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Calcium in PDB 4ibl: Rubidium Sites in Blood Coagulation Factor Viia

Enzymatic activity of Rubidium Sites in Blood Coagulation Factor Viia

All present enzymatic activity of Rubidium Sites in Blood Coagulation Factor Viia:
3.4.21.21;

Protein crystallography data

The structure of Rubidium Sites in Blood Coagulation Factor Viia, PDB code: 4ibl was solved by K.Vadivel, A.Schmidt, D.Cascio, K.Padmanabhan, S.P.Bajaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.24 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.900, 81.060, 126.420, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.5

Other elements in 4ibl:

The structure of Rubidium Sites in Blood Coagulation Factor Viia also contains other interesting chemical elements:

Rubidium (Rb) 6 atoms
Magnesium (Mg) 3 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rubidium Sites in Blood Coagulation Factor Viia (pdb code 4ibl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Rubidium Sites in Blood Coagulation Factor Viia, PDB code: 4ibl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4ibl

Go back to Calcium Binding Sites List in 4ibl
Calcium binding site 1 out of 4 in the Rubidium Sites in Blood Coagulation Factor Viia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rubidium Sites in Blood Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca204

b:60.5
occ:1.00
O L:HOH342 2.3 41.8 1.0
O L:HOH422 2.4 35.6 1.0
OE12 L:CGU29 2.7 28.1 1.0
RB L:RB205 2.9 48.7 0.7
O L:HOH344 2.9 38.2 1.0
OE21 L:CGU26 3.0 32.1 1.0
OE11 L:CGU29 3.1 28.5 1.0
CD1 L:CGU29 3.2 27.8 1.0
O L:HOH340 3.3 36.3 1.0
CD2 L:CGU26 3.9 27.4 1.0
OE22 L:CGU26 4.1 22.2 1.0
O L:HOH339 4.7 31.1 1.0
CG L:CGU29 4.8 24.9 1.0
OE12 L:CGU25 4.9 31.7 1.0

Calcium binding site 2 out of 4 in 4ibl

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Calcium binding site 2 out of 4 in the Rubidium Sites in Blood Coagulation Factor Viia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rubidium Sites in Blood Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca208

b:71.3
occ:1.00
O L:HOH402 2.3 37.6 1.0
OE21 L:CGU20 2.3 42.6 1.0
OE12 L:CGU20 2.4 44.2 1.0
O L:HOH403 2.4 47.3 1.0
O L:HOH404 2.9 42.2 1.0
CD1 L:CGU20 3.2 41.3 1.0
OE21 L:CGU6 3.2 43.6 1.0
CD2 L:CGU20 3.3 40.2 1.0
O L:HOH427 3.6 39.6 1.0
CG L:CGU20 3.7 40.1 1.0
CD2 L:CGU6 3.9 42.9 1.0
OE11 L:CGU20 4.1 43.2 1.0
OE22 L:CGU6 4.3 45.8 1.0
OE11 L:CGU6 4.3 43.3 1.0
O L:HOH428 4.4 42.3 1.0
OE22 L:CGU20 4.4 43.1 1.0
O L:ARG15 4.9 30.0 1.0
CG L:CGU6 4.9 35.5 1.0

Calcium binding site 3 out of 4 in 4ibl

Go back to Calcium Binding Sites List in 4ibl
Calcium binding site 3 out of 4 in the Rubidium Sites in Blood Coagulation Factor Viia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rubidium Sites in Blood Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca210

