Iron in PDB 6jp1: An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links

The structure of An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links, PDB code: 6jp1 was solved by Y.W.Lin, H.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.44 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.406, 33.604, 72.886, 90.00, 117.87, 90.00
R / Rfree (%)	17.1 / 22

The binding sites of Iron atom in the An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links (pdb code 6jp1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links, PDB code: 6jp1:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:12.2 occ:1.00 FE A:HEM201 0.0 12.2 1.0 ND A:HEM201 2.1 12.8 1.0 NC A:HEM201 2.1 12.5 1.0 NB A:HEM201 2.1 11.5 1.0 NA A:HEM201 2.1 11.9 1.0 NE2 A:HIS93 2.1 11.1 1.0 O A:HOH323 2.2 16.5 1.0 C1D A:HEM201 3.0 12.7 1.0 C4B A:HEM201 3.0 11.7 1.0 C1C A:HEM201 3.1 12.2 1.0 C1A A:HEM201 3.1 12.3 1.0 C4C A:HEM201 3.1 12.7 1.0 C4D A:HEM201 3.1 13.3 1.0 CE1 A:HIS93 3.1 11.1 1.0 C4A A:HEM201 3.1 11.9 1.0 CD2 A:HIS93 3.1 12.0 1.0 C1B A:HEM201 3.1 11.7 1.0 CHD A:HEM201 3.4 13.0 1.0 CHC A:HEM201 3.4 11.6 1.0 CHA A:HEM201 3.4 12.8 1.0 CHB A:HEM201 3.5 11.5 1.0 O A:HOH359 3.9 27.8 1.0 C2D A:HEM201 4.2 13.0 1.0 ND1 A:HIS93 4.2 11.8 1.0 CG A:HIS93 4.3 12.5 1.0 C3B A:HEM201 4.3 11.9 1.0 C3D A:HEM201 4.4 14.3 1.0 C3C A:HEM201 4.4 12.4 1.0 C2C A:HEM201 4.4 12.1 1.0 C2A A:HEM201 4.4 13.4 1.0 C2B A:HEM201 4.4 11.8 1.0 C3A A:HEM201 4.4 12.7 1.0 CG2 A:VAL68 4.6 18.9 1.0 CE1 A:HIS64 4.6 32.0 1.0 NE2 A:HIS64 4.9 32.0 1.0

Iron binding site 2 out of 2 in the An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of An X-Ray Structure of Met Sperm Whale F43Y/T67R Myoglobin with Tyr- Heme Double Cross-Links within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:11.7 occ:1.00 FE B:HEM1001 0.0 11.7 1.0 NC B:HEM1001 2.1 12.3 1.0 NA B:HEM1001 2.1 11.5 1.0 ND B:HEM1001 2.1 12.0 1.0 NB B:HEM1001 2.1 11.2 1.0 NE2 B:HIS93 2.1 12.3 1.0 O B:HOH1112 2.2 19.7 1.0 C4B B:HEM1001 3.0 10.8 1.0 C1D B:HEM1001 3.0 12.5 1.0 C1C B:HEM1001 3.1 12.0 1.0 C1A B:HEM1001 3.1 11.6 1.0 C4C B:HEM1001 3.1 13.2 1.0 CD2 B:HIS93 3.1 12.9 1.0 C4D B:HEM1001 3.1 12.3 1.0 C4A B:HEM1001 3.1 11.2 1.0 C1B B:HEM1001 3.2 11.5 1.0 CE1 B:HIS93 3.2 13.2 1.0 CHC B:HEM1001 3.4 11.3 1.0 CHD B:HEM1001 3.4 12.9 1.0 CHA B:HEM1001 3.5 12.1 1.0 CHB B:HEM1001 3.5 11.5 1.0 O B:HOH1155 4.1 27.2 1.0 C3B B:HEM1001 4.2 11.0 1.0 CG B:HIS93 4.3 12.4 1.0 ND1 B:HIS93 4.3 12.1 1.0 C2D B:HEM1001 4.3 12.8 1.0 C3D B:HEM1001 4.4 12.8 1.0 C3C B:HEM1001 4.4 13.5 1.0 C2C B:HEM1001 4.4 12.8 1.0 C2A B:HEM1001 4.4 11.8 1.0 C2B B:HEM1001 4.4 11.2 1.0 C3A B:HEM1001 4.4 11.8 1.0 CE1 B:HIS64 4.5 22.9 1.0 CG2 B:VAL68 4.5 14.0 1.0 NE2 B:HIS64 4.8 24.9 1.0

C.Liu, H.Yuan, F.Liao, C.W.Wei, K.J.Du, S.Q.Gao, X.Tan, Y.W.Lin. Unique Tyr-Heme Double Cross-Links in F43Y/T67R Myoglobin: An Artificial Enzyme with A Peroxidase Activity Comparable to That of Native Peroxidases. Chem.Commun.(Camb.) V. 55 6610 2019.
ISSN: ESSN 1364-548X
PubMed: 31119219
DOI: 10.1039/C9CC02714A