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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

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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

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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

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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

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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

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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

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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

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