2 A:HIS293 3.1 16.7 1.0 CD2 A:HIS336 3.1 23.4 1.0 CHA A:HEM519 3.4 18.6 1.0 CHD A:HEM519 3.4 19.4 1.0 CHC A:HEM519 3.4 20.8 1.0 CHB A:HEM519 3.4 19.2 1.0 ND1 A:HIS336 4.1 24.7 1.0 ND1 A:HIS293 4.1 15.3 1.0 CG A:HIS293 4.2 16.9 1.0 CG A:HIS336 4.2 24.7 1.0 C2A A:HEM519 4.2 15.9 1.0 C3A A:HEM519 4.3 15.0 1.0 C2D A:HEM519 4.3 21.5 1.0 C2C A:HEM519 4.3 21.2 1.0 C3D A:HEM519 4.3 21.2 1.0 C3C A:HEM519 4.3 21.4 1.0 C2B A:HEM519 4.3 20.7 1.0 C3B A:HEM519 4.3 21.2 1.0 CBC A:HEM518 4.9 14.7 1.0

Iron binding site 6 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe515 b:20.5 occ:1.00 FE B:HEM515 0.0 20.5 1.0 NC B:HEM515 1.9 15.6 1.0 NZ B:LYS133 1.9 17.9 1.0 NA B:HEM515 2.0 14.0 1.0 ND B:HEM515 2.0 15.6 1.0 NB B:HEM515 2.0 18.4 1.0 O1 B:SO41502 2.0 36.5 1.0 C1D B:HEM515 3.0 15.7 1.0 C4C B:HEM515 3.0 17.6 1.0 C1C B:HEM515 3.0 19.9 1.0 C4D B:HEM515 3.0 11.7 1.0 C1A B:HEM515 3.0 16.7 1.0 C4A B:HEM515 3.0 17.6 1.0 C1B B:HEM515 3.1 16.9 1.0 C4B B:HEM515 3.1 19.0 1.0 CE B:LYS133 3.1 14.3 1.0 S B:SO41502 3.3 43.4 1.0 CHD B:HEM515 3.3 16.0 1.0 CHA B:HEM515 3.4 13.0 1.0 CHC B:HEM515 3.4 17.2 1.0 CHB B:HEM515 3.4 18.6 1.0 O4 B:SO41502 3.7 44.5 1.0 O2 B:SO41502 3.9 42.3 1.0 C2C B:HEM515 4.2 17.6 1.0 C2D B:HEM515 4.2 14.9 1.0 NE2 B:HIS282 4.2 18.6 1.0 C3C B:HEM515 4.2 17.5 1.0 C3A B:HEM515 4.3 15.6 1.0 C3D B:HEM515 4.3 16.2 1.0 C2A B:HEM515 4.3 16.9 1.0 O B:HOH1614 4.3 22.0 1.0 C2B B:HEM515 4.3 15.3 1.0 C3B B:HEM515 4.4 18.2 1.0 O3 B:SO41502 4.4 40.5 1.0 CD B:LYS133 4.5 17.4 1.0 CMD B:HEM517 4.9 15.3 1.0 CD2 B:HIS282 4.9 14.8 1.0 O B:HOH1534 5.0 18.9 1.0

