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Calcium in PDB 6f39: C1R Homodimer CUB1-Egf-CUB2

Enzymatic activity of C1R Homodimer CUB1-Egf-CUB2

All present enzymatic activity of C1R Homodimer CUB1-Egf-CUB2:
3.4.21.41;

Protein crystallography data

The structure of C1R Homodimer CUB1-Egf-CUB2, PDB code: 6f39 was solved by J.O.M.Almitairi, U.Venkatraman Girija, C.M.Furze, X.Simpson-Gray, F.Badakshi, J.E.Marshall, D.A.Mitchell, P.C.E.Moody, R.Wallis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.06 / 5.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.563, 54.620, 138.180, 90.00, 99.90, 90.00
R / Rfree (%) 30.8 / 33.8

Other elements in 6f39:

The structure of C1R Homodimer CUB1-Egf-CUB2 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the C1R Homodimer CUB1-Egf-CUB2 (pdb code 6f39). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the C1R Homodimer CUB1-Egf-CUB2, PDB code: 6f39:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6f39

Go back to Calcium Binding Sites List in 6f39
Calcium binding site 1 out of 6 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:0.2
occ:1.00
 O A:SER104 2.5 0.5 1.0
OD1 A:ASP57 2.7 0.3 1.0
CG2 A:THR101 2.7 0.9 1.0
OD2 A:ASP57 2.8 0.7 1.0
CG A:ASP57 3.1 0.5 1.0
C A:SER104 3.1 0.3 1.0
OD1 A:ASN105 3.2 0.7 1.0
N A:ASN105 3.3 0.1 1.0
CA A:ASN105 3.4 0.1 1.0
OD1 A:ASP102 3.4 0.9 1.0
O A:ASP102 3.7 0.9 1.0
CB A:ASN105 3.8 0.4 1.0
CG A:ASN105 3.9 0.3 1.0
CB A:THR101 3.9 0.5 1.0
CE1 A:TYR21 3.9 0.3 1.0
OG1 A:THR101 4.1 0.7 1.0
N A:ASP102 4.2 0.4 1.0
CA A:SER104 4.3 0.6 1.0
N A:SER104 4.3 0.9 1.0
OE1 A:GLU49 4.4 0.5 1.0
CA A:THR101 4.4 0.9 1.0
OH A:TYR21 4.4 0.9 1.0
C A:ASP102 4.4 0.3 1.0
OD1 A:ASN23 4.5 0.0 1.0
OE2 A:GLU107 4.5 0.8 1.0
C A:THR101 4.5 0.1 1.0
CG A:ASN23 4.5 0.2 1.0
CB A:ASP57 4.6 0.6 1.0
CG A:ASP102 4.6 0.2 1.0
CZ A:TYR21 4.7 0.9 1.0
C A:ASN105 4.7 0.7 1.0
CB A:ASN23 4.8 0.8 1.0
CD1 A:TYR21 4.9 0.4 1.0
CA A:ASP102 4.9 0.7 1.0
ND2 A:ASN23 4.9 0.1 1.0
C A:PHE103 5.0 0.1 1.0

Calcium binding site 2 out of 6 in 6f39

Go back to Calcium Binding Sites List in 6f39
Calcium binding site 2 out of 6 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:0.5
occ:1.00
 O A:GLY154 2.2 0.3 1.0
O A:TYR151 2.2 0.9 1.0
OD1 A:ASP127 2.2 0.0 1.0
OD2 A:ASP127 2.3 0.9 1.0
CG A:ASP127 2.5 0.7 1.0
C A:GLY154 2.9 0.8 1.0
N A:GLY154 3.2 0.7 1.0
CA A:GLY154 3.2 0.0 1.0
OD1 A:ASP125 3.2 0.5 1.0
O A:LEU126 3.4 0.4 1.0
C A:TYR151 3.4 0.6 1.0
CB A:ASP127 3.9 0.3 1.0
N A:TYR151 4.0 0.4 1.0
N A:TYR155 4.0 0.1 1.0
CG A:ASP125 4.1 0.4 1.0
C A:LEU126 4.2 0.4 1.0
N A:GLY153 4.2 0.4 1.0
OD2 A:ASP125 4.3 0.2 1.0
CA A:TYR151 4.3 0.4 1.0
N A:VAL152 4.4 0.5 1.0
CA A:ASP127 4.4 0.5 1.0
C A:GLY153 4.4 0.3 1.0
CB A:TYR155 4.5 0.4 1.0
CA A:VAL152 4.6 0.5 1.0
CA A:TYR155 4.6 0.1 1.0
N A:ASP127 4.6 0.3 1.0
OD1 A:ASN150 4.7 0.0 1.0
C A:VAL152 4.8 0.9 1.0
CD1 A:TYR155 4.9 0.5 1.0
CA A:GLY153 5.0 0.9 1.0

Calcium binding site 3 out of 6 in 6f39

Go back to Calcium Binding Sites List in 6f39
Calcium binding site 3 out of 6 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:0.3
occ:1.00
 OD2 A:ASP226 2.4 0.6 1.0
N A:ASP277 3.1 0.3 1.0
CG A:ASP226 3.2 0.4 1.0
O A:SER275 3.2 0.7 1.0
OD2 A:ASP277 3.4 0.1 1.0
OD2 A:ASP273 3.4 0.7 1.0
OH A:TYR197 3.4 0.5 1.0
CB A:ASP226 3.5 0.0 1.0
CG A:ASP277 3.6 0.4 1.0
CB A:ASP277 3.7 0.9 1.0
CA A:ASP277 3.9 0.3 1.0
OG A:SER278 3.9 0.1 1.0
C A:GLY276 4.0 0.6 1.0
CA A:GLY276 4.0 0.8 1.0
N A:SER278 4.0 0.7 1.0
OD1 A:ASP226 4.2 0.7 1.0
C A:SER275 4.2 0.2 1.0
OD1 A:ASP277 4.4 0.2 1.0
CZ A:TYR197 4.4 0.9 1.0
C A:ASP277 4.4 0.2 1.0
CG A:ASP273 4.5 0.2 1.0
N A:GLY276 4.6 0.9 1.0
CE2 A:TYR197 4.6 0.2 1.0
CB A:SER278 4.8 0.6 1.0
CA A:ASP226 4.8 0.9 1.0
OD1 A:ASP273 4.9 0.9 1.0

Calcium binding site 4 out of 6 in 6f39

Go back to Calcium Binding Sites List in 6f39
Calcium binding site 4 out of 6 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:0.0
occ:1.00
 OD1 B:ASN23 2.6 0.6 1.0
CG2 B:THR101 2.7 0.1 1.0
CB B:ASN105 2.8 0.6 1.0
CG B:ASN23 2.9 0.2 1.0
CG B:ASN105 3.0 0.7 1.0
ND2 B:ASN105 3.1 0.3 1.0
OD2 B:ASP57 3.1 0.9 1.0
ND2 B:ASN23 3.2 0.6 1.0
CE1 B:TYR21 3.3 0.6 1.0
N B:ASN105 3.5 0.2 1.0
CA B:ASN105 3.6 0.0 1.0
O B:ASP102 3.7 0.9 1.0
CB B:ASN23 3.8 0.3 1.0
CD1 B:TYR21 3.8 0.9 1.0
OD1 B:ASN105 3.9 0.3 1.0
CG B:ASP57 3.9 0.1 1.0
OD1 B:ASP102 4.0 0.1 1.0
OD1 B:ASP57 4.0 0.2 1.0
CB B:THR101 4.0 0.4 1.0
C B:SER104 4.1 0.5 1.0
OG1 B:THR101 4.2 0.8 1.0
O B:SER104 4.3 0.6 1.0
CA B:ASN23 4.3 0.8 1.0
CZ B:TYR21 4.4 0.5 1.0
OH B:TYR21 4.6 0.3 1.0
OE1 B:GLU49 4.7 0.1 1.0
N B:ASP102 4.7 0.8 1.0
C B:ASP102 4.7 0.6 1.0
CA B:THR101 4.8 0.4 1.0
C B:THR101 4.8 0.1 1.0
N B:ASN23 4.9 0.4 1.0
N B:SER104 5.0 0.2 1.0

Calcium binding site 5 out of 6 in 6f39

Go back to Calcium Binding Sites List in 6f39
Calcium binding site 5 out of 6 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:0.5
occ:1.00
 OD1 B:ASP127 2.1 0.7 1.0
O B:GLY154 2.3 0.2 1.0
CA B:ASP127 2.5 0.0 1.0
O B:LEU126 2.5 0.1 1.0
C B:GLY154 2.8 0.5 1.0
CG B:ASP127 2.9 0.4 1.0
CB B:ASP127 3.1 0.6 1.0
C B:LEU126 3.3 0.5 1.0
N B:ASP127 3.3 0.0 1.0
CA B:GLY154 3.3 0.3 1.0
N B:GLU128 3.4 0.6 1.0
C B:ASP127 3.4 0.5 1.0
CD1 B:TYR155 3.5 0.5 1.0
CB B:TYR155 3.6 0.6 1.0
N B:TYR155 3.6 0.8 1.0
O B:TYR151 3.7 0.8 1.0
CG B:TYR155 3.9 0.3 1.0
N B:GLY154 4.0 0.7 1.0
OD2 B:ASP127 4.1 0.2 1.0
CA B:TYR155 4.1 0.9 1.0
N B:TYR151 4.3 0.2 1.0
CE1 B:TYR155 4.5 0.5 1.0
O B:ASP127 4.6 0.0 1.0
CA B:LEU126 4.7 0.8 1.0
CA B:GLU128 4.8 0.1 1.0
C B:TYR151 4.8 0.6 1.0
CA B:ASN150 4.9 0.2 1.0

Calcium binding site 6 out of 6 in 6f39

Go back to Calcium Binding Sites List in 6f39
Calcium binding site 6 out of 6 in the C1R Homodimer CUB1-Egf-CUB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of C1R Homodimer CUB1-Egf-CUB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:0.1
occ:1.00
 OH B:TYR197 2.2 0.3 1.0
OD2 B:ASP273 2.2 0.7 1.0
CB B:ASP226 2.7 0.6 1.0
OD2 B:ASP226 2.9 0.4 1.0
CG B:ASP273 3.1 0.7 1.0
OD2 B:ASP236 3.2 0.7 1.0
CG B:ASP226 3.2 1.0 1.0
OD1 B:ASP273 3.3 0.1 1.0
O B:SER275 3.4 0.3 1.0
CZ B:TYR197 3.5 0.8 1.0
CG B:ASP236 3.7 0.3 1.0
CB B:TYR235 4.0 0.7 1.0
CA B:ASP226 4.0 0.7 1.0
OD1 B:ASP236 4.0 0.9 1.0
CE2 B:TYR197 4.2 0.5 1.0
N B:ASP226 4.3 0.0 1.0
CB B:ASP273 4.4 0.9 1.0
CE1 B:TYR197 4.5 0.7 1.0
OD1 B:ASP226 4.5 0.7 1.0
C B:SER275 4.5 0.1 1.0
O B:ASP226 4.6 0.2 1.0
CA B:GLY276 4.6 0.6 1.0
CB B:ASP236 4.6 0.3 1.0
N B:ASP236 4.6 0.5 1.0
C B:ASP226 4.7 0.7 1.0
CG B:TYR235 4.7 0.4 1.0
N B:ASP277 4.7 0.5 1.0
CD2 B:TYR235 5.0 0.9 1.0
OG B:SER278 5.0 0.1 1.0

Reference:

J.O.M.Almitairi, U.Venkatraman Girija, C.M.Furze, X.Simpson-Gray, F.Badakshi, J.E.Marshall, W.J.Schwaeble, D.A.Mitchell, P.C.E.Moody, R.Wallis. Structure of the C1R-C1S Interaction of the C1 Complex of Complement Activation. Proc. Natl. Acad. Sci. V. 115 768 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29311313
DOI: 10.1073/PNAS.1718709115
Page generated: Wed Jul 9 14:05:05 2025

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