Iron in PDB 4b3w: Crystal Structure of Human Cytoglobin H(E7)Q Mutant

The structure of Crystal Structure of Human Cytoglobin H(E7)Q Mutant, PDB code: 4b3w was solved by M.Gabba, S.Abbruzzetti, F.Spyrakis, F.Forti, S.Bruno, A.Mozzarelli, F.J.Luque, C.Viappiani, P.Cozzini, M.Nardini, F.Germani, M.Bolognesi, L.Moens, S.Dewilde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.74 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.844, 70.054, 102.072, 90.00, 90.00, 90.00
R / Rfree (%)	20.658 / 27.727

The binding sites of Iron atom in the Crystal Structure of Human Cytoglobin H(E7)Q Mutant (pdb code 4b3w). 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 Human Cytoglobin H(E7)Q Mutant, PDB code: 4b3w:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Human Cytoglobin H(E7)Q Mutant


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 Human Cytoglobin H(E7)Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:26.5 occ:1.00 FE A:HEM200 0.0 26.5 1.0 NA A:HEM200 2.0 27.3 1.0 ND A:HEM200 2.1 28.2 1.0 NE2 A:HIS113 2.1 31.5 1.0 NB A:HEM200 2.1 24.5 1.0 NC A:HEM200 2.1 25.1 1.0 CE1 A:HIS113 2.9 32.0 1.0 C4A A:HEM200 3.0 27.0 1.0 C1B A:HEM200 3.1 25.1 1.0 C1D A:HEM200 3.1 28.5 1.0 C1A A:HEM200 3.1 28.9 1.0 C4D A:HEM200 3.1 30.4 1.0 C4C A:HEM200 3.1 25.8 1.0 C4B A:HEM200 3.1 23.8 1.0 C1C A:HEM200 3.1 24.5 1.0 CD2 A:HIS113 3.2 31.4 1.0 C A:CYN300 3.2 51.0 1.0 CHB A:HEM200 3.4 26.5 1.0 N A:CYN300 3.4 51.7 1.0 CHD A:HEM200 3.4 27.1 1.0 CHA A:HEM200 3.4 30.5 1.0 CHC A:HEM200 3.5 24.2 1.0 ND1 A:HIS113 4.1 32.8 1.0 CG A:HIS113 4.2 32.5 1.0 C3A A:HEM200 4.3 28.4 1.0 C2A A:HEM200 4.3 29.8 1.0 C2B A:HEM200 4.3 24.6 1.0 C2D A:HEM200 4.3 30.6 1.0 C3D A:HEM200 4.3 32.3 1.0 C3C A:HEM200 4.3 25.8 1.0 C3B A:HEM200 4.3 23.7 1.0 C2C A:HEM200 4.3 24.9 1.0 NE2 A:GLN81 4.7 31.5 1.0 CD2 A:HIS117 5.0 38.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Human Cytoglobin H(E7)Q Mutant


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 Human Cytoglobin H(E7)Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:52.5 occ:1.00 FE2 A:FC6400 0.0 52.5 1.0 C24 A:FC6400 1.8 55.5 1.0 C11 A:FC6400 1.8 51.9 1.0 C23 A:FC6400 1.8 54.7 1.0 C21 A:FC6400 1.8 49.7 1.0 C22 A:FC6400 1.8 53.9 1.0 C26 A:FC6400 1.8 50.8 1.0 N24 A:FC6400 3.0 57.9 1.0 N25 A:FC6400 3.0 47.8 1.0 N11 A:FC6400 3.0 51.9 1.0 N22 A:FC6400 3.0 54.6 1.0 N23 A:FC6400 3.0 56.7 1.0 N21 A:FC6400 3.0 47.8 1.0 NE A:ARG155 4.6 27.2 1.0 CB B:SER55 4.6 41.1 1.0 CZ A:ARG155 4.8 28.2 1.0 NH2 A:ARG155 4.8 28.5 1.0 OG B:SER55 4.9 39.4 1.0 CG A:LYS125 4.9 28.8 1.0 N B:SER55 4.9 39.0 1.0 CD B:PRO54 4.9 37.9 1.0 CE A:LYS125 5.0 31.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Human Cytoglobin H(E7)Q Mutant


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 Human Cytoglobin H(E7)Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:29.2 occ:1.00 FE B:HEM200 0.0 29.2 1.0 NE2 B:HIS113 2.0 30.4 1.0 NA B:HEM200 2.0 31.3 1.0 NB B:HEM200 2.1 28.2 1.0 ND B:HEM200 2.1 31.5 1.0 NC B:HEM200 2.1 28.3 1.0 C B:CYN300 2.9 44.5 1.0 CD2 B:HIS113 3.0 30.8 1.0 CE1 B:HIS113 3.0 31.7 1.0 C1A B:HEM200 3.1 34.1 1.0 C4D B:HEM200 3.1 33.9 1.0 C4A B:HEM200 3.1 31.6 1.0 C4B B:HEM200 3.1 27.2 1.0 C1D B:HEM200 3.1 31.9 1.0 C1B B:HEM200 3.1 28.7 1.0 C1C B:HEM200 3.1 26.7 1.0 C4C B:HEM200 3.1 29.4 1.0 CHA B:HEM200 3.4 35.0 1.0 CHB B:HEM200 3.4 30.4 1.0 CHC B:HEM200 3.5 26.2 1.0 CHD B:HEM200 3.5 31.1 1.0 N B:CYN300 3.6 45.0 1.0 ND1 B:HIS113 4.1 32.8 1.0 CG B:HIS113 4.2 32.3 1.0 C2A B:HEM200 4.3 36.1 1.0 C3A B:HEM200 4.3 34.3 1.0 C3D B:HEM200 4.3 35.7 1.0 C3B B:HEM200 4.3 27.8 1.0 C2B B:HEM200 4.3 27.8 1.0 C2D B:HEM200 4.3 34.5 1.0 C2C B:HEM200 4.3 26.5 1.0 C3C B:HEM200 4.4 28.2 1.0 NE2 B:GLN81 4.6 38.8 1.0 CD2 B:HIS117 5.0 34.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Human Cytoglobin H(E7)Q Mutant


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 Human Cytoglobin H(E7)Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:50.3 occ:1.00 FE2 B:FC6400 0.0 50.3 1.0 C21 B:FC6400 1.8 53.4 1.0 C11 B:FC6400 1.8 49.7 1.0 C22 B:FC6400 1.8 50.6 1.0 C23 B:FC6400 1.8 51.4 1.0 C26 B:FC6400 1.8 49.5 1.0 C24 B:FC6400 1.8 46.8 1.0 N11 B:FC6400 3.0 48.9 1.0 N22 B:FC6400 3.0 51.5 1.0 N25 B:FC6400 3.0 56.0 1.0 N23 B:FC6400 3.0 51.5 1.0 N24 B:FC6400 3.0 44.1 1.0 N21 B:FC6400 3.0 49.5 1.0 CB A:SER55 4.3 33.2 1.0 OG A:SER55 4.3 30.7 1.0 NE B:ARG155 4.5 30.4 1.0 CZ B:ARG155 4.7 31.1 1.0 N A:SER55 4.7 32.0 1.0 NH2 B:ARG155 4.8 31.6 1.0 CD A:PRO54 4.9 31.6 1.0 CE B:LYS125 4.9 31.3 1.0 CD B:ARG155 4.9 30.4 1.0 CG B:LYS125 5.0 28.8 1.0

M.Gabba, S.Abbruzzetti, F.Spyrakis, F.Forti, S.Bruno, A.Mozzarelli, F.J.Luque, C.Viappiani, P.Cozzini, M.Nardini, F.Germani, M.Bolognesi, L.Moens, S.Dewilde. Co Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin. Plos One V. 8 49770 2013.
ISSN: ISSN 1932-6203
PubMed: 23308092
DOI: 10.1371/JOURNAL.PONE.0049770