Iodine in PDB 6ax6: The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus

All present enzymatic activity of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus:
1.14.11.4;

The structure of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus, PDB code: 6ax6 was solved by H.Guo, C.Tsai, M.D.Miller, S.Alvarado, J.A.Tainer, G.N.Phillips Jr., J.M.Kurie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.49 / 2.24
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.210, 109.210, 83.910, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 24

The structure of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100;

Binding sites:

The binding sites of Iodine atom in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus (pdb code 6ax6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 100 binding sites of Iodine where determined in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus, PDB code: 6ax6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I901 b:49.2 occ:1.00 N A:ILE882 3.7 33.1 1.0 CA A:PRO881 3.9 33.9 1.0 CG1 A:ILE882 4.0 33.5 1.0 CD1 A:LEU822 4.1 42.0 1.0 CB A:PRO881 4.2 33.9 1.0 CB A:TYR814 4.3 37.1 1.0 CD1 A:TYR814 4.3 39.1 1.0 C A:PRO881 4.4 37.7 1.0 O A:ASP815 4.6 39.6 1.0 CG A:TYR814 4.6 36.3 1.0 CD1 A:ILE882 4.8 32.8 1.0 CA A:ILE882 4.8 38.9 1.0 CB A:ILE882 4.8 33.5 1.0 O A:ILE882 4.8 31.9 1.0 CD2 A:LEU822 4.9 45.2 1.0 CG A:LEU822 4.9 44.1 1.0 CG2 A:ILE882 5.0 29.1 1.0

Iodine binding site 2 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I902 b:40.8 occ:0.64 I A:IOD902 0.0 40.8 0.6 NH1 A:ARG795 3.5 78.7 1.0 O A:HOH1010 3.7 37.1 1.0 I A:IOD902 3.7 0.2 0.4 N A:THR803 3.7 30.4 1.0 CB A:ALA791 4.0 24.9 1.0 CA A:LYS802 4.1 32.2 1.0 CB A:LYS802 4.3 34.1 1.0 C A:LYS802 4.4 39.5 1.0 O A:THR803 4.4 35.3 1.0 CD A:ARG795 4.5 44.4 1.0 CB A:THR803 4.6 33.3 1.0 CA A:THR803 4.6 30.5 1.0 CZ A:ARG795 4.7 67.8 1.0 CG A:ARG795 4.8 37.8 1.0 O A:ALA791 4.8 33.6 1.0 C A:ALA791 5.0 36.5 1.0 CA A:ALA791 5.0 33.9 1.0

Iodine binding site 3 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I902 b:0.2 occ:0.36 I A:IOD902 0.0 0.2 0.4 NH1 A:ARG795 3.2 78.7 1.0 O A:PHE787 3.3 40.4 1.0 I A:IOD902 3.7 40.8 0.6 CG A:PRO792 4.0 34.3 1.0 CB A:ALA791 4.1 24.9 1.0 CD A:PRO792 4.1 34.1 1.0 CZ A:ARG795 4.3 67.8 1.0 N A:PRO792 4.4 35.5 1.0 C A:PHE787 4.5 29.9 1.0 NH2 A:ARG795 4.6 60.2 1.0 C A:ALA791 4.8 36.5 1.0 CA A:PRO792 4.9 34.6 1.0 CB A:PRO792 5.0 36.8 1.0

Iodine binding site 4 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I903 b:61.9 occ:1.00 O A:HOH1013 3.6 44.2 1.0 N A:VAL863 3.6 32.9 1.0 CB A:LYS862 3.9 39.0 1.0 CA A:LYS862 3.9 34.3 1.0 CG2 A:VAL863 4.0 31.5 1.0 CG A:GLU839 4.0 40.5 1.0 CD A:GLU839 4.2 45.0 1.0 OE2 A:GLU839 4.3 51.8 1.0 CB A:VAL863 4.3 32.9 1.0 C A:LYS862 4.3 33.3 1.0 CA A:VAL863 4.5 35.7 1.0 CG A:LYS862 4.6 49.2 1.0 OE1 A:GLU839 4.7 53.8 1.0 CB A:GLU839 4.8 38.6 1.0

Iodine binding site 5 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I904 b:56.0 occ:0.43 I A:IOD904 0.0 56.0 0.4 I A:IOD904 2.5 53.0 0.6 N A:TYR774 3.6 31.7 1.0 CB A:ASP779 3.7 32.9 1.0 CD2 A:TYR774 3.8 39.8 1.0 O A:ALA809 3.8 33.0 1.0 CB A:LEU773 3.9 27.7 1.0 CB A:ALA809 4.0 27.9 1.0 CB A:TYR774 4.0 34.5 1.0 N A:LEU773 4.1 34.5 1.0 N A:ALA809 4.3 30.0 1.0 CA A:LEU773 4.3 36.0 1.0 C A:LEU773 4.3 36.7 1.0 CA A:ASP779 4.3 34.1 1.0 CA A:TYR774 4.3 35.2 1.0 CG A:TYR774 4.4 31.3 1.0 CA A:ALA809 4.5 23.4 1.0 C A:ALA809 4.6 31.2 1.0 CE2 A:TYR774 4.8 39.6 1.0 CG A:LEU773 4.9 34.2 1.0 CG A:ASP779 5.0 43.6 1.0

Iodine binding site 6 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I904 b:53.0 occ:0.57 I A:IOD904 0.0 53.0 0.6 I A:IOD904 2.5 56.0 0.4 CB A:ASP779 3.8 32.9 1.0 CB A:ALA809 3.8 27.9 1.0 CA A:ASP779 4.0 34.1 1.0 O A:ASP779 4.0 39.0 1.0 CG2 A:ILE806 4.1 31.8 1.0 CD1 A:TRP782 4.2 31.5 1.0 C A:ASP779 4.5 32.2 1.0 CB A:TRP782 4.6 30.9 1.0 N A:ALA809 4.7 30.0 1.0 CG A:TRP782 4.8 32.7 1.0 CA A:ALA809 4.9 23.4 1.0 CD1 A:ILE806 4.9 39.0 1.0 CB A:ILE806 4.9 39.9 1.0

Iodine binding site 7 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:27.4 occ:0.61 I A:IOD905 0.0 27.4 0.6 I A:IOD905 3.4 24.3 0.1 NZ B:LYS804 3.6 41.0 1.0 N B:LYS802 3.7 32.0 1.0 CG B:LYS802 3.8 49.6 1.0 I A:IOD905 3.9 21.4 0.1 CB B:LYS802 4.0 35.9 1.0 CD1 B:TYR801 4.0 24.2 1.0 CD2 A:HIS826 4.1 24.2 1.0 CE1 B:TYR801 4.3 30.8 1.0 CA B:TYR801 4.4 29.1 1.0 CA B:LYS802 4.5 36.4 1.0 CE B:LYS804 4.5 47.0 1.0 CB A:HIS826 4.5 25.6 1.0 CG A:HIS826 4.6 28.2 1.0 C B:TYR801 4.6 30.7 1.0 O B:ASN800 4.7 35.9 1.0 O B:LYS802 4.7 33.7 1.0 CG B:TYR801 4.8 27.2 1.0

Iodine binding site 8 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:21.4 occ:0.14 I A:IOD905 0.0 21.4 0.1 I A:IOD905 2.3 29.6 0.1 O A:ASP827 3.5 34.1 1.0 I A:IOD905 3.9 27.4 0.6 C A:ASP827 4.1 34.7 1.0 CE1 B:TYR801 4.1 30.8 1.0 NZ B:LYS804 4.1 41.0 1.0 CA A:SER828 4.2 36.6 1.0 CG A:LYS872 4.3 32.5 1.0 CB A:HIS826 4.3 25.6 1.0 N A:SER828 4.3 33.6 1.0 CE B:LYS804 4.3 47.0 1.0 O A:HIS826 4.5 31.7 1.0 CB A:SER828 4.6 32.9 1.0 CD A:LYS872 4.6 31.6 1.0 C A:HIS826 4.7 32.3 1.0 CE A:LYS872 4.8 28.4 1.0 CD1 B:TYR801 4.8 24.2 1.0 OH B:TYR801 4.9 32.8 1.0 CZ B:TYR801 5.0 31.7 1.0 N A:ASP827 5.0 30.4 1.0

Iodine binding site 9 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:29.6 occ:0.14 I A:IOD905 0.0 29.6 0.1 I A:IOD905 2.3 21.4 0.1 O A:HOH1011 3.4 43.1 1.0 CE B:LYS804 3.7 47.0 1.0 CE A:LYS872 3.7 28.4 1.0 CD A:LYS872 4.0 31.6 1.0 NZ B:LYS804 4.0 41.0 1.0 NZ A:LYS872 4.2 35.7 1.0 OG A:SER828 4.2 44.7 1.0 CA A:SER828 4.2 36.6 1.0 OH B:TYR801 4.3 32.8 1.0 CB A:SER828 4.4 32.9 1.0 CG A:LYS872 4.4 32.5 1.0 O A:ASP827 4.6 34.1 1.0 CE1 B:TYR801 4.7 30.8 1.0 CD B:LYS804 4.7 49.2 1.0 CG B:LYS804 4.7 39.7 1.0 CZ B:TYR801 5.0 31.7 1.0

Iodine binding site 10 out of 100 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:24.3 occ:0.11 I A:IOD905 0.0 24.3 0.1 N A:HIS826 3.4 30.7 1.0 I A:IOD905 3.4 27.4 0.6 CA A:HIS825 3.8 31.0 1.0 CB A:HIS825 3.9 21.5 1.0 CD2 A:HIS826 4.0 24.2 1.0 C A:HIS825 4.1 33.4 1.0 O A:HIS826 4.3 31.7 1.0 CB A:HIS826 4.3 25.6 1.0 CA A:HIS826 4.3 24.0 1.0 CG A:HIS826 4.5 28.2 1.0 C A:HIS826 4.8 32.3 1.0 CE1 A:TYR876 4.8 29.8 1.0 O A:PRO824 4.9 32.3 1.0

H.F.Guo, C.L.Tsai, M.Terajima, X.Tan, P.Banerjee, M.D.Miller, X.Liu, J.Yu, J.Byemerwa, S.Alvarado, T.S.Kaoud, K.N.Dalby, N.Bota-Rabassedas, Y.Chen, M.Yamauchi, J.A.Tainer, G.N.Phillips, J.M.Kurie. Pro-Metastatic Collagen Lysyl Hydroxylase Dimer Assemblies Stabilized By FE2+-Binding. Nat Commun V. 9 512 2018.
ISSN: ESSN 2041-1723
PubMed: 29410444
DOI: 10.1038/S41467-018-02859-Z