Iron in PDB 1urv: Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination

The structure of Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination, PDB code: 1urv was solved by D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.940, 70.429, 100.913, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.5

The binding sites of Iron atom in the Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination (pdb code 1urv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination, PDB code: 1urv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination


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 Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1172 b:18.6 occ:1.00 FE A:HEM1172 0.0 18.6 1.0 NE2 A:HIS113 2.0 17.1 1.0 NB A:HEM1172 2.0 18.4 1.0 NC A:HEM1172 2.0 18.1 1.0 ND A:HEM1172 2.0 18.7 1.0 NA A:HEM1172 2.1 19.0 1.0 NE2 A:HIS81 2.2 18.8 1.0 CE1 A:HIS113 2.8 20.3 1.0 C1B A:HEM1172 3.0 18.9 1.0 C4C A:HEM1172 3.0 19.7 1.0 C4B A:HEM1172 3.0 19.0 1.0 C1D A:HEM1172 3.0 19.1 1.0 C1C A:HEM1172 3.1 18.9 1.0 C4A A:HEM1172 3.1 20.3 1.0 C4D A:HEM1172 3.1 19.1 1.0 CD2 A:HIS81 3.1 17.4 1.0 CD2 A:HIS113 3.1 19.4 1.0 C1A A:HEM1172 3.1 19.0 1.0 CE1 A:HIS81 3.2 17.2 1.0 CHB A:HEM1172 3.4 21.3 1.0 CHD A:HEM1172 3.4 17.0 1.0 CHC A:HEM1172 3.4 18.0 1.0 CHA A:HEM1172 3.5 18.8 1.0 ND1 A:HIS113 4.0 19.4 1.0 CG A:HIS113 4.1 18.8 1.0 C2B A:HEM1172 4.2 18.4 1.0 C3C A:HEM1172 4.3 18.4 1.0 C3B A:HEM1172 4.3 18.0 1.0 C2C A:HEM1172 4.3 20.2 1.0 CG A:HIS81 4.3 18.5 1.0 C2D A:HEM1172 4.3 17.9 1.0 C3D A:HEM1172 4.3 20.5 1.0 C3A A:HEM1172 4.3 21.9 1.0 ND1 A:HIS81 4.3 16.4 1.0 C2A A:HEM1172 4.3 21.4 1.0 CG2 A:VAL85 4.7 18.8 1.0 CD2 A:HIS117 5.0 22.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination


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 Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1173 b:21.4 occ:1.00 FE2 A:FC61173 0.0 21.4 1.0 C26 A:FC61173 1.8 21.8 1.0 C21 A:FC61173 1.8 24.0 1.0 C11 A:FC61173 1.8 21.1 1.0 C24 A:FC61173 1.8 20.1 1.0 C23 A:FC61173 1.8 23.6 1.0 C22 A:FC61173 1.8 21.0 1.0 N21 A:FC61173 3.0 23.2 1.0 N11 A:FC61173 3.0 18.1 1.0 N25 A:FC61173 3.0 24.7 1.0 N24 A:FC61173 3.0 15.1 1.0 N22 A:FC61173 3.0 8.6 1.0 N23 A:FC61173 3.0 20.9 1.0 NE A:ARG155 4.4 13.5 1.0 OG B:SER55 4.7 18.9 1.0 CZ A:ARG155 4.7 15.1 1.0 CB B:SER55 4.7 19.4 1.0 NH2 A:ARG155 4.8 14.1 1.0 CD2 A:TYR159 4.9 21.5 1.0 N B:SER55 4.9 18.8 1.0 CD A:ARG155 4.9 15.0 1.0 O A:HOH2056 4.9 48.2 1.0 CD A:LYS125 5.0 23.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination


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 Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1172 b:20.9 occ:1.00 FE B:HEM1172 0.0 20.9 1.0 NC B:HEM1172 1.9 20.9 1.0 NA B:HEM1172 2.0 18.3 1.0 NB B:HEM1172 2.0 17.4 1.0 ND B:HEM1172 2.1 22.2 1.0 NE2 B:HIS113 2.2 36.9 1.0 NE2 B:HIS81 2.3 18.0 0.6 C1C B:HEM1172 3.0 18.9 1.0 C4C B:HEM1172 3.0 22.5 1.0 C4B B:HEM1172 3.0 18.7 1.0 C1A B:HEM1172 3.0 19.5 1.0 C4A B:HEM1172 3.1 19.1 1.0 C1B B:HEM1172 3.1 20.3 1.0 C4D B:HEM1172 3.1 19.0 1.0 C1D B:HEM1172 3.1 22.8 1.0 CE1 B:HIS113 3.2 40.8 1.0 CE1 B:HIS81 3.2 18.0 0.6 CD2 B:HIS113 3.2 37.5 1.0 CD2 B:HIS81 3.3 19.0 0.6 CHC B:HEM1172 3.3 16.1 1.0 CHA B:HEM1172 3.4 19.8 1.0 CHD B:HEM1172 3.4 23.3 1.0 CHB B:HEM1172 3.5 20.3 1.0 NE2 B:HIS81 4.1 18.9 0.5 C2C B:HEM1172 4.2 22.0 1.0 C3C B:HEM1172 4.2 23.7 1.0 C3B B:HEM1172 4.3 18.8 1.0 C2A B:HEM1172 4.3 20.1 1.0 C3A B:HEM1172 4.3 20.2 1.0 C2B B:HEM1172 4.3 18.7 1.0 ND1 B:HIS113 4.3 40.6 1.0 C3D B:HEM1172 4.3 22.1 1.0 ND1 B:HIS81 4.3 19.1 0.6 CG B:HIS113 4.3 31.6 1.0 C2D B:HEM1172 4.3 25.4 1.0 CG B:HIS81 4.4 18.7 0.6 CE1 B:HIS81 4.5 17.9 0.5 CD2 B:HIS117 4.6 29.8 1.0 CG2 B:VAL85 4.7 21.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination


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 Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1173 b:25.6 occ:1.00 FE2 B:FC61173 0.0 25.6 1.0 C24 B:FC61173 1.8 24.9 1.0 C22 B:FC61173 1.8 24.4 1.0 C21 B:FC61173 1.8 22.9 1.0 C11 B:FC61173 1.8 24.4 1.0 C23 B:FC61173 1.8 23.4 1.0 C26 B:FC61173 1.8 25.5 1.0 N25 B:FC61173 3.0 21.9 1.0 N22 B:FC61173 3.0 26.3 1.0 N24 B:FC61173 3.0 28.8 1.0 N21 B:FC61173 3.0 27.9 1.0 N23 B:FC61173 3.0 14.5 1.0 N11 B:FC61173 3.0 18.6 1.0 NE B:ARG155 4.4 18.6 1.0 CB A:SER55 4.4 17.4 1.0 CE B:LYS125 4.6 21.3 1.0 OG A:SER55 4.7 16.3 1.0 CZ B:ARG155 4.7 15.9 1.0 CD1 B:TYR159 4.8 24.7 1.0 N A:SER55 4.8 17.5 1.0 CG B:LYS125 4.8 18.8 1.0 CD B:ARG155 4.9 19.4 1.0 NH2 B:ARG155 4.9 14.1 1.0 CD A:PRO54 4.9 16.7 1.0

D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Crystal Structure of Cytoglobin: the Fourth Globin Type Discovered in Man Displays Heme Hexa-Coordination. J.Mol.Biol. V. 336 917 2004.
ISSN: ISSN 0022-2836
PubMed: 15095869
DOI: 10.1016/J.JMB.2003.12.063