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Sodium in PDB 6f1c: C1RC1S Complex

Enzymatic activity of C1RC1S Complex

All present enzymatic activity of C1RC1S Complex:
3.4.21.41; 3.4.21.42;

Protein crystallography data

The structure of C1RC1S Complex, PDB code: 6f1c 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) 97.75 / 4.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.779, 124.265, 195.499, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 30.5

Other elements in 6f1c:

The structure of C1RC1S Complex also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the C1RC1S Complex (pdb code 6f1c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the C1RC1S Complex, PDB code: 6f1c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6f1c

Go back to Sodium Binding Sites List in 6f1c
Sodium binding site 1 out of 6 in the C1RC1S Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C1RC1S Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:0.0
occ:1.00
 O A:ARG279 2.6 0.2 1.0
O A:ARG195 2.8 0.8 1.0
OG A:SER190 3.0 0.2 1.0
O A:GLU192 3.1 0.6 1.0
O A:LEU191 3.1 0.6 1.0
C A:GLU192 3.6 0.8 1.0
C A:ARG279 3.7 0.8 1.0
CA A:TYR193 3.8 0.7 1.0
N A:TYR197 3.8 0.7 1.0
CB A:TYR197 3.8 0.6 1.0
CB A:SER190 3.8 0.0 1.0
CA A:TYR197 3.8 0.6 1.0
N A:TYR193 3.8 0.7 1.0
O A:SER190 3.9 0.8 1.0
C A:LEU191 4.0 0.9 1.0
C A:ARG195 4.0 1.0 1.0
CA A:GLY280 4.0 0.4 1.0
C A:SER196 4.0 0.6 1.0
CB A:TYR193 4.0 0.8 1.0
C A:SER190 4.1 0.2 1.0
O A:SER196 4.3 0.9 1.0
CD1 A:TYR193 4.3 0.6 1.0
N A:GLY280 4.4 0.4 1.0
N A:LEU191 4.4 0.0 1.0
CD2 A:TYR197 4.5 0.1 1.0
CA A:SER190 4.6 0.1 1.0
N A:GLU192 4.6 0.0 1.0
CA A:GLU192 4.6 0.6 1.0
N A:ARG195 4.7 0.7 1.0
CG A:TYR197 4.7 0.8 1.0
CA A:SER196 4.7 0.6 1.0
CG A:TYR193 4.7 1.0 1.0
N A:SER196 4.8 0.4 1.0
CA A:LEU191 4.8 0.8 1.0
CA A:ARG279 4.9 0.8 1.0
C A:PRO194 4.9 0.8 1.0
CA A:ARG195 4.9 0.1 1.0

Sodium binding site 2 out of 6 in 6f1c

Go back to Sodium Binding Sites List in 6f1c
Sodium binding site 2 out of 6 in the C1RC1S Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C1RC1S Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:0.6
occ:1.00
 O C:ARG279 2.5 0.6 1.0
O C:ARG195 2.8 0.1 1.0
O C:GLU192 3.0 0.1 1.0
OG C:SER190 3.1 0.1 1.0
O C:LEU191 3.1 0.6 1.0
C C:GLU192 3.5 0.1 1.0
C C:ARG279 3.7 0.0 1.0
CA C:TYR193 3.7 0.2 1.0
N C:TYR197 3.8 0.2 1.0
CB C:TYR197 3.8 0.6 1.0
N C:TYR193 3.8 0.6 1.0
CA C:TYR197 3.8 0.9 1.0
CB C:SER190 3.9 0.2 1.0
C C:ARG195 3.9 0.6 1.0
O C:SER190 4.0 0.5 1.0
C C:LEU191 4.0 0.2 1.0
C C:SER196 4.0 0.9 1.0
CB C:TYR193 4.0 0.0 1.0
CA C:GLY280 4.1 0.3 1.0
C C:SER190 4.1 0.7 1.0
O C:SER196 4.3 0.9 1.0
CD1 C:TYR193 4.3 0.2 1.0
N C:GLY280 4.4 0.7 1.0
N C:LEU191 4.5 0.6 1.0
CD2 C:TYR197 4.5 0.8 1.0
CA C:GLU192 4.6 0.6 1.0
N C:GLU192 4.6 0.8 1.0
N C:ARG195 4.6 0.2 1.0
CA C:SER196 4.6 0.7 1.0
CA C:SER190 4.6 0.5 1.0
CG C:TYR197 4.7 0.9 1.0
CG C:TYR193 4.7 0.1 1.0
N C:SER196 4.7 1.0 1.0
CA C:ARG279 4.8 0.1 1.0
C C:PRO194 4.8 0.1 1.0
CA C:LEU191 4.9 0.1 1.0
CA C:ARG195 4.9 0.9 1.0
CA C:PRO194 5.0 0.6 1.0