Iron binding site 7 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe516 b:17.2 occ:1.00 FE B:HEM516 0.0 17.2 1.0 ND B:HEM516 1.9 15.9 1.0 NB B:HEM516 1.9 16.4 1.0 NA B:HEM516 1.9 15.9 1.0 NC B:HEM516 2.0 17.2 1.0 NE2 B:HIS171 2.0 16.6 1.0 NE2 B:HIS318 2.0 16.6 1.0 CE1 B:HIS171 3.0 15.0 1.0 C1B B:HEM516 3.0 15.4 1.0 C4A B:HEM516 3.0 14.6 1.0 C1D B:HEM516 3.0 16.1 1.0 C4D B:HEM516 3.0 15.9 1.0 CE1 B:HIS318 3.0 16.2 1.0 C4C B:HEM516 3.0 13.8 1.0 CD2 B:HIS171 3.0 14.9 1.0 C1A B:HEM516 3.0 15.1 1.0 CD2 B:HIS318 3.0 16.3 1.0 C4B B:HEM516 3.0 12.9 1.0 C1C B:HEM516 3.1 14.1 1.0 CHB B:HEM516 3.3 14.0 1.0 CHD B:HEM516 3.4 15.0 1.0 CHA B:HEM516 3.4 15.4 1.0 CHC B:HEM516 3.5 13.7 1.0 ND1 B:HIS171 4.1 17.1 1.0 ND1 B:HIS318 4.1 15.1 1.0 CG B:HIS171 4.1 15.9 1.0 CG B:HIS318 4.2 16.2 1.0 C2B B:HEM516 4.2 14.7 1.0 C3A B:HEM516 4.2 13.8 1.0 C3B B:HEM516 4.2 12.7 1.0 C3D B:HEM516 4.2 16.3 1.0 C2D B:HEM516 4.2 16.1 1.0 C2A B:HEM516 4.3 14.1 1.0 C3C B:HEM516 4.3 14.1 1.0 C2C B:HEM516 4.3 13.9 1.0 CE B:MET305 4.5 15.4 1.0

Iron binding site 8 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe517 b:14.7 occ:1.00 FE B:HEM517 0.0 14.7 1.0 ND B:HEM517 2.0 14.1 1.0 NC B:HEM517 2.0 16.3 1.0 NA B:HEM517 2.0 13.7 1.0 NB B:HEM517 2.0 13.7 1.0 NE2 B:HIS214 2.0 12.4 1.0 NE2 B:HIS101 2.0 13.2 1.0 CE1 B:HIS214 2.9 12.7 1.0 CE1 B:HIS101 3.0 16.0 1.0 C1C B:HEM517 3.0 13.2 1.0 C4C B:HEM517 3.0 14.9 1.0 C1A B:HEM517 3.0 14.5 1.0 C1D B:HEM517 3.0 14.1 1.0 C4A B:HEM517 3.0 14.1 1.0 C1B B:HEM517 3.0 15.8 1.0 C4D B:HEM517 3.0 13.8 1.0 C4B B:HEM517 3.1 12.3 1.0 CD2 B:HIS101 3.1 14.7 1.0 CD2 B:HIS214 3.1 13.7 1.0 CHD B:HEM517 3.4 14.9 1.0 CHC B:HEM517 3.4 14.1 1.0 CHB B:HEM517 3.4 14.1 1.0 CHA B:HEM517 3.4 14.2 1.0 ND1 B:HIS214 4.1 14.0 1.0 ND1 B:HIS101 4.1 14.9 1.0 CG B:HIS214 4.2 13.9 1.0 CG B:HIS101 4.2 15.8 1.0 C2C B:HEM517 4.2 12.9 1.0 C2D B:HEM517 4.2 15.6 1.0 C2A B:HEM517 4.3 14.7 1.0 C3D B:HEM517 4.3 13.9 1.0 C3A B:HEM517 4.3 14.2 1.0 C3C B:HEM517 4.3 15.1 1.0 C2B B:HEM517 4.3 13.2 1.0 C3B B:HEM517 4.3 13.8 1.0

