Calcium in PDB 4l3z: Nitrite Complex of Tvnir, Second Middle Dose Data Set
Enzymatic activity of Nitrite Complex of Tvnir, Second Middle Dose Data Set
All present enzymatic activity of Nitrite Complex of Tvnir, Second Middle Dose Data Set:
1.7.2.2;
Protein crystallography data
The structure of Nitrite Complex of Tvnir, Second Middle Dose Data Set, PDB code: 4l3z
was solved by
A.A.Trofimov,
K.M.Polyakov,
V.A.Lazarenko,
A.N.Popov,
T.V.Tikhonova,
A.V.Tikhonov,
V.O.Popov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.07 /
1.85
|
Space group
|
P 21 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
194.920,
194.920,
194.920,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.5 /
17.4
|
Other elements in 4l3z:
The structure of Nitrite Complex of Tvnir, Second Middle Dose Data Set also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Nitrite Complex of Tvnir, Second Middle Dose Data Set
(pdb code 4l3z). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Nitrite Complex of Tvnir, Second Middle Dose Data Set, PDB code: 4l3z:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 4l3z
Go back to
Calcium Binding Sites List in 4l3z
Calcium binding site 1 out
of 4 in the Nitrite Complex of Tvnir, Second Middle Dose Data Set
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Nitrite Complex of Tvnir, Second Middle Dose Data Set within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca610
b:16.4
occ:1.00
|
OE1
|
A:GLN360
|
2.3
|
17.9
|
1.0
|
OE2
|
A:GLU302
|
2.3
|
15.1
|
1.0
|
O
|
A:LYS358
|
2.3
|
12.4
|
1.0
|
O
|
A:TYR303
|
2.4
|
13.5
|
1.0
|
OE1
|
A:GLU302
|
2.4
|
14.3
|
1.0
|
O
|
A:HOH965
|
2.5
|
16.8
|
1.0
|
O
|
A:HOH868
|
2.6
|
14.9
|
1.0
|
CD
|
A:GLU302
|
2.7
|
14.5
|
1.0
|
CD
|
A:GLN360
|
3.5
|
18.0
|
1.0
|
C
|
A:TYR303
|
3.5
|
13.3
|
1.0
|
C
|
A:LYS358
|
3.5
|
12.1
|
1.0
|
N
|
A:TYR303
|
3.9
|
12.6
|
1.0
|
NE2
|
A:GLN360
|
4.1
|
18.9
|
1.0
|
CA
|
A:LEU359
|
4.2
|
11.6
|
1.0
|
CG
|
A:GLU302
|
4.3
|
13.6
|
1.0
|
OH
|
A:TYR335
|
4.3
|
13.5
|
1.0
|
N
|
A:LEU359
|
4.3
|
10.8
|
1.0
|
OD1
|
A:ASN304
|
4.3
|
13.4
|
0.5
|
N
|
A:GLN360
|
4.3
|
12.3
|
1.0
|
CA
|
A:TYR303
|
4.4
|
13.5
|
1.0
|
N
|
A:ASN304
|
4.5
|
13.7
|
1.0
|
C
|
A:LEU359
|
4.5
|
11.7
|
1.0
|
OD1
|
A:ASP346
|
4.5
|
15.7
|
1.0
|
OD2
|
A:ASP346
|
4.5
|
16.3
|
1.0
|
CE1
|
A:PHE328
|
4.6
|
14.2
|
1.0
|
CA
|
A:LYS358
|
4.6
|
12.0
|
1.0
|
CB
|
A:LYS358
|
4.6
|
11.7
|
1.0
|
CA
|
A:ASN304
|
4.7
|
14.7
|
1.0
|
CG
|
A:GLN360
|
4.7
|
16.8
|
1.0
|
CB
|
A:GLN360
|
4.8
|
14.5
|
1.0
|
N
|
A:LYS358
|
4.9
|
12.9
|
1.0
|
OD1
|
A:ASN304
|
4.9
|
16.3
|
0.5
|
CG
|
A:ASP346
|
4.9
|
15.1
|
1.0
|
C
|
A:GLU302
|
4.9
|
12.9
|
1.0
|
CG
|
A:LYS358
|
5.0
|
11.7
|
1.0
|
|
Calcium binding site 2 out
of 4 in 4l3z
Go back to
Calcium Binding Sites List in 4l3z
Calcium binding site 2 out
of 4 in the Nitrite Complex of Tvnir, Second Middle Dose Data Set
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Nitrite Complex of Tvnir, Second Middle Dose Data Set within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca611
b:14.1
occ:0.50
|
O
|
A:HOH1034
|
2.3
|
25.4
|
1.0
|
O
|
A:PRO116
|
2.3
|
11.1
|
1.0
|
O3
|
A:GOL613
|
2.4
|
14.8
|
1.0
|
O
|
A:HOH911
|
2.4
|
10.6
|
1.0
|
O2A
|
A:HEC603
|
2.5
|
10.4
|
1.0
|
O
|
A:HOH928
|
2.7
|
17.1
|
1.0
|
C
|
A:PRO116
|
3.4
|
11.1
|
1.0
|
C3
|
A:GOL613
|
3.5
|
16.0
|
1.0
|
O1A
|
A:HEC604
|
3.7
|
14.6
|
1.0
|
CGA
|
A:HEC603
|
3.7
|
10.6
|
1.0
|
OG
|
A:SER84
|
4.0
|
11.0
|
1.0
|
CB
|
A:SER84
|
4.0
|
11.2
|
1.0
|
O
|
A:HOH1111
|
4.0
|
17.4
|
0.5
|
CD
|
A:PRO116
|
4.1
|
10.3
|
1.0
|
O
|
A:HOH1020
|
4.2
|
10.1
|
0.5
|
O2
|
A:GOL613
|
4.2
|
14.0
|
0.5
|
N
|
A:PRO116
|
4.2
|
10.6
|
1.0
|
CA
|
A:PRO116
|
4.2
|
11.1
|
1.0
|
CG
|
A:PRO116
|
4.3
|
10.8
|
1.0
|
N
|
A:ARG117
|
4.3
|
10.3
|
1.0
|
CAA
|
A:HEC603
|
4.4
|
9.4
|
1.0
|
CB
|
A:PRO116
|
4.4
|
10.8
|
1.0
|
CA
|
A:ARG117
|
4.4
|
9.9
|
1.0
|
C2
|
A:GOL613
|
4.4
|
16.8
|
1.0
|
O1A
|
A:HEC603
|
4.4
|
11.4
|
1.0
|
CGA
|
A:HEC604
|
4.5
|
16.0
|
1.0
|
CA
|
A:SER84
|
4.7
|
10.9
|
1.0
|
CB
|
A:GLU115
|
4.7
|
12.4
|
1.0
|
OE1
|
A:GLU115
|
4.7
|
15.6
|
1.0
|
CBA
|
A:HEC603
|
4.7
|
10.0
|
1.0
|
C
|
A:GLU115
|
4.8
|
10.7
|
1.0
|
|
Calcium binding site 3 out
of 4 in 4l3z
Go back to
Calcium Binding Sites List in 4l3z
Calcium binding site 3 out
of 4 in the Nitrite Complex of Tvnir, Second Middle Dose Data Set
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Nitrite Complex of Tvnir, Second Middle Dose Data Set within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca610
b:15.3
occ:1.00
|
O
|
B:LYS358
|
2.3
|
11.6
|
1.0
|
OE1
|
B:GLN360
|
2.3
|
16.4
|
1.0
|
O
|
B:TYR303
|
2.3
|
10.8
|
1.0
|
OE2
|
B:GLU302
|
2.4
|
11.5
|
1.0
|
O
|
B:HOH989
|
2.5
|
16.1
|
1.0
|
O
|
B:HOH892
|
2.5
|
15.7
|
1.0
|
OE1
|
B:GLU302
|
2.5
|
10.4
|
1.0
|
CD
|
B:GLU302
|
2.8
|
11.0
|
1.0
|
CD
|
B:GLN360
|
3.5
|
15.6
|
1.0
|
C
|
B:LYS358
|
3.5
|
10.5
|
1.0
|
C
|
B:TYR303
|
3.6
|
10.8
|
1.0
|
N
|
B:TYR303
|
4.0
|
10.1
|
1.0
|
NE2
|
B:GLN360
|
4.1
|
17.0
|
1.0
|
CA
|
B:LEU359
|
4.2
|
10.1
|
1.0
|
OH
|
B:TYR335
|
4.3
|
11.8
|
1.0
|
N
|
B:LEU359
|
4.3
|
10.1
|
1.0
|
N
|
B:GLN360
|
4.3
|
10.3
|
1.0
|
CG
|
B:GLU302
|
4.4
|
11.1
|
1.0
|
OD1
|
B:ASN304
|
4.4
|
12.4
|
0.5
|
C
|
B:LEU359
|
4.4
|
10.8
|
1.0
|
CA
|
B:TYR303
|
4.4
|
10.4
|
1.0
|
OD1
|
B:ASP346
|
4.5
|
14.3
|
1.0
|
N
|
B:ASN304
|
4.5
|
10.9
|
1.0
|
OD2
|
B:ASP346
|
4.5
|
13.1
|
1.0
|
CE2
|
B:PHE328
|
4.5
|
10.1
|
1.0
|
CA
|
B:LYS358
|
4.6
|
10.1
|
1.0
|
CB
|
B:LYS358
|
4.6
|
10.3
|
1.0
|
CA
|
B:ASN304
|
4.6
|
11.9
|
1.0
|
CG
|
B:GLN360
|
4.7
|
15.4
|
1.0
|
OD1
|
B:ASN304
|
4.7
|
13.1
|
0.5
|
CB
|
B:GLN360
|
4.8
|
12.2
|
1.0
|
CG
|
B:ASP346
|
4.9
|
12.5
|
1.0
|
N
|
B:LYS358
|
4.9
|
9.7
|
1.0
|
C
|
B:GLU302
|
5.0
|
10.3
|
1.0
|
|
Calcium binding site 4 out
of 4 in 4l3z
Go back to
Calcium Binding Sites List in 4l3z
Calcium binding site 4 out
of 4 in the Nitrite Complex of Tvnir, Second Middle Dose Data Set
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Nitrite Complex of Tvnir, Second Middle Dose Data Set within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca611
b:11.2
occ:0.50
|
O
|
B:HOH1060
|
1.9
|
6.8
|
0.5
|
O
|
B:PRO116
|
2.3
|
9.1
|
1.0
|
O1
|
B:GOL613
|
2.4
|
12.7
|
1.0
|
O
|
B:HOH935
|
2.4
|
10.2
|
1.0
|
O1A
|
B:HEC603
|
2.6
|
9.4
|
1.0
|
O
|
B:HOH952
|
2.6
|
17.7
|
1.0
|
O1A
|
B:HEC604
|
3.0
|
12.4
|
0.5
|
C
|
B:PRO116
|
3.4
|
8.6
|
1.0
|
C1
|
B:GOL613
|
3.5
|
12.9
|
1.0
|
O1A
|
B:HEC604
|
3.6
|
8.6
|
0.5
|
CGA
|
B:HEC603
|
3.7
|
9.2
|
1.0
|
CGA
|
B:HEC604
|
3.9
|
11.0
|
0.5
|
O
|
B:HOH1137
|
3.9
|
14.3
|
0.5
|
O2A
|
B:HEC604
|
4.0
|
11.4
|
0.5
|
OG
|
B:SER84
|
4.1
|
9.7
|
1.0
|
O
|
B:HOH1046
|
4.1
|
8.9
|
0.5
|
O2
|
B:GOL613
|
4.1
|
10.4
|
0.5
|
CB
|
B:SER84
|
4.1
|
9.4
|
1.0
|
CD
|
B:PRO116
|
4.2
|
8.0
|
1.0
|
N
|
B:PRO116
|
4.2
|
8.0
|
1.0
|
CG
|
B:PRO116
|
4.2
|
8.4
|
1.0
|
CA
|
B:PRO116
|
4.2
|
8.3
|
1.0
|
CB
|
B:PRO116
|
4.3
|
8.0
|
1.0
|
N
|
B:ARG117
|
4.3
|
8.3
|
1.0
|
CAA
|
B:HEC603
|
4.3
|
7.8
|
1.0
|
C2
|
B:GOL613
|
4.4
|
13.7
|
1.0
|
CA
|
B:ARG117
|
4.4
|
8.0
|
1.0
|
O2A
|
B:HEC603
|
4.4
|
9.8
|
1.0
|
CGA
|
B:HEC604
|
4.5
|
8.6
|
0.5
|
OE1
|
B:GLU115
|
4.6
|
13.0
|
1.0
|
CB
|
B:GLU115
|
4.7
|
9.2
|
1.0
|
CBA
|
B:HEC603
|
4.7
|
8.5
|
1.0
|
CA
|
B:SER84
|
4.7
|
9.5
|
1.0
|
C
|
B:GLU115
|
4.8
|
7.9
|
1.0
|
|
Reference:
A.A.Trofimov,
K.M.Polyakov,
V.A.Lazarenko,
A.N.Popov,
T.V.Tikhonova,
A.V.Tikhonov,
V.O.Popov.
Investigation of the X-Ray-Induced Nitrite Reduction Catalysed By Cytochrome C Nitrite Reductase From the Bacterium Thioalkalivibrio Nitratireducens To Be Published.
Page generated: Sun Jul 14 09:25:13 2024
|