Atomistry » Iron » PDB 3s6b-3sxt » 3sid
Atomistry »
  Iron »
    PDB 3s6b-3sxt »
      3sid »

Iron in PDB 3sid: Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy

Protein crystallography data

The structure of Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy, PDB code: 3sid was solved by R.B.Cooley, D.J.Arp, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.74 / 1.40
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 82.009, 82.009, 46.440, 90.00, 90.00, 120.00
R / Rfree (%) 11.5 / 15.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy (pdb code 3sid). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy, PDB code: 3sid:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3sid

Go back to Iron Binding Sites List in 3sid
Iron binding site 1 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy


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 Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:9.0
occ:1.00
OE2 A:GLU71 2.0 9.9 1.0
OE1 A:GLU162 2.0 9.6 1.0
N3 A:AZI300 2.2 8.7 0.5
OE2 A:GLU128 2.2 8.5 1.0
O A:HOH183 2.2 11.8 0.5
ND1 A:HIS165 2.2 9.1 1.0
OE1 A:GLU128 2.3 8.5 1.0
CD A:GLU128 2.6 7.6 1.0
N2 A:AZI300 2.9 9.9 0.5
CD A:GLU71 2.9 8.5 1.0
CD A:GLU162 3.0 8.9 1.0
CE1 A:HIS165 3.1 9.6 1.0
OE1 A:GLU71 3.3 12.0 1.0
CG A:HIS165 3.3 7.5 1.0
OE2 A:GLU162 3.5 9.6 1.0
FE A:FE201 3.5 11.1 1.0
CB A:HIS165 3.7 7.8 1.0
N1 A:AZI300 3.9 11.5 0.5
CG A:GLU128 4.1 8.2 1.0
OE1 A:GLU131 4.1 13.6 0.5
CG2 A:ILE67 4.2 11.9 1.0
CG A:GLU162 4.2 8.6 1.0
CA A:GLU162 4.3 7.9 1.0
NE2 A:HIS165 4.3 8.5 1.0
CG A:GLU71 4.3 8.8 1.0
CD2 A:HIS165 4.4 8.5 1.0
CB A:GLU162 4.4 8.5 1.0
CE1 A:HIS74 4.4 12.3 1.0
CE2 A:TYR45 4.6 11.6 1.0
OH A:TYR45 4.6 14.1 1.0
OE1 A:GLU40 4.7 13.3 1.0
CD A:GLU131 4.8 11.2 0.5
O A:HOH204 4.8 12.1 0.5
OE2 A:GLU131 4.9 14.4 0.5
CB A:GLU128 5.0 8.6 1.0
CZ A:TYR45 5.0 12.5 1.0
O A:GLU162 5.0 9.0 1.0

Iron binding site 2 out of 4 in 3sid

Go back to Iron Binding Sites List in 3sid
Iron binding site 2 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy


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 Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:11.1
occ:1.00
O A:HOH204 1.9 12.1 0.5
OE2 A:GLU37 2.0 8.8 0.5
N3 A:AZI300 2.0 8.7 0.5
O A:HOH183 2.0 11.8 0.5
OE1 A:GLU40 2.1 13.3 1.0
OE1 A:GLU71 2.1 12.0 1.0
OE2 A:GLU162 2.1 9.6 1.0
OE1 A:GLU37 2.2 11.1 0.5
OE2 A:GLU131 2.3 14.4 0.5
N2 A:AZI300 2.7 9.9 0.5
CD A:GLU37 2.9 9.3 0.5
CD A:GLU71 3.0 8.5 1.0
CD A:GLU37 3.1 10.6 0.5
CD A:GLU40 3.1 12.7 1.0
CD A:GLU162 3.1 8.9 1.0
CD A:GLU131 3.1 11.2 0.5
OE1 A:GLU37 3.2 13.1 0.5
OE2 A:GLU37 3.2 14.1 0.5
OE1 A:GLU131 3.4 13.6 0.5
OE1 A:GLU162 3.4 9.6 1.0
OE2 A:GLU40 3.5 17.1 1.0
FE A:FE200 3.5 9.0 1.0
OE2 A:GLU71 3.5 9.9 1.0
N1 A:AZI300 3.7 11.5 0.5
CG A:GLU71 4.2 8.8 1.0
ND1 A:HIS74 4.2 11.0 1.0
CG A:GLU37 4.2 9.4 0.5
CG A:GLU162 4.4 8.6 1.0
CG A:GLU131 4.4 9.6 0.5
CG A:GLU40 4.5 10.6 1.0
CG A:GLU37 4.5 8.7 0.5
CE1 A:HIS74 4.6 12.3 1.0
CB A:GLU71 4.7 9.5 1.0
OE1 A:GLU128 4.8 8.5 1.0
CB A:GLU40 4.8 10.1 1.0
CE2 A:TYR136 4.8 14.7 1.0
CA A:GLU37 4.9 9.9 0.5
CA A:GLU37 4.9 9.8 0.5
CB A:GLU37 4.9 9.6 0.5
OE2 A:GLU128 4.9 8.5 1.0
CG A:GLU131 5.0 9.4 0.5

Iron binding site 3 out of 4 in 3sid

Go back to Iron Binding Sites List in 3sid
Iron binding site 3 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:10.9
occ:1.00
OE1 B:GLU37 2.0 8.4 0.5
O B:HOH198 2.0 12.2 0.5
O B:HOH181 2.0 11.3 0.5
OE1 B:GLU71 2.1 12.1 1.0
N1 B:AZI300 2.1 7.8 0.5
OE2 B:GLU162 2.1 10.3 1.0
OE1 B:GLU40 2.1 13.6 1.0
OE1 B:GLU131 2.2 13.8 0.5
OE1 B:GLU37 2.3 11.4 0.5
N2 B:AZI300 2.7 10.1 0.5
CD B:GLU37 2.9 9.8 0.5
CD B:GLU71 3.0 9.1 1.0
CD B:GLU37 3.0 11.0 0.5
CD B:GLU162 3.1 10.1 1.0
CD B:GLU131 3.1 12.3 0.5
CD B:GLU40 3.1 13.0 1.0
OE2 B:GLU37 3.2 13.7 0.5
OE2 B:GLU37 3.2 12.8 0.5
OE2 B:GLU131 3.4 14.4 0.5
OE1 B:GLU162 3.4 9.0 1.0
OE2 B:GLU40 3.5 16.6 1.0
FE B:FE201 3.5 9.0 1.0
OE2 B:GLU71 3.5 10.5 1.0
N3 B:AZI300 3.7 10.7 0.5
CG B:GLU71 4.2 9.2 1.0
ND1 B:HIS74 4.2 10.7 1.0
CG B:GLU37 4.3 9.7 0.5
CG B:GLU162 4.4 8.7 1.0
CG B:GLU37 4.5 9.2 0.5
CG B:GLU40 4.5 10.2 1.0
CG B:GLU131 4.5 9.3 0.5
CE1 B:HIS74 4.6 10.8 1.0
CB B:GLU71 4.7 9.2 1.0
OE1 B:GLU128 4.8 8.4 1.0
CA B:GLU37 4.8 10.4 0.5
CE2 B:TYR136 4.8 14.9 1.0
CB B:GLU40 4.8 10.4 1.0
OE2 B:GLU128 4.9 9.4 1.0
CG B:GLU131 5.0 10.6 0.5
CB B:GLU37 5.0 9.9 0.5
CA B:GLU37 5.0 9.4 0.5
CB B:GLU37 5.0 9.6 0.5

Iron binding site 4 out of 4 in 3sid

Go back to Iron Binding Sites List in 3sid
Iron binding site 4 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:9.0
occ:1.00
OE2 B:GLU71 2.0 10.5 1.0
OE1 B:GLU162 2.0 9.0 1.0
N1 B:AZI300 2.1 7.8 0.5
O B:HOH181 2.2 11.3 0.5
OE2 B:GLU128 2.2 9.4 1.0
ND1 B:HIS165 2.2 8.8 1.0
OE1 B:GLU128 2.3 8.4 1.0
CD B:GLU128 2.6 7.7 1.0
N2 B:AZI300 2.9 10.1 0.5
CD B:GLU71 2.9 9.1 1.0
CD B:GLU162 3.0 10.1 1.0
CE1 B:HIS165 3.1 10.0 1.0
OE1 B:GLU71 3.2 12.1 1.0
CG B:HIS165 3.3 7.9 1.0
OE2 B:GLU162 3.5 10.3 1.0
FE B:FE200 3.5 10.9 1.0
CB B:HIS165 3.7 8.8 1.0
N3 B:AZI300 3.9 10.7 0.5
OE2 B:GLU131 4.1 14.4 0.5
CG B:GLU128 4.1 7.6 1.0
CG2 B:ILE67 4.2 11.4 1.0
CG B:GLU162 4.2 8.7 1.0
CA B:GLU162 4.3 7.1 1.0
NE2 B:HIS165 4.3 8.6 1.0
CG B:GLU71 4.3 9.2 1.0
CB B:GLU162 4.4 9.0 1.0
CD2 B:HIS165 4.4 8.9 1.0
CE1 B:HIS74 4.4 10.8 1.0
CE2 B:TYR45 4.5 11.8 1.0
OH B:TYR45 4.6 14.8 1.0
OE1 B:GLU40 4.7 13.6 1.0
OE1 B:GLU131 4.8 13.8 0.5
CD B:GLU131 4.8 12.3 0.5
O B:HOH198 4.9 12.2 0.5
CB B:GLU128 4.9 8.9 1.0
CZ B:TYR45 5.0 12.3 1.0

Reference:

R.B.Cooley, D.J.Arp, P.A.Karplus. Symerythrin Structures at Atomic Resolution and the Origins of Rubrerythrins and the Ferritin-Like Superfamily. J.Mol.Biol. V. 413 177 2011.
ISSN: ISSN 0022-2836
PubMed: 21872605
DOI: 10.1016/J.JMB.2011.08.019
Page generated: Sun Dec 13 15:21:11 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