Iron in PDB 6tjr: Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans

Protein crystallography data

The structure of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans, PDB code: 6tjr was solved by K.Kayastha, U.Ermler, C.Dahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.67 / 1.43
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 145.620, 145.620, 64.100, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 17.9

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans (pdb code 6tjr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans, PDB code: 6tjr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6tjr

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Iron binding site 1 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:14.1
occ:1.00
 FE1 A:SF4401 0.0 14.1 1.0
S2 A:SF4401 2.3 14.1 1.0
S4 A:SF4401 2.3 15.7 1.0
S3 A:SF4401 2.3 13.5 1.0
SG A:CYS180 2.3 15.3 1.0
FE2 A:SF4401 2.7 14.3 1.0
FE4 A:SF4401 2.7 14.6 1.0
FE3 A:SF4401 2.7 15.2 1.0
CB A:CYS180 3.2 12.9 1.0
N A:CYS180 3.9 12.0 1.0
CA A:CYS180 3.9 12.2 1.0
S1 A:SF4401 3.9 15.4 1.0
N A:CYS181 4.0 14.4 1.0
O A:HOH544 4.0 16.3 1.0
N A:LYS178 4.1 13.4 1.0
C A:CYS180 4.2 15.8 1.0
N A:SER177 4.2 13.7 1.0
C A:SER177 4.4 15.0 1.0
CB A:SER177 4.5 13.7 1.0
CA A:SER177 4.5 13.1 1.0
SG A:CYS176 4.5 14.8 1.0
SG A:CYS181 4.8 14.7 1.0
N A:CYS163 4.8 16.1 1.0
SG A:CYS163 4.9 16.1 1.0
N A:ILE179 4.9 12.9 1.0
C A:LYS178 4.9 15.3 1.0
CA A:LYS178 5.0 13.2 1.0
CA A:CYS163 5.0 15.2 1.0
CA A:CYS181 5.0 12.5 1.0

Iron binding site 2 out of 8 in 6tjr

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Iron binding site 2 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:14.3
occ:1.00
 FE2 A:SF4401 0.0 14.3 1.0
S1 A:SF4401 2.3 15.4 1.0
S4 A:SF4401 2.3 15.7 1.0
S3 A:SF4401 2.3 13.5 1.0
SG A:CYS176 2.3 14.8 1.0
FE1 A:SF4401 2.7 14.1 1.0
FE3 A:SF4401 2.7 15.2 1.0
FE4 A:SF4401 2.7 14.6 1.0
CB A:CYS176 3.5 13.8 1.0
S2 A:SF4401 3.9 14.1 1.0
CD A:ARG208 4.0 15.0 1.0
N A:SER177 4.0 13.7 1.0
N A:LYS178 4.0 13.4 1.0
CA A:CYS176 4.1 13.1 1.0
CD A:ARG167 4.1 17.2 1.0
NH1 A:ARG208 4.2 15.2 1.0
C A:CYS176 4.3 15.3 1.0
CA A:LYS178 4.6 13.2 1.0
CG A:ARG208 4.6 14.7 1.0
NE A:ARG208 4.7 15.6 1.0
SG A:CYS163 4.7 16.1 1.0
SG A:CYS180 4.8 15.3 1.0
CG A:ARG167 4.8 17.2 1.0
C A:SER177 4.8 15.0 1.0
CZ A:ARG208 4.8 17.2 1.0
SG A:CYS181 4.9 14.7 1.0
CA A:SER177 4.9 13.1 1.0
CB A:ARG208 4.9 14.5 1.0

Iron binding site 3 out of 8 in 6tjr

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Iron binding site 3 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:15.2
occ:1.00
 FE3 A:SF4401 0.0 15.2 1.0
SG A:CYS163 2.3 16.1 1.0
S4 A:SF4401 2.3 15.7 1.0
S2 A:SF4401 2.3 14.1 1.0
S1 A:SF4401 2.3 15.4 1.0
FE2 A:SF4401 2.7 14.3 1.0
FE4 A:SF4401 2.7 14.6 1.0
FE1 A:SF4401 2.7 14.1 1.0
CB A:CYS163 3.4 15.5 1.0
CA A:CYS163 3.5 15.2 1.0
N A:CYS163 3.6 16.1 1.0
O A:HOH648 3.9 17.4 1.0
S3 A:SF4401 3.9 13.5 1.0
CD A:ARG167 4.0 17.2 1.0
CB A:LEU162 4.6 14.6 1.0
C A:LEU162 4.6 18.2 1.0
O A:HOH544 4.6 16.3 1.0
CG A:ARG167 4.6 17.2 1.0
SG A:CYS181 4.7 14.7 1.0
NH1 A:ARG167 4.8 19.7 1.0
SG A:CYS180 4.8 15.3 1.0
SG A:CYS176 4.9 14.8 1.0
CB A:SER166 5.0 17.7 1.0

Iron binding site 4 out of 8 in 6tjr

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Iron binding site 4 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:14.6
occ:1.00
 FE4 A:SF4401 0.0 14.6 1.0
S3 A:SF4401 2.3 13.5 1.0
SG A:CYS181 2.3 14.7 1.0
S1 A:SF4401 2.3 15.4 1.0
S2 A:SF4401 2.3 14.1 1.0
FE1 A:SF4401 2.7 14.1 1.0
FE3 A:SF4401 2.7 15.2 1.0
FE2 A:SF4401 2.7 14.3 1.0
CB A:CYS181 3.3 12.8 1.0
N A:CYS181 3.6 14.4 1.0
CA A:CYS181 3.8 12.5 1.0
S4 A:SF4401 3.9 15.7 1.0
CB A:ARG208 4.3 14.5 1.0
O A:ASP206 4.4 17.6 1.0
CG A:ARG208 4.4 14.7 1.0
O A:HOH648 4.4 17.4 1.0
C A:CYS180 4.5 15.8 1.0
SG A:CYS163 4.6 16.1 1.0
CD A:ARG208 4.6 15.0 1.0
CD1 A:LEU162 4.7 16.1 1.0
N A:ARG208 4.7 14.0 1.0
SG A:CYS180 4.8 15.3 1.0
SG A:CYS176 4.9 14.8 1.0
CB A:CYS180 5.0 12.9 1.0

Iron binding site 5 out of 8 in 6tjr

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Iron binding site 5 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:16.1
occ:1.00
 FE1 B:SF4401 0.0 16.1 1.0
S3 B:SF4401 2.3 14.7 1.0
SG B:CYS181 2.3 17.5 1.0
S2 B:SF4401 2.3 16.1 1.0
S4 B:SF4401 2.3 16.8 1.0
FE3 B:SF4401 2.7 16.9 1.0
FE2 B:SF4401 2.7 16.2 1.0
FE4 B:SF4401 2.7 15.7 1.0
CB B:CYS181 3.3 15.4 1.0
N B:CYS181 3.6 15.5 1.0
CA B:CYS181 3.8 16.1 1.0
S1 B:SF4401 3.9 16.5 1.0
CB B:ARG208 4.3 14.0 1.0
CG B:ARG208 4.3 15.8 1.0
O B:ASP206 4.4 19.5 1.0
O B:HOH575 4.4 20.9 1.0
C B:CYS180 4.5 19.1 1.0
CD B:ARG208 4.6 15.8 1.0
SG B:CYS163 4.6 18.8 1.0
CD1 B:LEU162 4.7 20.9 1.0
N B:ARG208 4.7 15.2 1.0
SG B:CYS180 4.8 17.2 1.0
SG B:CYS176 4.8 15.7 1.0
CB B:CYS180 5.0 16.2 1.0

Iron binding site 6 out of 8 in 6tjr

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Iron binding site 6 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:16.2
occ:1.00
 FE2 B:SF4401 0.0 16.2 1.0
S4 B:SF4401 2.3 16.8 1.0
S1 B:SF4401 2.3 16.5 1.0
SG B:CYS180 2.3 17.2 1.0
S3 B:SF4401 2.3 14.7 1.0
FE4 B:SF4401 2.7 15.7 1.0
FE1 B:SF4401 2.7 16.1 1.0
FE3 B:SF4401 2.7 16.9 1.0
CB B:CYS180 3.2 16.2 1.0
N B:CYS180 3.9 14.5 1.0
S2 B:SF4401 3.9 16.1 1.0
CA B:CYS180 3.9 15.2 1.0
N B:CYS181 4.0 15.5 1.0
O B:HOH533 4.0 18.0 1.0
N B:LYS178 4.2 14.9 1.0
N B:SER177 4.2 15.2 1.0
C B:CYS180 4.2 19.1 1.0
C B:SER177 4.4 17.2 1.0
CB B:SER177 4.4 14.7 1.0
CA B:SER177 4.5 14.4 1.0
SG B:CYS176 4.5 15.7 1.0
N B:CYS163 4.8 17.7 1.0
SG B:CYS181 4.8 17.5 1.0
SG B:CYS163 4.9 18.8 1.0
CA B:CYS163 4.9 18.2 1.0
N B:ILE179 4.9 14.7 1.0
C B:LYS178 5.0 16.3 1.0
CA B:LYS178 5.0 14.7 1.0

Iron binding site 7 out of 8 in 6tjr

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Iron binding site 7 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:16.9
occ:1.00
 FE3 B:SF4401 0.0 16.9 1.0
S1 B:SF4401 2.3 16.5 1.0
SG B:CYS163 2.3 18.8 1.0
S2 B:SF4401 2.3 16.1 1.0
S4 B:SF4401 2.3 16.8 1.0
FE4 B:SF4401 2.7 15.7 1.0
FE1 B:SF4401 2.7 16.1 1.0
FE2 B:SF4401 2.7 16.2 1.0
CB B:CYS163 3.4 17.6 1.0
CA B:CYS163 3.5 18.2 1.0
N B:CYS163 3.6 17.7 1.0
O B:HOH575 3.9 20.9 1.0
S3 B:SF4401 3.9 14.7 1.0
CD B:ARG167 4.0 19.2 1.0
C B:LEU162 4.6 21.0 1.0
CB B:LEU162 4.6 17.4 1.0
CG B:ARG167 4.7 18.2 1.0
O B:HOH533 4.7 18.0 1.0
SG B:CYS181 4.7 17.5 1.0
NH1 B:ARG167 4.8 19.2 1.0
SG B:CYS180 4.8 17.2 1.0
SG B:CYS176 4.9 15.7 1.0
C B:CYS163 5.0 21.7 1.0

Iron binding site 8 out of 8 in 6tjr

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Iron binding site 8 out of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:15.7
occ:1.00
 FE4 B:SF4401 0.0 15.7 1.0
S2 B:SF4401 2.3 16.1 1.0
S1 B:SF4401 2.3 16.5 1.0
S3 B:SF4401 2.3 14.7 1.0
SG B:CYS176 2.3 15.7 1.0
FE2 B:SF4401 2.7 16.2 1.0
FE3 B:SF4401 2.7 16.9 1.0
FE1 B:SF4401 2.7 16.1 1.0
CB B:CYS176 3.5 15.2 1.0
S4 B:SF4401 3.9 16.8 1.0
N B:SER177 3.9 15.2 1.0
CD B:ARG208 4.0 15.8 1.0
N B:LYS178 4.0 14.9 1.0
CA B:CYS176 4.0 15.6 1.0
CD B:ARG167 4.2 19.2 1.0
NH1 B:ARG208 4.2 16.2 1.0
C B:CYS176 4.3 17.3 1.0
CA B:LYS178 4.6 14.7 1.0
CG B:ARG208 4.6 15.8 1.0
NE B:ARG208 4.7 14.2 1.0
SG B:CYS163 4.7 18.8 1.0
SG B:CYS180 4.7 17.2 1.0
C B:SER177 4.8 17.2 1.0
CG B:ARG167 4.8 18.2 1.0
CZ B:ARG208 4.8 17.0 1.0
CA B:SER177 4.9 14.4 1.0
SG B:CYS181 4.9 17.5 1.0
CB B:ARG208 4.9 14.0 1.0

Reference:

C.Ernst, K.Kayastha, T.Koch, S.S.Venceslau, I.A.C.Pereira, U.Demmer, U.Ermler, C.Dahl. Structural and Spectroscopic Characterization of A Hdra-Like Subunit From Hyphomicrobium Denitrificans. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32750208
DOI: 10.1111/FEBS.15505
Page generated: Sun Dec 13 17:09:42 2020

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