Calcium in PDB 2r7e: Crystal Structure Analysis of Coagulation Factor VIII

The structure of Crystal Structure Analysis of Coagulation Factor VIII, PDB code: 2r7e was solved by B.L.Stoddard, B.W.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.37 / 3.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	134.569, 134.569, 359.496, 90.00, 90.00, 90.00
R / Rfree (%)	27.9 / 34.7

The structure of Crystal Structure Analysis of Coagulation Factor VIII also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Calcium atom in the Crystal Structure Analysis of Coagulation Factor VIII (pdb code 2r7e). 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 Analysis of Coagulation Factor VIII, PDB code: 2r7e:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure Analysis of Coagulation Factor VIII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Coagulation Factor VIII within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2400 b:0.9 occ:1.00 O A:ALA112 2.7 0.6 1.0 OD2 A:ASP126 2.9 0.0 1.0 OD1 A:ASP116 3.2 0.6 1.0 OD2 A:ASP116 3.4 0.6 1.0 CB A:ASP126 3.4 0.1 1.0 CG A:LYS123 3.5 0.1 1.0 C A:ALA112 3.5 0.6 1.0 CG A:ASP116 3.5 0.6 1.0 CG A:ASP126 3.6 0.6 1.0 CB A:LYS123 3.9 0.1 1.0 CA A:LYS123 4.0 0.6 1.0 N A:GLU113 4.2 0.4 1.0 CD A:LYS123 4.3 0.1 1.0 CA A:ALA112 4.3 0.6 1.0 O A:GLU122 4.3 0.1 1.0 N A:ALA112 4.3 0.6 1.0 CA A:GLU113 4.4 0.4 1.0 CB A:ALA112 4.4 83.3 1.0 O A:GLU110 4.5 0.1 1.0 CD2 A:TYR114 4.7 0.7 1.0 N A:TYR114 4.7 0.1 1.0 CE2 A:TYR114 4.7 0.0 1.0 CE A:LYS123 4.7 0.1 1.0 OD1 A:ASP126 4.7 0.6 1.0 O A:TYR114 4.7 0.1 1.0 CB A:ASP116 4.8 0.6 1.0 O A:ASP126 4.8 0.4 1.0 N A:LYS123 4.9 0.5 1.0 CA A:ASP126 4.9 0.5 1.0 C A:GLU122 5.0 0.1 1.0 C A:GLU113 5.0 0.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure Analysis of Coagulation Factor VIII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Coagulation Factor VIII within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2402 b:1.0 occ:1.00 OG A:SER535 2.8 0.0 1.0 O A:SER535 2.8 1.0 1.0 N A:GLU540 3.0 0.6 1.0 OD1 A:ASN538 3.1 0.4 1.0 O A:GLU540 3.1 0.7 1.0 OD1 A:ASP542 3.1 0.8 1.0 C A:GLU540 3.1 0.9 1.0 CA A:GLU540 3.2 0.9 1.0 C A:SER535 3.3 0.7 1.0 N A:PHE536 3.8 0.6 1.0 CA A:PHE536 3.8 0.3 1.0 CB A:ASP542 3.8 0.8 1.0 CG A:ASP542 3.9 0.9 1.0 C A:MET539 3.9 0.6 1.0 N A:ASP542 3.9 0.5 1.0 N A:ARG541 3.9 0.7 1.0 N A:LEU543 4.0 0.5 1.0 CB A:SER535 4.0 0.4 1.0 N A:MET539 4.2 0.6 1.0 CG A:ASN538 4.2 0.9 1.0 CA A:SER535 4.2 1.0 1.0 N A:VAL537 4.2 0.5 1.0 CA A:ASP542 4.4 0.5 1.0 C A:PHE536 4.4 0.8 1.0 CA A:MET539 4.5 0.6 1.0 CB A:LEU543 4.5 1.0 1.0 C A:ARG541 4.6 0.4 1.0 O A:MET539 4.7 0.6 1.0 N A:ASN538 4.7 0.6 1.0 N A:SER535 4.7 0.9 1.0 CA A:ARG541 4.8 0.4 1.0 C A:ASP542 4.8 0.9 1.0 ND2 A:ASN538 4.8 0.8 1.0 CB A:GLU540 4.8 0.6 1.0 CA A:LEU543 4.8 0.7 1.0 OG A:SER534 4.8 0.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure Analysis of Coagulation Factor VIII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Coagulation Factor VIII within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2401 b:0.3 occ:1.00 OD1 A:ASP126 2.4 0.6 1.0 CB A:ASP125 3.0 0.9 1.0 CA A:ALA108 3.0 0.1 1.0 C A:ALA108 3.1 0.1 1.0 O A:LYS107 3.4 0.2 1.0 O A:ALA108 3.4 0.1 1.0 N A:ASP125 3.5 0.3 1.0 N A:ASP126 3.6 0.8 1.0 CA A:ASP125 3.6 0.3 1.0 N A:SER109 3.6 0.9 1.0 C A:ASP125 3.6 0.3 1.0 CG A:ASP126 3.7 0.6 1.0 N A:ALA108 4.0 0.1 1.0 O A:GLU122 4.0 0.1 1.0 CB A:ALA108 4.1 72.0 1.0 C A:LYS107 4.1 0.1 1.0 CG A:ASP125 4.3 0.9 1.0 O A:ASP125 4.3 0.3 1.0 CA A:ASP126 4.4 0.5 1.0 C A:GLU122 4.4 0.1 1.0 OD2 A:ASP125 4.5 0.4 1.0 CA A:SER109 4.5 0.1 1.0 OD2 A:ASP126 4.5 0.0 1.0 CB A:ASP126 4.5 0.1 1.0 C A:GLU124 4.7 0.4 1.0 N A:GLU124 4.8 0.7 1.0 CA A:GLU122 4.9 0.1 1.0

B.W.Shen, P.C.Spiegel, C.H.Chang, J.W.Huh, J.S.Lee, J.Kim, Y.H.Kim, B.L.Stoddard. The Tertiary Structure and Domain Organization of Coagulation Factor VIII. Blood V. 111 1240 2008.
ISSN: ISSN 0006-4971
PubMed: 17965321
DOI: 10.1182/BLOOD-2007-08-109918