Calcium in PDB 6mv4: Crystal Structure of Human Coagulation Factor Ixa

Enzymatic activity of Crystal Structure of Human Coagulation Factor Ixa

All present enzymatic activity of Crystal Structure of Human Coagulation Factor Ixa:
3.4.21.22;

Protein crystallography data

The structure of Crystal Structure of Human Coagulation Factor Ixa, PDB code: 6mv4 was solved by K.Vadivel, H.A.Schreuder, A.Liesum, S.P.Bajaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.64 / 1.37
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.758, 109.758, 112.458, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21

Other elements in 6mv4:

The structure of Crystal Structure of Human Coagulation Factor Ixa also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Coagulation Factor Ixa (pdb code 6mv4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human Coagulation Factor Ixa, PDB code: 6mv4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6mv4

Go back to Calcium Binding Sites List in 6mv4
Calcium binding site 1 out of 2 in the Crystal Structure of Human Coagulation Factor Ixa


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 Human Coagulation Factor Ixa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca311

b:17.7
occ:0.56
 CA H:CA311 0.0 17.7 0.6
OE2 H:GLU80 2.0 16.4 0.5
CA H:CA311 2.0 11.8 0.4
O H:GLU75 2.3 19.1 0.5
O H:HOH411 2.4 33.7 1.0
O H:GLU75 2.4 15.7 0.5
O H:ASN72 2.5 28.0 1.0
OE2 H:GLU77 2.6 16.6 0.5
OE2 H:GLU70 2.7 29.1 1.0
OE1 H:GLU70 2.9 30.0 1.0
CD H:GLU80 3.1 17.4 0.5
CD H:GLU70 3.1 28.6 1.0
CD H:GLU77 3.5 17.2 0.5
C H:GLU75 3.5 19.1 0.5
OE2 H:GLU80 3.6 16.7 0.5
C H:ASN72 3.6 25.7 1.0
C H:GLU75 3.6 17.3 0.5
C H:ILE73 3.6 23.1 0.5
CA H:ILE73 3.7 23.9 0.5
O H:ILE73 3.8 23.6 0.5
CG H:GLU80 3.8 17.4 0.5
N H:GLU75 3.8 18.9 0.5
N H:GLU77 3.8 16.9 0.5
CA H:ILE73 3.9 26.1 0.5
CG H:GLU77 3.9 16.8 0.5
N H:GLU74 4.0 21.5 0.5
OE1 H:GLU80 4.0 18.1 0.5
CA H:THR76 4.1 18.1 0.5
N H:ILE73 4.1 24.1 0.5
O H:HOH417 4.1 45.5 1.0
N H:ILE73 4.2 25.5 0.5
C H:ILE73 4.2 26.6 0.5
CB H:GLU77 4.2 16.7 0.5
C H:THR76 4.3 16.9 0.5
N H:THR76 4.3 17.6 0.5
N H:GLU75 4.3 21.0 0.5
CA H:GLU75 4.4 18.2 0.5
CD H:GLU80 4.4 18.0 0.5
CG H:GLU80 4.5 17.6 0.5
OE1 H:GLU77 4.5 16.9 0.5
OE2 H:GLU77 4.5 15.9 0.5
OE1 H:GLU77 4.5 18.3 0.5
CA H:GLU75 4.5 20.5 0.5
O H:ILE73 4.5 27.2 0.5
CG H:GLU70 4.6 27.2 1.0
N H:THR76 4.6 15.9 0.5
C H:GLU74 4.6 20.2 0.5
CA H:GLU77 4.7 17.0 0.5
CA H:GLU74 4.7 20.9 0.5
O H:HOH446 4.8 36.6 1.0
N H:ASN72 4.8 26.6 1.0
CA H:THR76 4.8 15.2 0.5
CA H:ASN72 4.8 25.4 1.0
N H:GLU74 4.8 25.1 0.5
CD H:GLU77 4.9 15.9 0.5
CB H:ILE73 5.0 23.5 0.5

Calcium binding site 2 out of 2 in 6mv4

Go back to Calcium Binding Sites List in 6mv4
Calcium binding site 2 out of 2 in the Crystal Structure of Human Coagulation Factor Ixa


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 Human Coagulation Factor Ixa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca311

b:11.8
occ:0.44
 CA H:CA311 0.0 11.8 0.4
OE2 H:GLU77 0.7 16.6 0.5
CD H:GLU77 1.7 17.2 0.5
CA H:CA311 2.0 17.7 0.6
OE2 H:GLU80 2.3 16.7 0.5
OE2 H:GLU70 2.4 29.1 1.0
O H:GLU75 2.4 15.7 0.5
CG H:GLU77 2.5 16.8 0.5
O H:ASN72 2.5 28.0 1.0
OE2 H:GLU77 2.5 15.9 0.5
OE1 H:GLU77 2.7 16.9 0.5
OE1 H:GLU77 2.8 18.3 0.5
CB H:GLU77 2.8 16.7 0.5
CD H:GLU77 2.9 15.9 0.5
OE2 H:GLU80 3.0 16.4 0.5
O H:GLU75 3.3 19.1 0.5
C H:GLU75 3.3 17.3 0.5
CD H:GLU80 3.4 18.0 0.5
CD H:GLU70 3.5 28.6 1.0
C H:ASN72 3.5 25.7 1.0
N H:ASN72 3.7 26.6 1.0
N H:GLU77 3.7 16.9 0.5
CG H:GLU80 3.8 17.6 0.5
CA H:GLU77 3.9 17.0 0.5
OE1 H:GLU70 3.9 30.0 1.0
CD H:GLU80 3.9 17.4 0.5
CA H:THR76 4.0 15.2 0.5
CG H:GLU80 4.1 17.4 0.5
N H:HIS71 4.1 27.1 1.0
N H:THR76 4.1 15.9 0.5
CA H:ASN72 4.2 25.4 1.0
N H:GLU77 4.2 15.4 0.5
N H:GLU75 4.3 18.9 0.5
CG H:GLU77 4.3 15.9 0.5
CA H:GLU75 4.3 18.2 0.5
O H:HOH411 4.4 33.7 1.0
C H:THR76 4.5 16.9 0.5
C H:GLU75 4.5 19.1 0.5
OE1 H:GLU80 4.5 17.4 0.5
C H:THR76 4.5 14.9 0.5
N H:ILE73 4.5 24.1 0.5
N H:ILE73 4.6 25.5 0.5
CB H:ASN72 4.6 27.9 1.0
C H:HIS71 4.6 27.0 1.0
CG H:GLU70 4.7 27.2 1.0
CA H:ILE73 4.7 23.9 0.5
CB H:GLU75 4.8 19.6 0.5
CB H:GLU77 4.8 16.1 0.5
CA H:GLU70 4.8 26.2 1.0
CA H:HIS71 4.8 26.5 1.0
C H:GLU77 4.8 17.6 0.5
CA H:THR76 4.9 18.1 0.5
CA H:ILE73 4.9 26.1 0.5
O H:GLU77 5.0 17.9 0.5
C H:GLU70 5.0 25.6 1.0
C H:ILE73 5.0 23.1 0.5

Reference:

K.Vadivel, H.A.Schreuder, A.Liesum, A.E.Schmidt, G.Goldsmith, S.P.Bajaj. Sodium-Site in Serine Protease Domain of Human Coagulation Factor Ixa: Evidence From the Crystal Structure and Molecular Dynamics Simulations Study. J. Thromb. Haemost. V. 17 574 2019.
ISSN: ESSN 1538-7836
PubMed: 30725510
DOI: 10.1111/JTH.14401
Page generated: Sat Dec 12 07:13:45 2020

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