b:21.0
occ:1.00
O L:GLN64 2.3 21.2 1.0
OD2 L:ASP46 2.4 20.5 1.0
OE1 L:GLN49 2.4 26.2 1.0
OD2 L:ASP63 2.5 27.6 1.0
O L:HOH336 2.5 23.2 1.0
O L:GLY47 2.5 23.8 1.0
O T:HOH428 2.5 21.2 1.0
OD1 L:ASP63 2.6 25.6 1.0
CG L:ASP63 2.8 26.3 1.0
C L:GLN64 3.5 20.6 1.0
CD L:GLN49 3.5 28.8 1.0
CG L:ASP46 3.6 23.3 1.0
C L:GLY47 3.7 26.7 1.0
NE2 L:GLN49 4.0 25.5 1.0
N L:GLN66 4.1 22.9 1.0
CB L:ASP46 4.1 23.5 1.0
N L:GLN49 4.2 24.7 1.0
N L:GLN64 4.2 20.6 1.0
CA L:LEU65 4.2 23.1 1.0
N L:LEU65 4.3 21.5 1.0
CA L:ASP48 4.3 27.8 1.0
CB L:ASP63 4.4 20.3 1.0
O L:HOH414 4.4 39.5 1.0
CA L:GLN64 4.5 20.4 1.0
N L:ASP48 4.5 26.6 1.0
C L:LEU65 4.6 23.9 1.0
OD1 L:ASP46 4.6 27.7 1.0
C L:ASP46 4.6 24.2 1.0
N L:GLY47 4.7 24.6 1.0
O L:SER67 4.7 19.5 1.0
O L:ASP46 4.7 26.1 1.0
C L:ASP48 4.8 26.9 1.0
C L:ASP63 4.8 21.2 1.0
CA L:GLY47 4.8 25.6 1.0
CG L:GLN49 4.8 26.2 1.0
O L:HOH365 5.0 36.8 1.0
OE1 T:GLN110 5.0 19.4 1.0
O L:HOH426 5.0 29.6 1.0

Calcium binding site 4 out of 4 in 4ibl

Go back to Calcium Binding Sites List in 4ibl
Calcium binding site 4 out of 4 in the Rubidium Sites in Blood Coagulation Factor Viia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rubidium Sites in Blood Coagulation Factor Viia within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca302

b:27.4
occ:1.00
OE2 H:GLU80 2.0 21.5 1.0
OE1 H:GLU70 2.2 15.0 1.0
O H:GLU75 2.2 19.6 1.0
O H:HOH469 2.2 20.4 1.0
O H:ASP72 2.3 14.7 1.0
O H:HOH429 2.3 13.2 1.0
CD H:GLU70 3.0 20.2 1.0
CD H:GLU80 3.1 23.2 1.0
OE2 H:GLU70 3.3 19.9 1.0
C H:GLU75 3.3 21.5 1.0
C H:ASP72 3.4 13.5 1.0
OE1 H:GLU80 3.8 23.3 1.0
N H:ASP72 3.8 14.6 1.0
CA H:HIS76 3.9 23.1 1.0
N H:HIS76 4.1 20.0 1.0
CG H:GLU80 4.2 17.9 1.0
CA H:ASP72 4.2 14.3 1.0
N H:GLU75 4.2 18.8 1.0
O H:HOH433 4.2 17.1 1.0
O H:HOH519 4.3 28.6 1.0
N H:LEU73 4.3 12.8 1.0
CA H:LEU73 4.3 14.4 1.0
N H:HIS71 4.4 12.4 1.0
CA H:GLU75 4.4 21.3 1.0
CG H:GLU70 4.4 17.3 1.0
CB H:ASP72 4.6 15.1 1.0
N H:ASP77 4.6 20.4 1.0
C H:LEU73 4.6 17.6 1.0
ND1 H:HIS76 4.6 28.7 1.0
C H:HIS76 4.7 23.1 1.0
C H:HIS71 4.9 13.9 1.0
CA H:GLU70 5.0 13.2 1.0
CB H:GLU75 5.0 22.2 1.0

Reference:

K.Vadivel, A.Schmidt, D.Cascio, K.Padmanabhan, S.P.Bajaj. Sodium Site in Blood Coagulation Factor Viia: Absence of Occupancy By Rubidium To Be Published.
Page generated: Sat Dec 12 04:51:37 2020

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