Sodium binding site 3 out of 6 in 6f1c

Go back to Sodium Binding Sites List in 6f1c
Sodium binding site 3 out of 6 in the C1RC1S Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of C1RC1S Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:0.2
occ:1.00
 O D:LYS179 2.6 0.5 1.0
O D:PRO175 2.8 0.9 1.0
O D:LYS266 2.8 0.8 1.0
OG D:SER174 2.9 0.2 1.0
N D:TYR181 3.5 0.2 1.0
N D:TYR177 3.6 0.6 1.0
CA D:TYR177 3.7 0.4 1.0
CA D:TYR181 3.8 0.9 1.0
CB D:SER174 3.8 0.1 1.0
C D:PRO180 3.8 0.3 1.0
C D:LYS179 3.8 0.9 1.0
CB D:TYR181 3.9 0.8 1.0
C D:PRO175 3.9 0.3 1.0
C D:LYS266 3.9 0.7 1.0
CB D:TYR177 4.0 0.1 1.0
CA D:GLY267 4.1 0.3 1.0
C D:ASN176 4.1 0.9 1.0
O D:SER174 4.1 0.2 1.0
CD1 D:TYR177 4.2 0.2 1.0
C D:SER174 4.2 0.1 1.0
O D:PRO180 4.2 0.4 1.0
CA D:PRO180 4.3 0.9 1.0
N D:GLY267 4.5 0.9 1.0
N D:PRO175 4.5 0.5 1.0
N D:PRO180 4.5 0.5 1.0
CG D:TYR177 4.6 0.8 1.0
CB D:ASN176 4.6 0.4 1.0
N D:ASN176 4.6 0.0 1.0
CD2 D:TYR181 4.6 0.3 1.0
CA D:SER174 4.6 0.0 1.0
CA D:ASN176 4.6 0.2 1.0
O D:ASN176 4.7 0.8 1.0
N D:LYS179 4.7 0.8 1.0
CG D:TYR181 4.7 0.6 1.0
C D:PRO178 4.8 0.5 1.0
O D:LYS265 4.8 0.3 1.0
CA D:PRO175 4.8 0.3 1.0
CA D:LYS179 4.9 0.6 1.0
N D:TRP268 5.0 1.0 1.0

Sodium binding site 4 out of 6 in 6f1c

Go back to Sodium Binding Sites List in 6f1c
Sodium binding site 4 out of 6 in the C1RC1S Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of C1RC1S Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na305

b:0.4
occ:1.00
 O D:GLN15 2.7 0.6 1.0
O D:PRO11 2.8 0.9 1.0
OG D:SER10 2.9 0.0 1.0
O D:THR106 3.0 0.8 1.0
C D:THR106 3.6 0.8 1.0
C D:ASN12 3.7 0.4 1.0
N D:TYR13 3.7 1.0 1.0
O D:ASN12 3.7 0.3 1.0
C D:GLN15 3.8 0.1 1.0
CB D:TYR17 3.8 0.7 1.0
N D:TYR17 3.8 0.3 1.0
CA D:TYR13 3.8 0.5 1.0
C D:PRO11 3.9 0.7 1.0
CB D:SER10 3.9 0.8 1.0
CA D:TYR17 4.0 0.1 1.0
C D:ALA16 4.0 0.1 1.0
CA D:GLY107 4.2 0.2 1.0
N D:GLN15 4.2 0.6 1.0
N D:GLY107 4.2 0.6 1.0
O D:SER10 4.3 0.2 1.0
CD2 D:TYR17 4.3 0.5 1.0
C D:SER10 4.4 0.6 1.0
O D:ALA16 4.4 0.3 1.0
CA D:ASN12 4.4 0.6 1.0
CB D:ASN12 4.5 0.9 1.0
CA D:THR106 4.5 0.7 1.0
CB D:TYR13 4.5 0.1 1.0
N D:ASN12 4.5 0.1 1.0
CG D:TYR17 4.6 1.0 1.0
CA D:ALA16 4.6 0.1 1.0
N D:ALA16 4.6 0.4 1.0
C D:PRO14 4.6 0.3 1.0
CA D:GLN15 4.6 0.1 1.0
N D:PRO11 4.7 0.9 1.0
O D:PHE105 4.7 0.5 1.0
CA D:SER10 4.8 0.5 1.0
CA D:PRO14 4.9 0.2 1.0
CA D:PRO11 4.9 0.9 1.0

