Atomistry » Calcium » PDB 6f2y-6fhn » 6f39
Atomistry »
  Calcium »
    PDB 6f2y-6fhn »
      6f39 »

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: Tue Jul 16 07:36:31 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy