Atomistry » Iron » PDB 5ufj-5utb » 5ulg
Atomistry »
  Iron »
    PDB 5ufj-5utb »
      5ulg »

Iron in PDB 5ulg: Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate

Enzymatic activity of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate

All present enzymatic activity of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate:
3.1.1.64;

Protein crystallography data

The structure of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate, PDB code: 5ulg was solved by P.D.Kiser, K.Palczewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.85 / 2.10
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 175.319, 175.319, 86.653, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 20.7

Other elements in 5ulg:

The structure of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate (pdb code 5ulg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate, PDB code: 5ulg:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5ulg

Go back to Iron Binding Sites List in 5ulg
Iron binding site 1 out of 2 in the Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:33.2
occ:1.00
O2 A:PLM602 1.9 58.6 1.0
NE2 A:HIS180 2.2 32.9 1.0
NE2 A:HIS527 2.2 32.0 1.0
NE2 A:HIS313 2.3 29.9 1.0
NE2 A:HIS241 2.4 29.7 1.0
C1 A:PLM602 2.8 53.2 1.0
CE1 A:HIS180 3.0 31.3 1.0
CE1 A:HIS527 3.1 32.9 1.0
C2 A:PLM602 3.1 51.8 1.0
CD2 A:HIS313 3.1 31.7 1.0
CD2 A:HIS527 3.2 31.9 1.0
CD2 A:HIS180 3.2 33.7 1.0
CE1 A:HIS241 3.3 28.7 1.0
CE1 A:HIS313 3.3 29.7 1.0
CD2 A:HIS241 3.4 26.8 1.0
O1 A:PLM602 4.0 56.3 1.0
ND1 A:HIS527 4.2 33.0 1.0
ND1 A:HIS180 4.2 34.0 1.0
CG A:HIS527 4.2 32.6 1.0
CG A:HIS313 4.3 30.8 1.0
CG A:HIS180 4.3 33.3 1.0
C3 A:PLM602 4.3 58.4 1.0
ND1 A:HIS313 4.4 31.6 1.0
C4 A:PLM602 4.4 58.5 1.0
ND1 A:HIS241 4.4 31.0 1.0
CG A:HIS241 4.5 26.9 1.0
CG1 A:VAL134 4.8 35.5 1.0

Iron binding site 2 out of 2 in 5ulg

Go back to Iron Binding Sites List in 5ulg
Iron binding site 2 out of 2 in the Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:30.2
occ:1.00
O1 B:PLM602 1.9 50.1 1.0
NE2 B:HIS527 2.2 32.0 1.0
NE2 B:HIS180 2.2 35.0 1.0
NE2 B:HIS313 2.2 28.8 1.0
NE2 B:HIS241 2.3 29.0 1.0
C1 B:PLM602 2.9 49.9 1.0
CE1 B:HIS527 3.1 30.1 1.0
CE1 B:HIS180 3.1 34.5 1.0
CD2 B:HIS313 3.1 29.0 1.0
CD2 B:HIS527 3.2 33.3 1.0
C2 B:PLM602 3.2 50.5 1.0
CE1 B:HIS241 3.2 28.8 1.0
CE1 B:HIS313 3.3 29.5 1.0
CD2 B:HIS180 3.3 31.8 1.0
CD2 B:HIS241 3.3 29.2 1.0
O2 B:PLM602 4.1 49.4 1.0
ND1 B:HIS527 4.2 31.2 1.0
CG B:HIS527 4.3 32.7 1.0
ND1 B:HIS180 4.3 34.9 1.0
C4 B:PLM602 4.3 52.3 1.0
CG B:HIS313 4.3 27.5 1.0
C3 B:PLM602 4.3 54.6 1.0
ND1 B:HIS313 4.3 28.6 1.0
ND1 B:HIS241 4.4 32.4 1.0
CG B:HIS180 4.4 35.5 1.0
CG B:HIS241 4.4 29.2 1.0
CG1 B:VAL134 4.9 35.1 1.0

Reference:

P.D.Kiser, J.Zhang, M.Badiee, J.Kinoshita, N.S.Peachey, G.P.Tochtrop, K.Palczewski. Rational Tuning of Visual Cycle Modulator Pharmacodynamics. J. Pharmacol. Exp. Ther. V. 362 131 2017.
ISSN: ESSN 1521-0103
PubMed: 28476927
DOI: 10.1124/JPET.117.240721
Page generated: Sun Dec 13 16:13:28 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy