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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6ax6:

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

Iodine (I) 100 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus, PDB code: 6ax6:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6ax6

Go back to Iron Binding Sites List in 6ax6
Iron binding site 1 out of 2 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe934

b:69.6
occ:1.00
O A:HOH1015 2.3 59.6 1.0
NE2 A:HIS877 2.3 34.7 1.0
NE2 A:HIS825 2.4 34.8 1.0
OD1 A:ASP827 2.5 36.5 1.0
CE1 A:HIS877 3.2 33.0 1.0
CE1 A:HIS825 3.3 33.3 1.0
I A:IOD935 3.3 61.2 0.4
CG A:ASP827 3.3 32.6 1.0
CD2 A:HIS877 3.4 33.1 1.0
CD2 A:HIS825 3.4 28.3 1.0
OD2 A:ASP827 3.5 35.5 1.0
ND1 A:HIS877 4.4 30.7 1.0
CZ A:PHE893 4.4 26.6 1.0
ND1 A:HIS825 4.4 30.0 1.0
CG A:HIS877 4.5 31.9 1.0
CE1 A:PHE893 4.5 23.1 1.0
CG A:HIS825 4.5 26.6 1.0
CB A:ASP827 4.7 30.9 1.0

Iron binding site 2 out of 2 in 6ax6

Go back to Iron Binding Sites List in 6ax6
Iron binding site 2 out of 2 in the The Crystal Structure of A Lysyl Hydroxylase From Acanthamoeba Polyphaga Mimivirus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
B:Fe935

b:51.9
occ:1.00
O B:HOH1024 2.1 48.8 1.0
NE2 B:HIS877 2.2 30.8 1.0
OD1 B:ASP827 2.4 27.2 1.0
NE2 B:HIS825 2.4 26.0 1.0
CE1 B:HIS877 3.1 31.6 1.0
CG B:ASP827 3.2 26.9 1.0
OD2 B:ASP827 3.2 32.7 1.0
CD2 B:HIS877 3.3 24.6 1.0
CE1 B:HIS825 3.3 28.6 1.0
CD2 B:HIS825 3.4 23.2 1.0
I B:IOD919 3.5 0.1 1.0
ND1 B:HIS877 4.2 23.6 1.0
CG B:HIS877 4.4 27.4 1.0
ND1 B:HIS825 4.4 32.2 1.0
CG B:HIS825 4.5 20.5 1.0
CB B:ASP827 4.6 28.8 1.0
CZ B:PHE893 4.6 25.4 1.0
CE1 B:PHE893 4.7 22.1 1.0

Reference:

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
Page generated: Sun Dec 13 16:20:55 2020

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