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Calcium in PDB 6x0i: Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp

Enzymatic activity of Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp

All present enzymatic activity of Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp:
1.14.13.196;

Protein crystallography data

The structure of Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp, PDB code: 6x0i was solved by J.J.Tanner, A.C.Campbell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.21 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.507, 154.868, 90.483, 90.00, 109.25, 90.00
R / Rfree (%) 16.8 / 21.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp (pdb code 6x0i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp, PDB code: 6x0i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6x0i

Go back to Calcium Binding Sites List in 6x0i
Calcium binding site 1 out of 4 in the Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:42.9
occ:1.00
 O A:ASP288 2.4 32.2 1.0
C A:ASP288 3.6 23.4 1.0
OG B:SER138 3.7 28.5 0.5
CB A:ASP288 4.0 38.5 1.0
O B:HOH887 4.2 37.1 1.0
OD2 A:ASP288 4.3 69.3 1.0
CG A:ASP288 4.3 57.7 1.0
CA A:ASP288 4.4 29.1 1.0
CB B:SER138 4.4 27.0 0.5
CB B:SER138 4.5 27.0 0.6
OE2 D:GLU333 4.6 27.6 1.0
O B:HOH837 4.6 44.8 1.0
N A:SER289 4.6 19.3 1.0
O B:ASN136 4.7 19.6 1.0
CA A:SER289 4.7 14.1 1.0
C A:SER289 4.8 21.8 1.0
N A:PRO290 4.8 20.6 1.0
CD A:PRO290 4.9 17.2 1.0
OG B:SER138 4.9 26.3 0.6

Calcium binding site 2 out of 4 in 6x0i

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Calcium binding site 2 out of 4 in the Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:36.3
occ:1.00
 O C:HOH774 2.4 38.6 1.0
O B:HOH912 2.5 36.1 1.0
O B:ASP288 2.5 31.8 1.0
OD2 B:ASP288 2.6 24.4 0.4
O A:HOH771 2.8 34.5 1.0
CG B:ASP288 3.2 29.8 0.4
C B:ASP288 3.7 27.7 1.0
OD1 B:ASP288 3.8 34.8 0.4
OG A:SER138 3.9 23.8 0.5
CB B:ASP288 4.0 32.9 0.6
CB B:ASP288 4.0 32.3 0.4
CA B:ASP288 4.4 26.8 0.6
CA B:ASP288 4.4 27.1 0.4
OE2 C:GLU333 4.4 23.7 1.0
OD2 B:ASP288 4.4 39.0 0.6
CG B:ASP288 4.4 34.6 0.6
CB A:SER138 4.5 20.3 0.5
CB A:SER138 4.5 20.1 0.5
O A:HOH910 4.6 45.3 1.0
O A:HOH904 4.6 25.9 1.0
N B:SER289 4.7 26.1 1.0
OG A:SER138 4.7 20.6 0.5
O A:HOH890 4.8 38.0 1.0
CA B:SER289 4.8 18.1 1.0
O C:HOH734 4.8 41.0 1.0
O A:ASN136 4.8 18.8 1.0
C B:SER289 4.9 15.4 1.0
N B:PRO290 4.9 16.5 1.0

Calcium binding site 3 out of 4 in 6x0i

Go back to Calcium Binding Sites List in 6x0i
Calcium binding site 3 out of 4 in the Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:56.9
occ:1.00
 O C:ASP288 2.6 34.9 1.0
C C:ASP288 3.8 28.5 1.0
OG D:SER138 3.8 33.3 1.0
CB C:ASP288 4.1 36.6 1.0
CG C:ASP288 4.4 52.2 1.0
OE1 B:GLU333 4.4 25.5 1.0
OD2 C:ASP288 4.5 62.7 1.0
CB D:SER138 4.5 23.9 1.0
CA C:ASP288 4.5 30.8 1.0
O D:ASN136 4.8 23.0 1.0
N C:SER289 4.8 25.6 1.0
N C:PRO290 4.9 18.2 1.0
C C:SER289 4.9 17.9 1.0
CA C:SER289 4.9 18.1 1.0
O D:HOH906 4.9 40.8 1.0
CD C:PRO290 4.9 16.5 1.0

Calcium binding site 4 out of 4 in 6x0i

Go back to Calcium Binding Sites List in 6x0i
Calcium binding site 4 out of 4 in the Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Oxidized Sida Ornithine Hydroxylase with the Fad "in" and Complexed with Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca604

b:52.7
occ:1.00
 O C:HOH918 2.3 37.9 1.0
O C:HOH739 2.5 27.2 1.0
O D:ASP288 2.5 42.3 1.0
OG C:SER138 3.6 19.5 0.6
C D:ASP288 3.7 36.1 1.0
OE2 A:GLU333 4.2 30.2 1.0
O C:HOH863 4.2 26.5 1.0
CB D:ASP288 4.3 53.9 1.0
CB C:SER138 4.3 20.3 0.6
CB C:SER138 4.3 20.4 0.4
O C:ASN136 4.5 22.4 1.0
O A:HOH924 4.5 48.2 1.0
CG D:ASP288 4.5 64.6 1.0
CA D:ASP288 4.6 39.8 1.0
N D:PRO290 4.6 19.9 1.0
OD2 D:ASP288 4.6 68.8 1.0
CA D:SER289 4.6 18.1 1.0
N D:SER289 4.6 19.8 1.0
C D:SER289 4.7 21.1 1.0
CD D:PRO290 4.7 16.2 1.0
OG C:SER138 4.8 18.0 0.4
CA D:PRO290 4.9 18.4 1.0

Reference:

A.C.Campbell, K.M.Stiers, J.S.Martin Del Campo, R.Mehra-Chaudhary, P.Sobrado, J.J.Tanner. Trapping Conformational States of A Flavin-Dependent N -Monooxygenase in Crystallo Reveals Protein and Flavin Dynamics. J.Biol.Chem. V. 295 13239 2020.
ISSN: ESSN 1083-351X
PubMed: 32723870
DOI: 10.1074/JBC.RA120.014750
Page generated: Tue Jul 16 17:39:45 2024

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