Calcium in PDB 5ya6: Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii
Protein crystallography data
The structure of Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii, PDB code: 5ya6
was solved by
V.A.Meshcheryakov,
M.Wolf,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.00 /
1.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
37.090,
73.660,
107.290,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.3 /
20
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii
(pdb code 5ya6). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii, PDB code: 5ya6:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 5ya6
Go back to
Calcium Binding Sites List in 5ya6
Calcium binding site 1 out
of 2 in the Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:10.1
occ:1.00
|
OD1
|
A:ASP139
|
2.3
|
9.3
|
1.0
|
OD1
|
A:ASN150
|
2.4
|
10.7
|
1.0
|
OD1
|
A:ASP141
|
2.4
|
11.1
|
1.0
|
OG
|
A:SER143
|
2.4
|
10.2
|
1.0
|
OD1
|
A:ASP153
|
2.4
|
8.1
|
1.0
|
O
|
A:HOH504
|
2.4
|
10.6
|
1.0
|
OD2
|
A:ASP153
|
2.5
|
8.6
|
1.0
|
CG
|
A:ASP153
|
2.8
|
8.6
|
1.0
|
CG
|
A:ASP141
|
3.3
|
14.1
|
1.0
|
CG
|
A:ASN150
|
3.3
|
14.4
|
1.0
|
CG
|
A:ASP139
|
3.5
|
14.9
|
1.0
|
CB
|
A:SER143
|
3.5
|
10.6
|
1.0
|
ND2
|
A:ASN150
|
3.7
|
16.8
|
1.0
|
OD2
|
A:ASP141
|
3.8
|
16.4
|
1.0
|
OD2
|
A:ASP139
|
4.1
|
11.4
|
1.0
|
N
|
A:SER143
|
4.1
|
10.1
|
1.0
|
N
|
A:ASP141
|
4.2
|
12.1
|
1.0
|
N
|
A:ALA140
|
4.2
|
10.5
|
1.0
|
O
|
A:HOH443
|
4.2
|
13.2
|
1.0
|
N
|
A:ASN150
|
4.3
|
10.9
|
1.0
|
CB
|
A:ASP153
|
4.3
|
9.1
|
1.0
|
CA
|
A:SER143
|
4.4
|
10.0
|
1.0
|
CB
|
A:ASP141
|
4.5
|
13.1
|
1.0
|
CA
|
A:ASP139
|
4.5
|
10.1
|
1.0
|
CB
|
A:ASP139
|
4.6
|
10.9
|
1.0
|
CB
|
A:ASN150
|
4.6
|
12.5
|
1.0
|
O
|
A:HOH522
|
4.6
|
18.8
|
1.0
|
N
|
A:LEU144
|
4.7
|
11.6
|
1.0
|
CA
|
A:ASP141
|
4.7
|
12.7
|
1.0
|
O
|
A:ASN150
|
4.7
|
10.4
|
1.0
|
CA
|
A:ASN150
|
4.8
|
11.5
|
1.0
|
C
|
A:ASN150
|
4.8
|
11.7
|
1.0
|
O
|
A:VAL148
|
4.8
|
10.6
|
1.0
|
N
|
A:GLY142
|
4.8
|
11.1
|
1.0
|
C
|
A:ASP139
|
4.9
|
11.5
|
1.0
|
C
|
A:ASP141
|
4.9
|
12.0
|
1.0
|
C
|
A:SER143
|
5.0
|
11.1
|
1.0
|
|
Calcium binding site 2 out
of 2 in 5ya6
Go back to
Calcium Binding Sites List in 5ya6
Calcium binding site 2 out
of 2 in the Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Archaeal Flagellin FLAB1 From Methanocaldococcus Jannaschii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:17.4
occ:1.00
|
OD1
|
B:ASP139
|
2.3
|
15.6
|
1.0
|
OD1
|
B:ASN150
|
2.4
|
18.5
|
1.0
|
OD1
|
B:ASP153
|
2.4
|
16.9
|
1.0
|
OD1
|
B:ASP141
|
2.4
|
18.9
|
1.0
|
OG
|
B:SER143
|
2.4
|
15.2
|
1.0
|
OD2
|
B:ASP153
|
2.4
|
14.2
|
1.0
|
O
|
B:HOH478
|
2.4
|
18.7
|
1.0
|
CG
|
B:ASP153
|
2.7
|
15.2
|
1.0
|
CG
|
B:ASN150
|
3.3
|
18.6
|
1.0
|
CG
|
B:ASP141
|
3.4
|
23.0
|
1.0
|
CG
|
B:ASP139
|
3.4
|
15.1
|
1.0
|
CB
|
B:SER143
|
3.5
|
15.6
|
1.0
|
ND2
|
B:ASN150
|
3.8
|
20.9
|
1.0
|
OD2
|
B:ASP141
|
3.9
|
24.1
|
1.0
|
N
|
B:SER143
|
4.0
|
16.8
|
1.0
|
OD2
|
B:ASP139
|
4.2
|
16.6
|
1.0
|
N
|
B:ASN150
|
4.2
|
15.5
|
1.0
|
CB
|
B:ASP153
|
4.2
|
15.6
|
1.0
|
O
|
B:HOH422
|
4.3
|
25.0
|
1.0
|
N
|
B:ASP141
|
4.3
|
22.4
|
1.0
|
CA
|
B:ASP139
|
4.3
|
16.7
|
1.0
|
CA
|
B:SER143
|
4.3
|
15.7
|
1.0
|
CB
|
B:ASP139
|
4.3
|
16.0
|
1.0
|
CB
|
B:ASP141
|
4.5
|
22.4
|
1.0
|
CB
|
B:ASN150
|
4.5
|
17.8
|
1.0
|
C
|
B:ASP139
|
4.5
|
18.2
|
1.0
|
N
|
B:ALA140
|
4.5
|
21.4
|
1.0
|
N
|
B:GLY142
|
4.5
|
19.2
|
1.0
|
O
|
B:ASN150
|
4.6
|
17.0
|
1.0
|
CA
|
B:ASN150
|
4.6
|
16.5
|
1.0
|
CA
|
B:ASP141
|
4.7
|
22.2
|
1.0
|
C
|
B:ASN150
|
4.7
|
18.4
|
1.0
|
N
|
B:LEU144
|
4.7
|
16.0
|
1.0
|
O
|
B:VAL148
|
4.7
|
13.9
|
1.0
|
C
|
B:ASP141
|
4.8
|
21.1
|
1.0
|
O
|
B:LYS151
|
5.0
|
22.3
|
1.0
|
C
|
B:SER143
|
5.0
|
14.4
|
1.0
|
|
Reference:
V.A.Meshcheryakov,
S.Shibata,
M.T.Schreiber,
A.Villar-Briones,
K.F.Jarrell,
S.I.Aizawa,
M.Wolf.
High-Resolution Archaellum Structure Reveals A Conserved Metal-Binding Site. Embo Rep. V. 20 2019.
ISSN: ESSN 1469-3178
PubMed: 30898768
DOI: 10.15252/EMBR.201846340
Page generated: Sat Dec 12 05:54:17 2020
|