Copper in PDB 5k8d: Crystal Structure of Rfviiifc

The structure of Crystal Structure of Rfviiifc, PDB code: 5k8d was solved by N.Leksa, C.Quan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.60 / 4.19
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	136.295, 136.295, 365.098, 90.00, 90.00, 90.00
R / Rfree (%)	29.8 / 36.2

The structure of Crystal Structure of Rfviiifc also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Copper atom in the Crystal Structure of Rfviiifc (pdb code 5k8d). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Rfviiifc, PDB code: 5k8d:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Crystal Structure of Rfviiifc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Rfviiifc within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu808 b:0.5 occ:1.00 ND1 A:HIS315 1.9 0.4 1.0 CE1 A:HIS267 1.9 0.4 1.0 ND1 A:HIS267 2.1 0.8 1.0 SG A:CYS310 2.2 0.2 1.0 CG A:HIS315 2.5 0.5 1.0 NE2 A:HIS267 2.7 0.8 1.0 CB A:HIS315 2.8 0.4 1.0 CE1 A:HIS315 2.9 0.4 1.0 CG A:HIS267 3.1 0.8 1.0 CB A:CYS310 3.2 0.8 1.0 CD2 A:HIS267 3.4 0.4 1.0 CD2 A:HIS315 3.6 0.1 1.0 NE2 A:HIS315 3.7 0.4 1.0 ND1 A:HIS232 3.7 0.6 1.0 CE1 A:HIS232 4.0 0.0 1.0 CD1 A:ILE312 4.1 0.8 1.0 CA A:HIS315 4.1 0.4 1.0 CG A:MET320 4.2 0.8 1.0 CB A:HIS267 4.2 0.5 1.0 CG1 A:ILE312 4.3 0.9 1.0 CB A:MET320 4.4 0.0 1.0 CA A:CYS310 4.6 0.3 1.0 O A:VAL266 4.6 0.1 1.0 CA A:HIS267 4.7 0.8 1.0 C A:HIS315 4.8 0.3 1.0 SD A:MET320 4.8 0.0 1.0 CG A:HIS232 4.9 0.8 1.0 C A:CYS310 4.9 0.8 1.0

Copper binding site 2 out of 2 in the Crystal Structure of Rfviiifc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Rfviiifc within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2610 b:0.4 occ:1.00 SG B:CYS2000 1.9 0.0 1.0 ND1 B:HIS1954 2.0 0.9 1.0 ND1 B:HIS2005 2.7 0.1 1.0 CE1 B:HIS1954 2.8 0.2 1.0 CD1 B:ILE2002 2.9 0.4 1.0 CB B:HIS2005 2.9 0.1 1.0 CG B:HIS1954 3.2 0.6 1.0 CB B:CYS2000 3.2 0.4 1.0 CG B:HIS2005 3.2 0.8 1.0 CB B:ILE2002 3.6 0.5 1.0 CB B:HIS1954 3.7 0.2 1.0 CG1 B:ILE2002 3.7 1.0 1.0 CA B:HIS1954 3.8 0.2 1.0 CE1 B:HIS2005 3.9 0.4 1.0 NE2 B:HIS1954 4.0 0.7 1.0 SD B:MET2010 4.0 0.3 1.0 CD2 B:HIS1954 4.2 0.9 1.0 CG2 B:ILE2002 4.3 0.3 1.0 CA B:HIS2005 4.4 0.2 1.0 CD2 B:HIS2005 4.5 0.8 1.0 CA B:CYS2000 4.6 0.3 1.0 N B:HIS1954 4.6 0.8 1.0 N B:SER1955 4.7 0.0 1.0 N B:ILE2002 4.7 0.2 1.0 CA B:ILE2002 4.8 0.7 1.0 C B:HIS1954 4.8 0.5 1.0 NE2 B:HIS2005 4.8 0.2 1.0 CG B:MET2010 4.9 0.4 1.0 C B:CYS2000 4.9 0.9 1.0 C B:HIS2005 4.9 0.8 1.0

N.C.Leksa, P.L.Chiu, G.M.Bou-Assaf, C.Quan, Z.Liu, A.B.Goodman, M.G.Chambers, S.E.Tsutakawa, M.Hammel, R.T.Peters, T.Walz, J.D.Kulman. The Structural Basis For the Functional Comparability of Factor VIII and the Long-Acting Variant Recombinant Factor VIII Fc Fusion Protein. J. Thromb. Haemost. V. 15 1167 2017.
ISSN: ESSN 1538-7836
PubMed: 28397397
DOI: 10.1111/JTH.13700