Atomistry » Calcium » PDB 5k21-5kfu » 5k8d
Atomistry »
  Calcium »
    PDB 5k21-5kfu »
      5k8d »

Calcium in PDB 5k8d: Crystal Structure of Rfviiifc

Protein crystallography data

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

Other elements in 5k8d:

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

Copper (Cu) 2 atoms

Calcium Binding Sites:

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 5k8d

Go back to Calcium Binding Sites List in 5k8d
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 5k8d

Go back to Calcium Binding Sites List in 5k8d
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 5k8d

Go back to Calcium Binding Sites List in 5k8d
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

Reference:

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
Page generated: Sat Dec 12 05:33:03 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy