Sodium in PDB 6f1h: C1RC1S Complex
Enzymatic activity of C1RC1S Complex
Protein crystallography data
The structure of C1RC1S Complex, PDB code: 6f1h
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)
|
80.65 /
4.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.209,
88.340,
197.559,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
30.4 /
34
|
Other elements in 6f1h:
The structure of C1RC1S Complex also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the C1RC1S Complex
(pdb code 6f1h). 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: 6f1h:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6f1h
Go back to
Sodium Binding Sites List in 6f1h
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:0.8
occ:1.00
|
O
|
A:ARG279
|
2.5
|
0.1
|
1.0
|
OG
|
A:SER190
|
2.7
|
0.3
|
1.0
|
O
|
A:ARG195
|
2.8
|
0.8
|
1.0
|
O
|
A:GLU192
|
3.3
|
0.4
|
1.0
|
O
|
A:LEU191
|
3.4
|
0.3
|
1.0
|
C
|
A:ARG279
|
3.6
|
0.9
|
1.0
|
CB
|
A:SER190
|
3.6
|
1.0
|
1.0
|
CA
|
A:TYR193
|
3.7
|
0.8
|
1.0
|
C
|
A:GLU192
|
3.7
|
0.4
|
1.0
|
CB
|
A:TYR197
|
3.8
|
0.8
|
1.0
|
CA
|
A:GLY280
|
3.8
|
0.2
|
1.0
|
N
|
A:TYR197
|
3.8
|
0.2
|
1.0
|
N
|
A:TYR193
|
3.9
|
0.1
|
1.0
|
CA
|
A:TYR197
|
3.9
|
0.9
|
1.0
|
CD1
|
A:TYR193
|
3.9
|
0.3
|
1.0
|
C
|
A:ARG195
|
4.0
|
0.7
|
1.0
|
O
|
A:SER190
|
4.0
|
0.7
|
1.0
|
CB
|
A:TYR193
|
4.0
|
0.2
|
1.0
|
C
|
A:SER190
|
4.1
|
0.6
|
1.0
|
C
|
A:SER196
|
4.2
|
0.9
|
1.0
|
N
|
A:GLY280
|
4.2
|
0.1
|
1.0
|
C
|
A:LEU191
|
4.2
|
0.6
|
1.0
|
CD2
|
A:TYR197
|
4.4
|
0.5
|
1.0
|
CG
|
A:TYR193
|
4.4
|
0.1
|
1.0
|
CA
|
A:SER190
|
4.5
|
1.0
|
1.0
|
O
|
A:SER196
|
4.5
|
0.8
|
1.0
|
N
|
A:ARG195
|
4.6
|
0.2
|
1.0
|
N
|
A:LEU191
|
4.6
|
0.6
|
1.0
|
CG
|
A:TYR197
|
4.6
|
0.6
|
1.0
|
C
|
A:PRO194
|
4.7
|
0.1
|
1.0
|
CA
|
A:SER196
|
4.8
|
0.5
|
1.0
|
CA
|
A:ARG279
|
4.8
|
0.5
|
1.0
|
CA
|
A:GLU192
|
4.8
|
0.8
|
1.0
|
N
|
A:SER196
|
4.9
|
0.2
|
1.0
|
CA
|
A:PRO194
|
4.9
|
0.4
|
1.0
|
N
|
A:GLU192
|
4.9
|
0.4
|
1.0
|
CA
|
A:ARG195
|
4.9
|
0.1
|
1.0
|
C
|
A:GLY280
|
4.9
|
0.1
|
1.0
|
N
|
A:TRP281
|
4.9
|
0.6
|
1.0
|
CE1
|
A:TYR193
|
5.0
|
0.7
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6f1h
Go back to
Sodium Binding Sites List in 6f1h
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:Na305
b:0.7
occ:1.00
|
O
|
C:LEU191
|
2.5
|
0.9
|
1.0
|
OG
|
C:SER190
|
2.5
|
0.1
|
1.0
|
O
|
C:SER190
|
2.9
|
0.4
|
1.0
|
O
|
C:GLU192
|
2.9
|
0.7
|
1.0
|
C
|
C:GLU192
|
3.0
|
0.6
|
1.0
|
N
|
C:TYR193
|
3.1
|
0.9
|
1.0
|
C
|
C:SER190
|
3.1
|
0.3
|
1.0
|
C
|
C:LEU191
|
3.1
|
0.2
|
1.0
|
CA
|
C:TYR193
|
3.2
|
0.4
|
1.0
|
CB
|
C:SER190
|
3.3
|
0.9
|
1.0
|
CB
|
C:TYR193
|
3.3
|
0.6
|
1.0
|
O
|
C:ARG195
|
3.5
|
0.9
|
1.0
|
N
|
C:LEU191
|
3.6
|
0.9
|
1.0
|
O
|
C:ARG279
|
3.7
|
0.1
|
1.0
|
CA
|
C:SER190
|
3.7
|
0.7
|
1.0
|
N
|
C:GLU192
|
3.8
|
0.9
|
1.0
|
CA
|
C:GLU192
|
3.9
|
0.1
|
1.0
|
CA
|
C:LEU191
|
4.0
|
0.3
|
1.0
|
CD1
|
C:TYR193
|
4.1
|
0.8
|
1.0
|
CG
|
C:TYR193
|
4.2
|
0.2
|
1.0
|
N
|
C:SER190
|
4.5
|
0.1
|
1.0
|
CB
|
C:TYR197
|
4.5
|
0.4
|
1.0
|
C
|
C:ARG195
|
4.6
|
0.7
|
1.0
|
CA
|
C:TYR197
|
4.6
|
0.7
|
1.0
|
CA
|
C:GLY280
|
4.6
|
0.7
|
1.0
|
C
|
C:TYR193
|
4.7
|
0.8
|
1.0
|
CB
|
C:GLU192
|
4.7
|
0.1
|
1.0
|
C
|
C:ARG279
|
4.7
|
0.8
|
1.0
|
N
|
C:ARG195
|
4.8
|
0.1
|
1.0
|
N
|
C:TYR197
|
4.8
|
0.0
|
1.0
|
C
|
C:SER196
|
4.9
|
0.4
|
1.0
|
O
|
C:SER196
|
4.9
|
0.6
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6f1h
Go back to
Sodium Binding Sites List in 6f1h
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:0.6
occ:1.00
|
O
|
D:PRO178
|
3.1
|
0.2
|
1.0
|
CG
|
D:LYS266
|
3.5
|
0.7
|
1.0
|
CB
|
D:LYS266
|
3.6
|
1.0
|
1.0
|
CA
|
D:LYS266
|
3.7
|
0.4
|
1.0
|
C
|
D:PRO178
|
4.3
|
0.8
|
1.0
|
CD
|
D:LYS266
|
4.3
|
0.4
|
1.0
|
N
|
D:LYS266
|
4.6
|
0.8
|
1.0
|
CD
|
D:PRO180
|
4.8
|
0.4
|
1.0
|
C
|
D:LYS266
|
4.8
|
0.6
|
1.0
|
CA
|
D:LYS179
|
4.8
|
0.8
|
1.0
|
O
|
D:LYS266
|
4.9
|
0.1
|
1.0
|
N
|
D:PRO180
|
4.9
|
0.8
|
1.0
|
C
|
D:LYS179
|
4.9
|
0.8
|
1.0
|
CG
|
D:PRO180
|
5.0
|
0.1
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6f1h
Go back to
Sodium Binding Sites List in 6f1h
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:0.8
occ:1.00
|
O
|
D:GLN15
|
2.4
|
0.9
|
1.0
|
OG
|
D:SER10
|
2.7
|
0.5
|
1.0
|
O
|
D:THR106
|
2.8
|
0.6
|
1.0
|
O
|
D:PRO11
|
3.3
|
0.1
|
1.0
|
C
|
D:THR106
|
3.4
|
0.1
|
1.0
|
C
|
D:GLN15
|
3.5
|
0.3
|
1.0
|
N
|
D:TYR17
|
3.7
|
0.2
|
1.0
|
CB
|
D:SER10
|
3.7
|
0.7
|
1.0
|
C
|
D:ALA16
|
3.8
|
0.8
|
1.0
|
CA
|
D:TYR13
|
3.9
|
0.3
|
1.0
|
CB
|
D:TYR17
|
3.9
|
0.3
|
1.0
|
CA
|
D:GLY107
|
3.9
|
0.4
|
1.0
|
N
|
D:TYR13
|
4.0
|
0.0
|
1.0
|
O
|
D:ASN12
|
4.0
|
0.3
|
1.0
|
N
|
D:GLY107
|
4.0
|
0.1
|
1.0
|
CA
|
D:TYR17
|
4.0
|
0.8
|
1.0
|
C
|
D:ASN12
|
4.0
|
0.6
|
1.0
|
N
|
D:GLN15
|
4.2
|
1.0
|
1.0
|
CA
|
D:ALA16
|
4.2
|
0.6
|
1.0
|
O
|
D:ALA16
|
4.3
|
0.4
|
1.0
|
C
|
D:PRO11
|
4.3
|
0.2
|
1.0
|
CD2
|
D:TYR17
|
4.3
|
0.6
|
1.0
|
N
|
D:ALA16
|
4.3
|
0.6
|
1.0
|
CA
|
D:THR106
|
4.3
|
0.7
|
1.0
|
CB
|
D:TYR13
|
4.5
|
0.0
|
1.0
|
O
|
D:SER10
|
4.5
|
0.1
|
1.0
|
C
|
D:SER10
|
4.5
|
0.8
|
1.0
|
CA
|
D:GLN15
|
4.5
|
0.3
|
1.0
|
C
|
D:PRO14
|
4.5
|
0.7
|
1.0
|
O
|
D:PHE105
|
4.6
|
0.4
|
1.0
|
CD1
|
D:TYR13
|
4.6
|
0.9
|
1.0
|
CG
|
D:TYR17
|
4.6
|
0.6
|
1.0
|
CA
|
D:SER10
|
4.7
|
0.0
|
1.0
|
CA
|
D:PRO14
|
4.8
|
0.7
|
1.0
|
CA
|
D:ASN12
|
4.9
|
0.1
|
1.0
|
N
|
D:PRO11
|
4.9
|
0.4
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6f1h
Go back to
Sodium Binding Sites List in 6f1h
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:0.0
occ:1.00
|
OG
|
B:SER10
|
2.6
|
0.7
|
1.0
|
O
|
B:GLN15
|
2.6
|
0.3
|
1.0
|
O
|
B:THR106
|
2.7
|
0.8
|
1.0
|
O
|
B:PRO11
|
3.1
|
0.9
|
1.0
|
C
|
B:THR106
|
3.5
|
0.9
|
1.0
|
CA
|
B:TYR13
|
3.5
|
0.5
|
1.0
|
N
|
B:TYR13
|
3.6
|
0.6
|
1.0
|
CB
|
B:SER10
|
3.7
|
0.2
|
1.0
|
C
|
B:GLN15
|
3.8
|
1.0
|
1.0
|
C
|
B:ASN12
|
3.8
|
0.7
|
1.0
|
O
|
B:ASN12
|
3.8
|
0.6
|
1.0
|
N
|
B:TYR17
|
4.1
|
0.5
|
1.0
|
C
|
B:PRO11
|
4.1
|
0.6
|
1.0
|
CB
|
B:TYR13
|
4.1
|
0.0
|
1.0
|
N
|
B:GLN15
|
4.2
|
0.7
|
1.0
|
CA
|
B:GLY107
|
4.2
|
0.7
|
1.0
|
CB
|
B:TYR17
|
4.2
|
0.7
|
1.0
|
O
|
B:SER10
|
4.2
|
0.2
|
1.0
|
N
|
B:GLY107
|
4.2
|
0.5
|
1.0
|
C
|
B:ALA16
|
4.2
|
0.9
|
1.0
|
C
|
B:SER10
|
4.3
|
0.2
|
1.0
|
CA
|
B:TYR17
|
4.3
|
0.5
|
1.0
|
CD1
|
B:TYR13
|
4.4
|
0.0
|
1.0
|
CA
|
B:THR106
|
4.4
|
0.9
|
1.0
|
C
|
B:PRO14
|
4.5
|
0.0
|
1.0
|
O
|
B:ALA16
|
4.5
|
0.2
|
1.0
|
CA
|
B:GLN15
|
4.6
|
0.3
|
1.0
|
CA
|
B:SER10
|
4.6
|
0.5
|
1.0
|
CA
|
B:PRO14
|
4.6
|
1.0
|
1.0
|
N
|
B:ALA16
|
4.7
|
0.6
|
1.0
|
CA
|
B:ALA16
|
4.7
|
0.9
|
1.0
|
CA
|
B:ASN12
|
4.7
|
0.5
|
1.0
|
CG
|
B:TYR13
|
4.7
|
0.6
|
1.0
|
N
|
B:PRO11
|
4.7
|
0.4
|
1.0
|
N
|
B:ASN12
|
4.8
|
0.3
|
1.0
|
CD2
|
B:TYR17
|
4.8
|
0.4
|
1.0
|
C
|
B:TYR13
|
4.8
|
0.2
|
1.0
|
O
|
B:PHE105
|
4.8
|
0.6
|
1.0
|
CB
|
B:ASN12
|
4.9
|
0.8
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6f1h
Go back to
Sodium Binding Sites List in 6f1h
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:0.2
occ:1.00
|
O
|
B:LYS179
|
2.5
|
0.3
|
1.0
|
O
|
B:LYS266
|
2.6
|
0.5
|
1.0
|
OG
|
B:SER174
|
3.0
|
0.7
|
1.0
|
O
|
B:PRO175
|
3.2
|
0.4
|
1.0
|
N
|
B:TYR181
|
3.2
|
0.8
|
1.0
|
CA
|
B:TYR181
|
3.5
|
0.8
|
1.0
|
C
|
B:PRO180
|
3.5
|
0.0
|
1.0
|
CB
|
B:TYR181
|
3.6
|
0.7
|
1.0
|
C
|
B:LYS179
|
3.7
|
0.7
|
1.0
|
C
|
B:LYS266
|
3.7
|
0.6
|
1.0
|
CA
|
B:GLY267
|
3.8
|
0.3
|
1.0
|
CB
|
B:SER174
|
3.9
|
0.6
|
1.0
|
CA
|
B:TYR177
|
4.0
|
0.4
|
1.0
|
CA
|
B:PRO180
|
4.0
|
0.3
|
1.0
|
N
|
B:TYR177
|
4.0
|
0.9
|
1.0
|
O
|
B:PRO180
|
4.0
|
0.6
|
1.0
|
N
|
B:GLY267
|
4.2
|
0.5
|
1.0
|
CB
|
B:TYR177
|
4.3
|
0.9
|
1.0
|
CD2
|
B:TYR181
|
4.3
|
0.9
|
1.0
|
C
|
B:PRO175
|
4.3
|
0.2
|
1.0
|
CD1
|
B:TYR177
|
4.3
|
0.9
|
1.0
|
N
|
B:PRO180
|
4.3
|
0.3
|
1.0
|
CG
|
B:TYR181
|
4.4
|
0.4
|
1.0
|
C
|
B:ASN176
|
4.5
|
0.4
|
1.0
|
O
|
B:SER174
|
4.6
|
0.9
|
1.0
|
O
|
B:LYS265
|
4.6
|
0.1
|
1.0
|
C
|
B:SER174
|
4.6
|
0.3
|
1.0
|
N
|
B:LYS179
|
4.7
|
0.1
|
1.0
|
C
|
B:PRO178
|
4.8
|
0.1
|
1.0
|
CG
|
B:TYR177
|
4.8
|
0.6
|
1.0
|
CA
|
B:LYS179
|
4.8
|
0.7
|
1.0
|
CA
|
B:SER174
|
4.9
|
0.4
|
1.0
|
N
|
B:PRO175
|
4.9
|
0.8
|
1.0
|
C
|
B:GLY267
|
4.9
|
0.4
|
1.0
|
O
|
B:ASN176
|
4.9
|
0.8
|
1.0
|
N
|
B:TRP268
|
5.0
|
0.1
|
1.0
|
CA
|
B:LYS266
|
5.0
|
0.5
|
1.0
|
CB
|
B:ASN176
|
5.0
|
0.5
|
1.0
|
C
|
B:TYR181
|
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 08:39:01 2024
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