Iron binding site 9 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe518 b:12.1 occ:1.00 FE B:HEM518 0.0 12.1 1.0 NC B:HEM518 1.9 12.8 1.0 NA B:HEM518 1.9 13.1 1.0 ND B:HEM518 1.9 13.6 1.0 NB B:HEM518 2.0 13.5 1.0 NE2 B:HIS304 2.0 13.7 1.0 NE2 B:HIS411 2.0 12.4 1.0 CE1 B:HIS411 2.9 12.2 1.0 C1C B:HEM518 3.0 14.0 1.0 CE1 B:HIS304 3.0 13.3 1.0 C1B B:HEM518 3.0 13.2 1.0 C4D B:HEM518 3.0 12.3 1.0 C4B B:HEM518 3.0 9.9 1.0 C4A B:HEM518 3.0 14.1 1.0 C1A B:HEM518 3.0 13.4 1.0 C1D B:HEM518 3.0 13.6 1.0 C4C B:HEM518 3.0 13.2 1.0 CD2 B:HIS304 3.0 12.2 1.0 CD2 B:HIS411 3.2 12.5 1.0 CHC B:HEM518 3.3 11.5 1.0 CHB B:HEM518 3.4 13.4 1.0 CHA B:HEM518 3.4 14.8 1.0 CHD B:HEM518 3.4 10.2 1.0 ND1 B:HIS411 4.1 13.8 1.0 ND1 B:HIS304 4.1 13.5 1.0 CG B:HIS304 4.2 14.3 1.0 C2C B:HEM518 4.2 12.5 1.0 C2A B:HEM518 4.2 14.2 1.0 C3A B:HEM518 4.2 13.1 1.0 C2B B:HEM518 4.2 12.0 1.0 CG B:HIS411 4.2 12.0 1.0 C3D B:HEM518 4.2 13.2 1.0 C3C B:HEM518 4.3 12.9 1.0 C2D B:HEM518 4.3 11.8 1.0 C3B B:HEM518 4.3 11.6 1.0

Iron binding site 10 out of 15 in the Cytochrome C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe519 b:15.9 occ:1.00 FE B:HEM519 0.0 15.9 1.0 NC B:HEM519 1.9 16.4 1.0 NA B:HEM519 1.9 16.9 1.0 ND B:HEM519 1.9 15.3 1.0 NB B:HEM519 2.0 16.2 1.0 NE2 B:HIS336 2.0 20.7 1.0 NE2 B:HIS293 2.0 15.8 1.0 CE1 B:HIS336 2.9 24.7 1.0 C4A B:HEM519 3.0 16.1 1.0 CE1 B:HIS293 3.0 13.4 1.0 C1B B:HEM519 3.0 15.1 1.0 C1C B:HEM519 3.0 14.4 1.0 C1A B:HEM519 3.0 16.1 1.0 C4D B:HEM519 3.0 17.7 1.0 C1D B:HEM519 3.0 17.8 1.0 C4C B:HEM519 3.0 15.4 1.0 C4B B:HEM519 3.0 15.4 1.0 CD2 B:HIS293 3.0 12.6 1.0 CD2 B:HIS336 3.1 22.9 1.0 CHB B:HEM519 3.4 14.7 1.0 CHC B:HEM519 3.4 14.5 1.0 CHA B:HEM519 3.4 15.8 1.0 CHD B:HEM519 3.4 15.8 1.0 ND1 B:HIS336 4.1 24.1 1.0 ND1 B:HIS293 4.1 13.9 1.0 CG B:HIS293 4.2 12.1 1.0 CG B:HIS336 4.2 24.9 1.0 C3A B:HEM519 4.2 15.3 1.0 C2A B:HEM519 4.2 15.8 1.0 C2B B:HEM519 4.2 15.7 1.0 C2C B:HEM519 4.2 16.2 1.0 C3D B:HEM519 4.2 19.2 1.0 C2D B:HEM519 4.3 18.8 1.0 C3C B:HEM519 4.3 16.4 1.0 C3B B:HEM519 4.3 15.0 1.0 CBC B:HEM518 4.8 12.2 1.0

O.Einsle, A.Messerschmidt, P.Stach, G.P.Bourenkov, H.D.Bartunik, R.Huber, P.M.Kroneck. Structure of Cytochrome C Nitrite Reductase. Nature V. 400 476 1999.
ISSN: ISSN 0028-0836
PubMed: 10440380
DOI: 10.1038/22802