Sodium binding site 5 out of 6 in 6f1c

Go back to Sodium Binding Sites List in 6f1c
Sodium binding site 5 out of 6 in the C1RC1S Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of C1RC1S Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:0.7
occ:1.00
 O B:GLN15 2.8 0.4 1.0
O B:PRO11 2.8 0.3 1.0
OG B:SER10 2.9 0.6 1.0
O B:THR106 2.9 0.1 1.0
C B:THR106 3.6 1.0 1.0
CB B:TYR17 3.7 0.3 1.0
N B:TYR13 3.8 0.7 1.0
C B:ASN12 3.8 0.2 1.0
O B:ASN12 3.8 0.9 1.0
N B:TYR17 3.8 0.8 1.0
C B:GLN15 3.8 0.5 1.0
CA B:TYR13 3.8 0.2 1.0
CB B:SER10 3.8 0.5 1.0
C B:PRO11 3.9 0.2 1.0
CA B:TYR17 3.9 0.6 1.0
C B:ALA16 4.1 0.7 1.0
CA B:GLY107 4.1 0.1 1.0
N B:GLY107 4.2 0.2 1.0
N B:GLN15 4.3 1.0 1.0
O B:SER10 4.3 0.5 1.0
CD2 B:TYR17 4.3 0.4 1.0
C B:SER10 4.3 0.8 1.0
O B:ALA16 4.4 0.9 1.0
CA B:THR106 4.5 0.6 1.0
CA B:ASN12 4.5 0.1 1.0
CB B:TYR13 4.5 1.0 1.0
CB B:ASN12 4.5 0.5 1.0
CG B:TYR17 4.5 0.8 1.0
N B:ASN12 4.6 0.8 1.0
CA B:ALA16 4.6 0.1 1.0
C B:PRO14 4.6 0.9 1.0
N B:ALA16 4.6 0.2 1.0
CA B:GLN15 4.7 0.7 1.0
N B:PRO11 4.7 0.7 1.0
O B:PHE105 4.7 0.8 1.0
CA B:SER10 4.7 0.0 1.0
CA B:PRO14 4.9 0.7 1.0
CA B:PRO11 4.9 0.7 1.0

Sodium binding site 6 out of 6 in 6f1c

Go back to Sodium Binding Sites List in 6f1c
Sodium binding site 6 out of 6 in the C1RC1S Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of C1RC1S Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:0.4
occ:1.00
 O B:LYS179 2.6 0.9 1.0
O B:LYS266 2.8 0.3 1.0
O B:PRO175 2.8 0.2 1.0
OG B:SER174 2.9 0.3 1.0
N B:TYR181 3.5 0.4 1.0
N B:TYR177 3.6 0.2 1.0
CA B:TYR177 3.6 0.7 1.0
CB B:SER174 3.8 0.1 1.0
CA B:TYR181 3.8 0.6 1.0
C B:LYS179 3.8 0.6 1.0
C B:PRO180 3.8 0.2 1.0
C B:PRO175 3.9 1.0 1.0
CB B:TYR181 3.9 0.5 1.0
C B:LYS266 3.9 0.6 1.0
CB B:TYR177 3.9 0.2 1.0
CA B:GLY267 4.1 0.7 1.0
C B:ASN176 4.1 0.0 1.0
O B:SER174 4.1 0.5 1.0
CD1 B:TYR177 4.2 0.8 1.0
C B:SER174 4.2 0.3 1.0
O B:PRO180 4.2 0.8 1.0
CA B:PRO180 4.3 0.7 1.0
N B:GLY267 4.5 0.0 1.0
N B:PRO175 4.5 0.3 1.0
N B:PRO180 4.5 0.4 1.0
CG B:TYR177 4.5 0.1 1.0
CB B:ASN176 4.6 0.4 1.0
N B:ASN176 4.6 0.4 1.0
CA B:ASN176 4.6 0.6 1.0
O B:ASN176 4.6 0.0 1.0
CA B:SER174 4.6 0.8 1.0
CD2 B:TYR181 4.6 0.8 1.0
N B:LYS179 4.7 0.2 1.0
C B:PRO178 4.7 0.0 1.0
CG B:TYR181 4.8 0.9 1.0
O B:LYS265 4.8 1.0 1.0
CA B:PRO175 4.8 0.7 1.0
CA B:LYS179 4.9 0.7 1.0
N B:TRP268 5.0 0.7 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 Oct 8 08:38:44 2024

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