Atomistry » Iron » PDB 1rte-1sdk » 1ryt
Atomistry »
  Iron »
    PDB 1rte-1sdk »
      1ryt »

Iron in PDB 1ryt: Rubrerythrin

Protein crystallography data

The structure of Rubrerythrin, PDB code: 1ryt was solved by F.Demare, D.M.Kurtz, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 50.400, 82.000, 100.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 25.6

Iron Binding Sites:

The binding sites of Iron atom in the Rubrerythrin (pdb code 1ryt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Rubrerythrin, PDB code: 1ryt:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 1ryt

Go back to Iron Binding Sites List in 1ryt
Iron binding site 1 out of 3 in the Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rubrerythrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:24.6
occ:0.90
OE1 A:GLU128 2.1 22.7 1.0
OE2 A:GLU53 2.1 28.3 1.0
OE1 A:GLU94 2.1 22.1 1.0
O A:HOH680 2.2 20.6 1.0
OE2 A:GLU94 2.3 24.3 1.0
ND1 A:HIS131 2.5 17.5 1.0
CD A:GLU94 2.5 24.6 1.0
CD A:GLU53 2.9 19.9 1.0
CD A:GLU128 3.0 24.2 1.0
FE A:FE601 3.2 22.7 0.9
OE1 A:GLU53 3.2 21.2 1.0
CE1 A:HIS131 3.3 16.1 1.0
OE2 A:GLU128 3.5 25.3 1.0
CG A:HIS131 3.6 14.6 1.0
CB A:HIS131 3.9 15.1 1.0
CG A:GLU94 4.0 20.1 1.0
CG A:GLU53 4.2 21.5 1.0
CG A:GLU128 4.3 18.4 1.0
CA A:GLU128 4.3 11.4 1.0
CB A:GLU128 4.4 13.1 1.0
OH A:TYR27 4.5 20.6 1.0
CE2 A:TYR27 4.5 15.0 1.0
NE2 A:HIS131 4.5 18.4 1.0
CG2 A:THR49 4.5 10.1 1.0
O A:HOH679 4.5 20.6 1.0
CD2 A:HIS131 4.7 16.2 1.0
OE1 A:GLU97 4.7 23.1 1.0
CB A:GLU94 4.8 18.7 1.0
CE1 A:HIS56 4.9 19.2 1.0
OE2 A:GLU97 4.9 28.0 1.0
ND1 A:HIS56 5.0 20.9 1.0
CZ A:TYR27 5.0 18.3 1.0

Iron binding site 2 out of 3 in 1ryt

Go back to Iron Binding Sites List in 1ryt
Iron binding site 2 out of 3 in the Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rubrerythrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:22.7
occ:0.90
O A:HOH680 1.9 20.6 1.0
OE2 A:GLU128 2.0 25.3 1.0
OE1 A:GLU20 2.1 30.8 1.0
OE1 A:GLU53 2.2 21.2 1.0
OE1 A:GLU97 2.2 23.1 1.0
OE2 A:GLU20 2.5 28.2 1.0
CD A:GLU20 2.6 28.4 1.0
CD A:GLU128 2.8 24.2 1.0
CD A:GLU97 3.0 25.4 1.0
CD A:GLU53 3.1 19.9 1.0
OE1 A:GLU128 3.1 22.7 1.0
OE2 A:GLU97 3.1 28.0 1.0
FE A:FE600 3.2 24.6 0.9
OE2 A:GLU53 3.5 28.3 1.0
CG A:GLU128 4.2 18.4 1.0
CG A:GLU20 4.2 23.2 1.0
ND1 A:HIS56 4.2 20.9 1.0
OE1 A:GLU94 4.2 22.1 1.0
CG A:GLU53 4.3 21.5 1.0
O A:HOH679 4.3 20.6 1.0
CG A:GLU97 4.4 26.8 1.0
OH A:TYR102 4.6 30.5 1.0
CE2 A:TYR102 4.6 32.2 1.0
CB A:GLU97 4.9 24.4 1.0
CE1 A:HIS56 4.9 19.2 1.0
CB A:GLU53 4.9 16.0 1.0
CD A:GLU94 4.9 24.6 1.0
OE2 A:GLU94 4.9 24.3 1.0
CB A:GLU20 5.0 16.7 1.0

Iron binding site 3 out of 3 in 1ryt

Go back to Iron Binding Sites List in 1ryt
Iron binding site 3 out of 3 in the Rubrerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rubrerythrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.8
occ:1.00
SG A:CYS161 2.1 14.7 1.0
SG A:CYS158 2.2 13.1 1.0
SG A:CYS174 2.3 19.9 1.0
SG A:CYS177 2.4 18.4 1.0
CB A:CYS174 3.2 16.7 1.0
CB A:CYS158 3.2 12.4 1.0
CB A:CYS161 3.3 17.5 1.0
CB A:CYS177 3.4 16.2 1.0
N A:CYS161 3.7 16.6 1.0
N A:CYS177 3.8 20.1 1.0
CA A:CYS161 4.0 14.1 1.0
CA A:CYS177 4.1 19.2 1.0
CB A:TYR163 4.4 16.5 1.0
CB A:ASN160 4.6 15.5 1.0
CA A:CYS174 4.6 17.1 1.0
CA A:CYS158 4.6 16.0 1.0
C A:CYS161 4.7 14.2 1.0
C A:ASN160 4.7 17.4 1.0
CB A:ALA176 4.7 16.2 1.0
N A:GLY162 4.7 14.3 1.0
N A:TYR163 4.8 17.7 1.0
C A:CYS177 4.8 19.6 1.0
C A:ALA176 4.9 21.4 1.0
N A:ALA178 5.0 19.9 1.0

Reference:

F.Demare, D.M.Kurtz Jr., P.Nordlund. The Structure of Desulfovibrio Vulgaris Rubrerythrin Reveals A Unique Combination of Rubredoxin-Like FES4 and Ferritin-Like Diiron Domains. Nat.Struct.Biol. V. 3 539 1996.
ISSN: ISSN 1072-8368
PubMed: 8646540
DOI: 10.1038/NSB0696-539
Page generated: Wed Jul 16 20:32:07 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy