Calcium in PDB 1qdb: Cytochrome C Nitrite Reductase
Protein crystallography data
The structure of Cytochrome C Nitrite Reductase, PDB code: 1qdb
was solved by
O.Einsle,
A.Messerschmidt,
P.Stach,
R.Huber,
P.M.H.Kroneck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
1.90
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.484,
185.344,
92.192,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
22
|
Other elements in 1qdb:
The structure of Cytochrome C Nitrite Reductase also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Cytochrome C Nitrite Reductase
(pdb code 1qdb). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Cytochrome C Nitrite Reductase, PDB code: 1qdb:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 1qdb
Go back to
Calcium Binding Sites List in 1qdb
Calcium binding site 1 out
of 3 in the Cytochrome C Nitrite Reductase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cytochrome C Nitrite Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca520
b:2.1
occ:1.00
|
O
|
A:TYR217
|
2.5
|
24.0
|
1.0
|
O
|
A:LYS279
|
2.5
|
23.2
|
1.0
|
OE1
|
A:GLN281
|
2.5
|
29.6
|
1.0
|
O
|
A:HOH1564
|
2.6
|
32.6
|
1.0
|
OE2
|
A:GLU216
|
2.7
|
21.6
|
1.0
|
OE1
|
A:GLU216
|
2.7
|
19.6
|
1.0
|
O
|
A:HOH1534
|
2.7
|
27.8
|
1.0
|
CD
|
A:GLU216
|
3.0
|
21.6
|
1.0
|
C
|
A:LYS279
|
3.6
|
24.4
|
1.0
|
CD
|
A:GLN281
|
3.6
|
28.1
|
1.0
|
C
|
A:TYR217
|
3.6
|
27.5
|
1.0
|
OH
|
A:TYR260
|
4.0
|
24.3
|
1.0
|
N
|
A:TYR217
|
4.2
|
25.2
|
1.0
|
CA
|
A:ALA280
|
4.2
|
24.4
|
1.0
|
NE2
|
A:GLN281
|
4.2
|
30.3
|
1.0
|
N
|
A:GLN281
|
4.3
|
21.9
|
1.0
|
N
|
A:ALA280
|
4.3
|
23.8
|
1.0
|
OD2
|
A:ASP267
|
4.4
|
29.8
|
1.0
|
C
|
A:ALA280
|
4.4
|
22.3
|
1.0
|
N
|
A:TYR218
|
4.5
|
26.2
|
1.0
|
CG
|
A:GLU216
|
4.5
|
18.5
|
1.0
|
OD1
|
A:ASP267
|
4.5
|
28.3
|
1.0
|
CA
|
A:TYR217
|
4.5
|
26.5
|
1.0
|
CA
|
A:TYR218
|
4.6
|
27.8
|
1.0
|
CA
|
A:LYS279
|
4.6
|
22.1
|
1.0
|
CB
|
A:LYS279
|
4.6
|
21.3
|
1.0
|
CB
|
A:TYR218
|
4.6
|
28.6
|
1.0
|
N
|
A:LYS279
|
4.8
|
21.1
|
1.0
|
CB
|
A:GLN281
|
4.8
|
24.5
|
1.0
|
CG
|
A:GLN281
|
4.8
|
28.6
|
1.0
|
CG
|
A:ASP267
|
4.8
|
31.5
|
1.0
|
CZ
|
A:TYR260
|
5.0
|
24.1
|
1.0
|
O
|
A:HOH1678
|
5.0
|
41.8
|
1.0
|
|
Calcium binding site 2 out
of 3 in 1qdb
Go back to
Calcium Binding Sites List in 1qdb
Calcium binding site 2 out
of 3 in the Cytochrome C Nitrite Reductase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cytochrome C Nitrite Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca520
b:2.1
occ:1.00
|
O
|
B:TYR217
|
2.5
|
13.9
|
1.0
|
O
|
B:LYS279
|
2.5
|
16.9
|
1.0
|
OE1
|
B:GLN281
|
2.5
|
22.2
|
1.0
|
O
|
B:HOH1535
|
2.6
|
19.0
|
1.0
|
O
|
B:HOH1610
|
2.6
|
25.3
|
1.0
|
OE2
|
B:GLU216
|
2.6
|
17.9
|
1.0
|
OE1
|
B:GLU216
|
2.6
|
14.8
|
1.0
|
CD
|
B:GLU216
|
3.0
|
19.0
|
1.0
|
CD
|
B:GLN281
|
3.6
|
24.1
|
1.0
|
C
|
B:TYR217
|
3.6
|
15.8
|
1.0
|
C
|
B:LYS279
|
3.6
|
18.1
|
1.0
|
OH
|
B:TYR260
|
3.9
|
17.2
|
1.0
|
N
|
B:TYR217
|
4.1
|
16.1
|
1.0
|
NE2
|
B:GLN281
|
4.2
|
25.6
|
1.0
|
CA
|
B:ALA280
|
4.3
|
15.5
|
1.0
|
OD2
|
B:ASP267
|
4.3
|
20.1
|
1.0
|
N
|
B:GLN281
|
4.3
|
15.6
|
1.0
|
N
|
B:ALA280
|
4.4
|
15.3
|
1.0
|
CG
|
B:GLU216
|
4.5
|
14.9
|
1.0
|
C
|
B:ALA280
|
4.5
|
16.2
|
1.0
|
N
|
B:TYR218
|
4.5
|
17.2
|
1.0
|
CA
|
B:TYR218
|
4.5
|
18.1
|
1.0
|
CA
|
B:TYR217
|
4.5
|
16.5
|
1.0
|
CB
|
B:TYR218
|
4.6
|
17.9
|
1.0
|
CA
|
B:LYS279
|
4.6
|
15.7
|
1.0
|
OD1
|
B:ASP267
|
4.6
|
18.8
|
1.0
|
CB
|
B:LYS279
|
4.7
|
17.8
|
1.0
|
N
|
B:LYS279
|
4.8
|
17.1
|
1.0
|
CB
|
B:GLN281
|
4.8
|
18.7
|
1.0
|
CG
|
B:GLN281
|
4.8
|
21.1
|
1.0
|
CG
|
B:ASP267
|
4.8
|
20.2
|
1.0
|
CZ
|
B:TYR260
|
4.8
|
18.2
|
1.0
|
CE1
|
B:PHE397
|
4.9
|
15.9
|
1.0
|
|
Calcium binding site 3 out
of 3 in 1qdb
Go back to
Calcium Binding Sites List in 1qdb
Calcium binding site 3 out
of 3 in the Cytochrome C Nitrite Reductase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cytochrome C Nitrite Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca520
b:2.1
occ:1.00
|
O
|
C:LYS279
|
2.4
|
9.3
|
1.0
|
O
|
C:TYR217
|
2.5
|
12.9
|
1.0
|
OE1
|
C:GLN281
|
2.5
|
17.1
|
1.0
|
O
|
C:HOH1546
|
2.6
|
12.6
|
1.0
|
O
|
C:HOH1543
|
2.6
|
13.6
|
1.0
|
OE2
|
C:GLU216
|
2.6
|
13.6
|
1.0
|
OE1
|
C:GLU216
|
2.6
|
13.3
|
1.0
|
CD
|
C:GLU216
|
3.0
|
15.0
|
1.0
|
C
|
C:LYS279
|
3.6
|
13.6
|
1.0
|
CD
|
C:GLN281
|
3.6
|
18.3
|
1.0
|
C
|
C:TYR217
|
3.6
|
15.7
|
1.0
|
OH
|
C:TYR260
|
3.9
|
13.3
|
1.0
|
N
|
C:TYR217
|
4.2
|
13.3
|
1.0
|
NE2
|
C:GLN281
|
4.2
|
21.7
|
1.0
|
CA
|
C:ALA280
|
4.2
|
13.4
|
1.0
|
N
|
C:GLN281
|
4.3
|
13.2
|
1.0
|
OD2
|
C:ASP267
|
4.3
|
16.2
|
1.0
|
N
|
C:ALA280
|
4.4
|
13.4
|
1.0
|
C
|
C:ALA280
|
4.4
|
14.2
|
1.0
|
CG
|
C:GLU216
|
4.5
|
9.7
|
1.0
|
N
|
C:TYR218
|
4.5
|
15.7
|
1.0
|
CA
|
C:TYR218
|
4.5
|
14.0
|
1.0
|
CA
|
C:TYR217
|
4.6
|
14.5
|
1.0
|
CB
|
C:TYR218
|
4.6
|
12.1
|
1.0
|
CA
|
C:LYS279
|
4.6
|
12.2
|
1.0
|
OD1
|
C:ASP267
|
4.6
|
13.7
|
1.0
|
CB
|
C:LYS279
|
4.7
|
11.7
|
1.0
|
N
|
C:LYS279
|
4.7
|
10.8
|
1.0
|
CB
|
C:GLN281
|
4.8
|
17.1
|
1.0
|
CG
|
C:GLN281
|
4.8
|
17.2
|
1.0
|
CG
|
C:ASP267
|
4.8
|
15.1
|
1.0
|
CE1
|
C:PHE397
|
4.8
|
12.5
|
1.0
|
CZ
|
C:TYR260
|
4.9
|
13.4
|
1.0
|
O
|
C:HOH1699
|
4.9
|
29.7
|
1.0
|
|
Reference:
O.Einsle,
A.Messerschmidt,
P.Stach,
G.P.Bourenkov,
H.D.Bartunik,
R.Huber,
P.M.Kroneck.
Structure of Cytochrome C Nitrite Reductase. Nature V. 400 476 1999.
ISSN: ISSN 0028-0836
PubMed: 10440380
DOI: 10.1038/22802
Page generated: Thu Jul 11 21:42:24 2024
|