Calcium 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:

Copper

(Cu)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Rfviiifc (pdb code 5k8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Rfviiifc, PDB code: 5k8d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Rfviiifc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rfviiifc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca805 b:0.5 occ:1.00 OD2 A:ASP126 2.3 0.1 1.0 OD2 A:ASP116 2.9 0.9 1.0 CG A:ASP126 3.0 0.9 1.0 O A:GLU122 3.1 0.4 1.0 O A:ALA112 3.2 0.6 1.0 CB A:ASP126 3.3 0.8 1.0 CG A:LYS123 3.5 0.3 1.0 CG2 A:THR118 3.6 0.0 1.0 CG A:ASP116 3.7 0.6 1.0 CA A:LYS123 3.9 0.8 1.0 OD1 A:ASP116 4.0 0.4 1.0 C A:GLU122 4.0 0.5 1.0 O A:LYS107 4.0 0.8 1.0 OE2 A:GLU110 4.1 0.9 1.0 OD1 A:ASP126 4.1 0.8 1.0 CB A:LYS123 4.3 0.6 1.0 N A:LYS123 4.3 0.8 1.0 CB A:LYS107 4.3 0.2 1.0 C A:ALA112 4.5 0.1 1.0 CE A:LYS123 4.6 0.1 1.0 CD A:LYS123 4.7 0.9 1.0 CD A:LYS107 4.8 0.9 1.0 NZ A:LYS107 4.8 0.9 1.0 CA A:ASP126 4.8 0.8 1.0 CB A:THR118 4.8 0.2 1.0 CA A:LYS107 4.9 0.7 1.0 CB A:ASP116 4.9 0.6 1.0 C A:LYS107 4.9 0.6 1.0 CE A:LYS107 4.9 0.9 1.0 CG A:LYS107 4.9 0.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Rfviiifc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rfviiifc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca806 b:0.2 occ:1.00 O A:SER535 2.6 0.1 1.0 OD1 A:ASP542 3.0 0.1 1.0 OD1 A:ASN538 3.1 0.5 1.0 C A:MET539 3.4 0.9 1.0 N A:GLU540 3.5 0.1 1.0 C A:SER535 3.6 0.6 1.0 N A:ASP542 3.6 0.3 1.0 N A:MET539 3.6 0.4 1.0 CB A:ASP542 3.6 0.5 1.0 O A:MET539 3.6 0.1 1.0 CG A:ASP542 3.7 0.8 1.0 N A:LEU543 3.8 0.9 1.0 CA A:MET539 3.8 0.5 1.0 N A:VAL537 3.8 0.0 1.0 OG A:SER535 3.9 0.9 1.0 N A:ASN538 3.9 0.3 1.0 C A:GLU540 3.9 0.2 1.0 N A:ARG541 3.9 0.7 1.0 CA A:PHE536 4.0 0.1 1.0 CA A:ASP542 4.1 0.2 1.0 CA A:GLU540 4.1 0.3 1.0 CG A:ASN538 4.1 0.3 1.0 N A:PHE536 4.2 0.7 1.0 O A:GLU540 4.3 0.8 1.0 C A:ASN538 4.4 0.3 1.0 C A:PHE536 4.4 0.8 1.0 C A:ASP542 4.5 0.0 1.0 OG A:SER534 4.5 0.8 1.0 CA A:ASN538 4.6 0.5 1.0 CA A:SER535 4.6 0.8 1.0 C A:ARG541 4.6 0.3 1.0 CA A:VAL537 4.7 0.7 1.0 CB A:VAL537 4.7 0.4 1.0 CB A:LEU543 4.7 0.6 1.0 CB A:SER535 4.8 0.6 1.0 CA A:LEU543 4.8 0.2 1.0 CA A:ARG541 4.8 0.1 1.0 C A:VAL537 4.8 0.2 1.0 N A:SER535 4.8 0.5 1.0 CG2 A:VAL537 4.8 0.7 1.0 ND2 A:ASN538 4.8 0.8 1.0 OD2 A:ASP542 4.9 0.5 1.0 CB A:ASN538 4.9 0.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Rfviiifc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rfviiifc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca807 b:0.5 occ:1.00 OD1 A:ASP126 2.3 0.8 1.0 CA A:ALA108 2.7 0.8 1.0 O A:LYS107 2.7 0.8 1.0 O A:ALA108 2.8 1.0 1.0 C A:ALA108 3.1 0.1 1.0 CB A:ASP125 3.3 0.4 1.0 CG A:ASP126 3.4 0.9 1.0 N A:ASP126 3.4 0.1 1.0 N A:ALA108 3.5 0.6 1.0 C A:LYS107 3.5 0.6 1.0 O A:GLU122 3.5 0.4 1.0 N A:ASP125 3.5 0.9 1.0 C A:ASP125 3.7 0.2 1.0 CA A:ASP125 3.7 0.3 1.0 CB A:ALA108 3.7 0.3 1.0 C A:GLU122 3.9 0.5 1.0 OD2 A:ASP126 4.1 0.1 1.0 CB A:ASP126 4.2 0.8 1.0 CA A:GLU122 4.3 0.8 1.0 CA A:ASP126 4.3 0.8 1.0 O A:GLU110 4.3 0.2 1.0 N A:SER109 4.4 0.6 1.0 O A:ASP125 4.4 1.0 1.0 CG A:ASP125 4.5 0.8 1.0 OD2 A:ASP125 4.6 1.0 1.0 O A:ARG121 4.6 0.5 1.0 N A:GLU124 4.7 0.6 1.0 C A:GLU124 4.7 0.7 1.0 C A:LYS123 4.7 0.4 1.0 N A:LYS123 4.7 0.8 1.0 CA A:LYS107 4.9 0.7 1.0 CA A:LYS123 5.0 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