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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:

Iron (Fe) 16 atoms

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: Sat Dec 12 04:56:18 2020

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