Atomistry » Iron » PDB 3pur-3qjs » 3qhc
Atomistry »
  Iron »
    PDB 3pur-3qjs »
      3qhc »

Iron in PDB 3qhc: Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite

Protein crystallography data

The structure of Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite, PDB code: 3qhc 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) 26.68 / 1.25
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 81.499, 81.499, 46.341, 90.00, 90.00, 120.00
R / Rfree (%) 11.5 / 14.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite (pdb code 3qhc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite, PDB code: 3qhc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3qhc

Go back to Iron Binding Sites List in 3qhc
Iron binding site 1 out of 6 in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite


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 Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe182

b:16.3
occ:0.50
 O A:HOH339 0.9 16.8 0.5
OE2 A:GLU37 1.9 9.7 0.4
O A:HOH204 2.2 13.6 1.0
OE1 A:GLU40 2.3 19.4 1.0
FE A:FE183 2.4 7.6 0.5
OE1 A:GLU131 2.4 23.0 1.0
OE1 A:GLU162 2.5 18.5 1.0
OE1 A:GLU71 2.6 14.6 1.0
CD A:GLU37 2.7 9.1 0.4
OE1 A:GLU37 2.7 12.5 0.4
CD A:GLU162 3.2 7.6 1.0
CD A:GLU71 3.2 9.4 1.0
CD A:GLU131 3.3 15.9 1.0
CD A:GLU40 3.3 12.2 1.0
OE2 A:GLU162 3.4 8.5 1.0
OE2 A:GLU37 3.4 8.9 0.6
FE A:FE181 3.5 8.2 1.0
OE1 A:GLU37 3.6 10.6 0.6
OE2 A:GLU71 3.6 11.8 1.0
OE2 A:GLU40 3.6 12.2 1.0
OE2 A:GLU131 3.7 15.7 1.0
CD A:GLU37 3.7 7.9 0.6
O A:HOH324 3.9 10.2 0.3
CG A:GLU37 4.1 7.5 0.4
CG A:GLU71 4.3 10.1 1.0
CG A:GLU162 4.5 7.4 1.0
ND1 A:HIS74 4.5 8.8 1.0
OH A:TYR136 4.5 20.9 0.7
CE2 A:TYR136 4.6 10.8 0.7
CG A:GLU131 4.6 10.1 1.0
CG A:GLU40 4.6 10.2 1.0
OE1 A:GLU128 4.6 7.7 1.0
CE2 A:TYR136 4.8 8.2 0.3
CB A:GLU71 4.8 9.0 1.0
OE2 A:GLU128 4.9 9.6 1.0
CB A:GLU37 4.9 9.0 0.4
CB A:GLU40 4.9 9.8 1.0
CB A:GLU131 4.9 9.5 1.0
CG A:GLU37 4.9 9.5 0.6
OH A:TYR136 5.0 7.4 0.3
CE1 A:HIS74 5.0 8.9 1.0
CA A:GLU37 5.0 9.4 0.4

Iron binding site 2 out of 6 in 3qhc

Go back to Iron Binding Sites List in 3qhc
Iron binding site 2 out of 6 in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite


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 Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe181

b:8.2
occ:1.00
 OE2 A:GLU162 2.0 8.5 1.0
OE2 A:GLU71 2.0 11.8 1.0
ND1 A:HIS165 2.2 7.1 1.0
OE2 A:GLU128 2.2 9.6 1.0
OE1 A:GLU128 2.2 7.7 1.0
O A:HOH204 2.3 13.6 1.0
CD A:GLU128 2.5 8.5 1.0
CD A:GLU71 2.8 9.4 1.0
CD A:GLU162 3.0 7.6 1.0
CE1 A:HIS165 3.1 8.3 1.0
OE1 A:GLU71 3.1 14.6 1.0
CG A:HIS165 3.3 6.9 1.0
FE A:FE182 3.5 16.3 0.5
OE1 A:GLU162 3.6 18.5 1.0
CB A:HIS165 3.6 6.8 1.0
CG A:GLU128 4.1 8.4 1.0
FE A:FE183 4.1 7.6 0.5
CG2 A:ILE67 4.2 10.1 1.0
CG A:GLU162 4.2 7.4 1.0
CG A:GLU71 4.2 10.1 1.0
CA A:GLU162 4.3 7.2 1.0
NE2 A:HIS165 4.3 8.1 1.0
CD2 A:HIS165 4.3 8.3 1.0
O A:HOH339 4.4 16.8 0.5
OE1 A:GLU131 4.4 23.0 1.0
CB A:GLU162 4.4 6.8 1.0
CE1 A:HIS74 4.5 8.9 1.0
OE1 A:GLU40 4.6 19.4 1.0
OH A:TYR45 4.6 13.4 1.0
CE2 A:TYR45 4.7 10.5 1.0
CB A:GLU128 4.9 7.7 1.0
ND1 A:HIS74 5.0 8.8 1.0
OE1 A:GLU37 5.0 12.5 0.4

Iron binding site 3 out of 6 in 3qhc

Go back to Iron Binding Sites List in 3qhc
Iron binding site 3 out of 6 in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite


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 Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe183

b:7.6
occ:0.50
 OE1 A:GLU37 1.1 12.5 0.4
OE1 A:GLU71 2.0 14.6 1.0
CD A:GLU37 2.0 9.1 0.4
OE1 A:GLU162 2.1 18.5 1.0
OE2 A:GLU37 2.1 8.9 0.6
ND1 A:HIS74 2.2 8.8 1.0
OE1 A:GLU37 2.2 10.6 0.6
O A:HOH339 2.4 16.8 0.5
FE A:FE182 2.4 16.3 0.5
CD A:GLU37 2.5 7.9 0.6
OE2 A:GLU37 2.5 9.7 0.4
CE1 A:HIS74 3.0 8.9 1.0
CD A:GLU162 3.0 7.6 1.0
CD A:GLU71 3.2 9.4 1.0
OE2 A:GLU162 3.2 8.5 1.0
CG A:GLU37 3.3 7.5 0.4
CG A:HIS74 3.3 7.7 1.0
CB A:HIS74 3.8 8.6 1.0
CG A:GLU37 4.0 9.5 0.6
OE2 A:GLU71 4.0 11.8 1.0
O A:HOH204 4.0 13.6 1.0
CA A:GLU71 4.0 7.8 1.0
CB A:GLU37 4.1 9.0 0.4
FE A:FE181 4.1 8.2 1.0
OE1 A:GLU40 4.1 19.4 1.0
CG A:GLU71 4.2 10.1 1.0
CG A:GLU162 4.2 7.4 1.0
NE2 A:HIS74 4.2 8.9 1.0
CB A:GLU71 4.2 9.0 1.0
OE1 A:GLU131 4.3 23.0 1.0
CD2 A:HIS74 4.4 8.7 1.0
CG2 A:ILE158 4.5 9.2 1.0
CE2 A:TYR136 4.6 10.8 0.7
CE2 A:TYR136 4.6 8.2 0.3
OH A:TYR136 4.6 7.4 0.3
O A:GLU71 4.6 9.5 1.0
OH A:TYR136 4.8 20.9 0.7
CB A:GLU37 4.8 8.4 0.6
C A:GLU71 4.8 8.6 1.0
CA A:GLU37 4.9 9.4 0.4
CA A:GLU37 4.9 9.4 0.6
N A:GLU71 5.0 8.1 1.0
CZ A:TYR136 5.0 5.0 0.3

Iron binding site 4 out of 6 in 3qhc

Go back to Iron Binding Sites List in 3qhc
Iron binding site 4 out of 6 in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite


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 Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe182

b:16.1
occ:0.50
 O B:HOH293 1.1 10.7 0.5
O B:HOH224 2.1 14.0 1.0
OE2 B:GLU37 2.1 10.8 0.4
OE1 B:GLU40 2.3 19.2 1.0
OE1 B:GLU131 2.4 23.1 1.0
FE B:FE183 2.4 7.7 0.5
OE1 B:GLU162 2.5 18.8 1.0
OE1 B:GLU71 2.7 14.8 1.0
CD B:GLU37 2.7 7.7 0.4
OE1 B:GLU37 2.8 12.4 0.4
CD B:GLU162 3.2 7.9 1.0
CD B:GLU71 3.2 9.4 1.0
CD B:GLU40 3.3 12.4 1.0
CD B:GLU131 3.3 16.0 1.0
OE2 B:GLU162 3.4 8.1 1.0
OE2 B:GLU37 3.4 8.7 0.6
FE B:FE181 3.5 8.2 1.0
OE2 B:GLU71 3.6 12.1 1.0
OE1 B:GLU37 3.6 11.5 0.6
OE2 B:GLU40 3.6 12.0 1.0
OE2 B:GLU131 3.7 15.9 1.0
CD B:GLU37 3.8 7.5 0.6
O B:HOH276 3.9 9.1 0.3
CG B:GLU37 4.2 6.8 0.4
CG B:GLU71 4.3 10.5 1.0
CG B:GLU162 4.5 7.1 1.0
ND1 B:HIS74 4.5 8.2 1.0
OH B:TYR136 4.5 19.4 0.7
CG B:GLU131 4.5 10.4 1.0
CE2 B:TYR136 4.6 11.0 0.7
CG B:GLU40 4.6 10.7 1.0
OE1 B:GLU128 4.6 7.5 1.0
OE2 B:GLU128 4.8 9.7 1.0
CE2 B:TYR136 4.8 8.7 0.3
CB B:GLU71 4.9 8.8 1.0
CB B:GLU40 4.9 9.5 1.0
CB B:GLU37 4.9 8.7 0.4
CB B:GLU131 4.9 9.0 1.0
OH B:TYR136 5.0 7.4 0.3
CE1 B:HIS74 5.0 8.7 1.0

Iron binding site 5 out of 6 in 3qhc

Go back to Iron Binding Sites List in 3qhc
Iron binding site 5 out of 6 in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe183

b:7.7
occ:0.50
 OE1 B:GLU37 1.1 12.4 0.4
OE1 B:GLU71 2.0 14.8 1.0
CD B:GLU37 2.1 7.7 0.4
OE1 B:GLU162 2.1 18.8 1.0
OE2 B:GLU37 2.1 8.7 0.6
ND1 B:HIS74 2.2 8.2 1.0
OE1 B:GLU37 2.2 11.5 0.6
O B:HOH293 2.3 10.7 0.5
FE B:FE182 2.4 16.1 0.5
CD B:GLU37 2.5 7.5 0.6
OE2 B:GLU37 2.6 10.8 0.4
CE1 B:HIS74 3.0 8.7 1.0
CD B:GLU162 3.0 7.9 1.0
CD B:GLU71 3.2 9.4 1.0
OE2 B:GLU162 3.2 8.1 1.0
CG B:HIS74 3.3 7.9 1.0
CG B:GLU37 3.4 6.8 0.4
CB B:HIS74 3.7 8.1 1.0
O B:HOH224 4.0 14.0 1.0
OE2 B:GLU71 4.0 12.1 1.0
CG B:GLU37 4.0 9.8 0.6
CA B:GLU71 4.0 7.8 1.0
CB B:GLU37 4.1 8.7 0.4
OE1 B:GLU40 4.1 19.2 1.0
FE B:FE181 4.1 8.2 1.0
NE2 B:HIS74 4.2 9.1 1.0
CG B:GLU71 4.2 10.5 1.0
CB B:GLU71 4.2 8.8 1.0
CG B:GLU162 4.3 7.1 1.0
OE1 B:GLU131 4.3 23.1 1.0
CD2 B:HIS74 4.4 8.7 1.0
CG2 B:ILE158 4.5 9.1 1.0
CE2 B:TYR136 4.5 11.0 0.7
CE2 B:TYR136 4.6 8.7 0.3
OH B:TYR136 4.6 7.4 0.3
O B:GLU71 4.6 9.6 1.0
OH B:TYR136 4.8 19.4 0.7
CB B:GLU37 4.8 8.9 0.6
C B:GLU71 4.9 8.5 1.0
CA B:GLU37 4.9 9.4 0.4
CZ B:TYR136 4.9 5.0 0.3
N B:GLU71 5.0 8.2 1.0
CA B:GLU37 5.0 9.2 0.6
O B:HOH276 5.0 9.1 0.3

Iron binding site 6 out of 6 in 3qhc

Go back to Iron Binding Sites List in 3qhc
Iron binding site 6 out of 6 in the Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Symerythrin From Cyanophora Paradoxa, Reduced with Dithionite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe181

b:8.2
occ:1.00
 OE2 B:GLU162 2.0 8.1 1.0
OE2 B:GLU71 2.0 12.1 1.0
ND1 B:HIS165 2.2 7.4 1.0
OE2 B:GLU128 2.2 9.7 1.0
OE1 B:GLU128 2.2 7.5 1.0
O B:HOH224 2.3 14.0 1.0
CD B:GLU128 2.5 8.0 1.0
CD B:GLU71 2.8 9.4 1.0
CD B:GLU162 3.1 7.9 1.0
CE1 B:HIS165 3.1 8.8 1.0
OE1 B:GLU71 3.1 14.8 1.0
CG B:HIS165 3.3 7.3 1.0
FE B:FE182 3.5 16.1 0.5
OE1 B:GLU162 3.6 18.8 1.0
CB B:HIS165 3.7 7.4 1.0
CG B:GLU128 4.0 8.9 1.0
FE B:FE183 4.1 7.7 0.5
CG2 B:ILE67 4.2 10.1 1.0
CG B:GLU162 4.2 7.1 1.0
CG B:GLU71 4.2 10.5 1.0
CA B:GLU162 4.3 7.1 1.0
NE2 B:HIS165 4.3 7.9 1.0
CD2 B:HIS165 4.4 8.6 1.0
OE1 B:GLU131 4.4 23.1 1.0
CB B:GLU162 4.4 7.0 1.0
CE1 B:HIS74 4.5 8.7 1.0
O B:HOH293 4.6 10.7 0.5
OE1 B:GLU40 4.6 19.2 1.0
OH B:TYR45 4.6 13.7 1.0
CE2 B:TYR45 4.7 10.3 1.0
CB B:GLU128 4.9 7.7 1.0
ND1 B:HIS74 5.0 8.2 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 Aug 4 18:40:30 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy