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Iron in PDB 6rr4: Structure of 25% Reduced Kpdyp

Protein crystallography data

The structure of Structure of 25% Reduced Kpdyp, PDB code: 6rr4 was solved by V.Pfanzagl, J.Beale, S.Hofbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.40 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.889, 76.647, 76.579, 90.00, 108.01, 90.00
R / Rfree (%) 16.9 / 18.1

Other elements in 6rr4:

The structure of Structure of 25% Reduced Kpdyp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of 25% Reduced Kpdyp (pdb code 6rr4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of 25% Reduced Kpdyp, PDB code: 6rr4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6rr4

Go back to Iron Binding Sites List in 6rr4
Iron binding site 1 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of 25% Reduced Kpdyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:3.1
occ:0.25
FE A:HEM401 0.0 3.1 0.2
FE A:HEM401 0.1 3.2 0.8
NC A:HEM401 2.0 3.0 0.2
ND A:HEM401 2.0 3.0 0.2
ND A:HEM401 2.0 3.0 0.8
NA A:HEM401 2.0 3.0 0.2
NB A:HEM401 2.0 3.0 0.2
NC A:HEM401 2.1 3.0 0.8
NA A:HEM401 2.1 3.0 0.8
NB A:HEM401 2.1 3.0 0.8
NE2 A:HIS215 2.2 3.9 1.0
O A:HOH508 2.6 35.6 1.0
C4D A:HEM401 3.0 3.0 0.8
C4B A:HEM401 3.0 3.0 0.8
C1D A:HEM401 3.0 3.0 0.8
C4C A:HEM401 3.0 3.0 0.2
C4D A:HEM401 3.0 3.0 0.2
C4C A:HEM401 3.0 3.0 0.8
C1D A:HEM401 3.0 3.0 0.2
C1B A:HEM401 3.0 3.0 0.8
C4B A:HEM401 3.0 3.0 0.2
C1C A:HEM401 3.0 3.0 0.8
C1B A:HEM401 3.0 3.0 0.2
CD2 A:HIS215 3.0 3.2 1.0
C1A A:HEM401 3.0 3.0 0.2
C1A A:HEM401 3.0 3.0 0.8
C4A A:HEM401 3.0 3.0 0.2
C4A A:HEM401 3.0 3.0 0.8
C1C A:HEM401 3.1 3.0 0.2
CE1 A:HIS215 3.1 3.0 1.0
HD2 A:HIS215 3.1 3.0 1.0
HE1 A:HIS215 3.3 3.0 1.0
CHC A:HEM401 3.4 3.5 0.8
CHD A:HEM401 3.4 3.4 0.8
CHA A:HEM401 3.4 3.3 0.8
CHB A:HEM401 3.4 3.4 0.8
CHA A:HEM401 3.4 3.3 0.2
CHD A:HEM401 3.4 3.4 0.2
CHC A:HEM401 3.4 3.5 0.2
CHB A:HEM401 3.4 3.4 0.2
HH11 A:ARG232 3.9 3.0 1.0
HE1 A:PHE248 4.0 3.0 1.0
HG21 A:VAL219 4.0 3.0 1.0
HE1 A:MET276 4.0 3.0 1.0
CG A:HIS215 4.2 3.9 1.0
ND1 A:HIS215 4.2 3.2 1.0
C3C A:HEM401 4.2 3.1 0.8
C3C A:HEM401 4.3 3.1 0.2
C2C A:HEM401 4.3 3.0 0.8
C3D A:HEM401 4.3 3.0 0.2
C2C A:HEM401 4.3 3.0 0.2
C3D A:HEM401 4.3 3.0 0.8
C2B A:HEM401 4.3 3.0 0.8
C3A A:HEM401 4.3 3.1 0.8
C3B A:HEM401 4.3 3.2 0.8
C3A A:HEM401 4.3 3.1 0.2
C2A A:HEM401 4.3 3.0 0.2
C2A A:HEM401 4.3 3.0 0.8
C2D A:HEM401 4.3 3.0 0.2
C2D A:HEM401 4.3 3.0 0.8
C2B A:HEM401 4.3 3.0 0.2
NH1 A:ARG232 4.3 3.0 1.0
C3B A:HEM401 4.3 3.1 0.2
HHA A:HEM401 4.3 3.0 0.2
HHC A:HEM401 4.4 3.0 0.2
HD3 A:ARG232 4.4 3.0 1.0
HHC A:HEM401 4.4 3.0 0.8
HHD A:HEM401 4.4 3.0 0.2
HHD A:HEM401 4.4 3.0 0.8
HHB A:HEM401 4.5 3.0 0.2
HHA A:HEM401 4.5 3.0 0.8
HHB A:HEM401 4.5 3.0 0.8
HH12 A:ARG232 4.5 3.0 1.0
HD2 A:ARG232 4.5 3.0 1.0
HG11 A:VAL219 4.6 3.0 1.0
O A:HOH526 4.6 27.4 1.0
OD1 A:ASP143 4.7 14.5 1.0
CE1 A:PHE248 4.7 3.0 1.0
CD A:ARG232 4.9 3.1 1.0
CG2 A:VAL219 4.9 3.0 1.0
CE A:MET276 5.0 3.0 1.0
HD1 A:PHE248 5.0 3.0 1.0

Iron binding site 2 out of 4 in 6rr4

Go back to Iron Binding Sites List in 6rr4
Iron binding site 2 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of 25% Reduced Kpdyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:3.2
occ:0.75
FE A:HEM401 0.0 3.2 0.8
FE A:HEM401 0.1 3.1 0.2
ND A:HEM401 1.9 3.0 0.2
ND A:HEM401 2.0 3.0 0.8
NA A:HEM401 2.0 3.0 0.2
NC A:HEM401 2.0 3.0 0.2
NB A:HEM401 2.0 3.0 0.2
NA A:HEM401 2.1 3.0 0.8
NC A:HEM401 2.1 3.0 0.8
NB A:HEM401 2.1 3.0 0.8
NE2 A:HIS215 2.2 3.9 1.0
O A:HOH508 2.6 35.6 1.0
C4D A:HEM401 2.9 3.0 0.8
C4D A:HEM401 3.0 3.0 0.2
C1D A:HEM401 3.0 3.0 0.8
C1D A:HEM401 3.0 3.0 0.2
C1A A:HEM401 3.0 3.0 0.2
C1A A:HEM401 3.0 3.0 0.8
C4C A:HEM401 3.0 3.0 0.2
C4C A:HEM401 3.0 3.0 0.8
C4B A:HEM401 3.0 3.0 0.8
C4A A:HEM401 3.0 3.0 0.2
C1B A:HEM401 3.0 3.0 0.8
C4A A:HEM401 3.0 3.0 0.8
C1B A:HEM401 3.0 3.0 0.2
C4B A:HEM401 3.1 3.0 0.2
CD2 A:HIS215 3.1 3.2 1.0
C1C A:HEM401 3.1 3.0 0.8
C1C A:HEM401 3.1 3.0 0.2
HD2 A:HIS215 3.2 3.0 1.0
CE1 A:HIS215 3.2 3.0 1.0
CHA A:HEM401 3.3 3.3 0.8
CHA A:HEM401 3.3 3.3 0.2
CHD A:HEM401 3.4 3.4 0.8
CHB A:HEM401 3.4 3.4 0.8
HE1 A:HIS215 3.4 3.0 1.0
CHC A:HEM401 3.4 3.5 0.8
CHD A:HEM401 3.4 3.4 0.2
CHB A:HEM401 3.4 3.4 0.2
CHC A:HEM401 3.5 3.5 0.2
HH11 A:ARG232 3.9 3.0 1.0
HE1 A:PHE248 4.0 3.0 1.0
HG21 A:VAL219 4.0 3.0 1.0
HE1 A:MET276 4.1 3.0 1.0
C3D A:HEM401 4.2 3.0 0.2
C3D A:HEM401 4.2 3.0 0.8
CG A:HIS215 4.2 3.9 1.0
C3A A:HEM401 4.3 3.1 0.8
C2A A:HEM401 4.3 3.0 0.2
C3A A:HEM401 4.3 3.1 0.2
NH1 A:ARG232 4.3 3.0 1.0
C2A A:HEM401 4.3 3.0 0.8
C2D A:HEM401 4.3 3.0 0.2
C3C A:HEM401 4.3 3.1 0.8
C2D A:HEM401 4.3 3.0 0.8
ND1 A:HIS215 4.3 3.2 1.0
C3C A:HEM401 4.3 3.1 0.2
C2C A:HEM401 4.3 3.0 0.8
C2B A:HEM401 4.3 3.0 0.8
C2C A:HEM401 4.3 3.0 0.2
HHA A:HEM401 4.3 3.0 0.2
C3B A:HEM401 4.3 3.2 0.8
C2B A:HEM401 4.3 3.0 0.2
HD3 A:ARG232 4.4 3.0 1.0
C3B A:HEM401 4.4 3.1 0.2
HHA A:HEM401 4.4 3.0 0.8
HHC A:HEM401 4.4 3.0 0.2
HHD A:HEM401 4.4 3.0 0.2
HHD A:HEM401 4.4 3.0 0.8
HH12 A:ARG232 4.4 3.0 1.0
HHB A:HEM401 4.4 3.0 0.2
HHB A:HEM401 4.5 3.0 0.8
HD2 A:ARG232 4.5 3.0 1.0
HHC A:HEM401 4.5 3.0 0.8
O A:HOH526 4.6 27.4 1.0
HG11 A:VAL219 4.6 3.0 1.0
OD1 A:ASP143 4.7 14.5 1.0
CE1 A:PHE248 4.7 3.0 1.0
CD A:ARG232 4.8 3.1 1.0
CG2 A:VAL219 4.9 3.0 1.0
CZ A:ARG232 5.0 12.4 1.0
HD1 A:PHE248 5.0 3.0 1.0

Iron binding site 3 out of 4 in 6rr4

Go back to Iron Binding Sites List in 6rr4
Iron binding site 3 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of 25% Reduced Kpdyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:3.1
occ:0.25
FE B:HEM401 0.0 3.1 0.2
FE B:HEM401 0.0 3.3 0.8
NC B:HEM401 2.0 3.0 0.2
NA B:HEM401 2.0 3.0 0.2
NB B:HEM401 2.0 3.0 0.2
ND B:HEM401 2.0 3.0 0.8
ND B:HEM401 2.0 3.0 0.2
NA B:HEM401 2.0 3.1 0.8
NB B:HEM401 2.1 3.0 0.8
NE2 B:HIS215 2.1 3.6 1.0
NC B:HEM401 2.1 3.0 0.8
O B:HOH501 2.6 25.5 1.0
C4D B:HEM401 3.0 3.0 0.8
C1D B:HEM401 3.0 3.0 0.8
C4B B:HEM401 3.0 3.0 0.8
C1B B:HEM401 3.0 3.0 0.2
C1A B:HEM401 3.0 3.0 0.8
C4B B:HEM401 3.0 3.0 0.2
C1B B:HEM401 3.0 3.0 0.8
C4C B:HEM401 3.0 3.0 0.2
C1D B:HEM401 3.0 3.0 0.2
CE1 B:HIS215 3.0 3.0 1.0
C4D B:HEM401 3.0 3.0 0.2
C4A B:HEM401 3.0 3.0 0.8
C4A B:HEM401 3.0 3.0 0.2
C1A B:HEM401 3.0 3.0 0.2
C4C B:HEM401 3.0 3.0 0.8
CD2 B:HIS215 3.0 3.1 1.0
C1C B:HEM401 3.1 3.0 0.2
C1C B:HEM401 3.1 3.0 0.8
HE1 B:HIS215 3.2 3.0 1.0
HD2 B:HIS215 3.2 3.0 1.0
CHA B:HEM401 3.4 3.3 0.8
CHD B:HEM401 3.4 3.4 0.8
CHA B:HEM401 3.4 3.3 0.2
CHD B:HEM401 3.4 3.4 0.2
CHB B:HEM401 3.4 3.4 0.2
CHC B:HEM401 3.4 3.5 0.2
CHB B:HEM401 3.4 3.4 0.8
CHC B:HEM401 3.5 3.5 0.8
HG21 B:VAL219 3.9 3.0 1.0
HE1 B:PHE248 3.9 3.0 1.0
HH11 B:ARG232 3.9 3.0 1.0
OD2 B:ASP143 4.1 22.6 0.5
ND1 B:HIS215 4.1 3.2 1.0
CG B:HIS215 4.2 3.9 1.0
C3A B:HEM401 4.2 3.1 0.8
HE1 B:MET276 4.2 3.0 1.0
C3D B:HEM401 4.2 3.0 0.8
C2A B:HEM401 4.2 3.1 0.8
C2D B:HEM401 4.2 3.0 0.8
C3B B:HEM401 4.2 3.1 0.8
C2B B:HEM401 4.3 3.0 0.8
C3C B:HEM401 4.3 3.1 0.2
C3C B:HEM401 4.3 3.1 0.8
C3A B:HEM401 4.3 3.1 0.2
C2C B:HEM401 4.3 3.0 0.2
C3D B:HEM401 4.3 3.0 0.2
C2B B:HEM401 4.3 3.0 0.2
C2A B:HEM401 4.3 3.1 0.2
C2C B:HEM401 4.3 3.0 0.8
C3B B:HEM401 4.3 3.1 0.2
C2D B:HEM401 4.3 3.0 0.2
NH1 B:ARG232 4.3 3.0 1.0
HHA B:HEM401 4.4 3.0 0.2
HHC B:HEM401 4.4 3.0 0.2
HD3 B:ARG232 4.4 3.0 1.0
HHB B:HEM401 4.4 3.0 0.2
HHD B:HEM401 4.5 3.0 0.2
HHA B:HEM401 4.5 3.0 0.8
HHD B:HEM401 4.5 3.0 0.8
HH12 B:ARG232 4.5 3.0 1.0
HHB B:HEM401 4.5 3.0 0.8
HHC B:HEM401 4.5 3.0 0.8
OD1 B:ASP143 4.6 9.0 0.5
HG11 B:VAL219 4.6 3.0 1.0
CE1 B:PHE248 4.6 3.1 1.0
HD2 B:ARG232 4.6 3.0 1.0
O B:HOH525 4.8 21.0 1.0
CG2 B:VAL219 4.8 3.0 1.0
HD1 B:HIS215 4.9 3.0 1.0
CD B:ARG232 4.9 3.0 1.0
HG23 B:VAL219 4.9 3.0 1.0
CZ B:ARG232 5.0 8.5 1.0

Iron binding site 4 out of 4 in 6rr4

Go back to Iron Binding Sites List in 6rr4
Iron binding site 4 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of 25% Reduced Kpdyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:3.3
occ:0.75
FE B:HEM401 0.0 3.3 0.8
FE B:HEM401 0.0 3.1 0.2
ND B:HEM401 1.9 3.0 0.8
NC B:HEM401 2.0 3.0 0.2
ND B:HEM401 2.0 3.0 0.2
NA B:HEM401 2.0 3.0 0.2
NB B:HEM401 2.0 3.0 0.2
NA B:HEM401 2.0 3.1 0.8
NB B:HEM401 2.1 3.0 0.8
NC B:HEM401 2.1 3.0 0.8
NE2 B:HIS215 2.1 3.6 1.0
O B:HOH501 2.6 25.5 1.0
C4D B:HEM401 2.9 3.0 0.8
C1D B:HEM401 2.9 3.0 0.8
C1D B:HEM401 3.0 3.0 0.2
C1A B:HEM401 3.0 3.0 0.8
C4D B:HEM401 3.0 3.0 0.2
C4C B:HEM401 3.0 3.0 0.2
C4B B:HEM401 3.0 3.0 0.8
C1B B:HEM401 3.0 3.0 0.2
C1A B:HEM401 3.0 3.0 0.2
C4B B:HEM401 3.0 3.0 0.2
C4C B:HEM401 3.0 3.0 0.8
C1B B:HEM401 3.0 3.0 0.8
C4A B:HEM401 3.0 3.0 0.8
C4A B:HEM401 3.0 3.0 0.2
CE1 B:HIS215 3.1 3.0 1.0
C1C B:HEM401 3.1 3.0 0.2
CD2 B:HIS215 3.1 3.1 1.0
C1C B:HEM401 3.1 3.0 0.8
HE1 B:HIS215 3.2 3.0 1.0
HD2 B:HIS215 3.2 3.0 1.0
CHA B:HEM401 3.4 3.3 0.8
CHD B:HEM401 3.4 3.4 0.8
CHA B:HEM401 3.4 3.3 0.2
CHD B:HEM401 3.4 3.4 0.2
CHB B:HEM401 3.4 3.4 0.2
CHC B:HEM401 3.4 3.5 0.2
CHB B:HEM401 3.5 3.4 0.8
CHC B:HEM401 3.5 3.5 0.8
HG21 B:VAL219 3.9 3.0 1.0
HE1 B:PHE248 3.9 3.0 1.0
HH11 B:ARG232 3.9 3.0 1.0
OD2 B:ASP143 4.1 22.6 0.5
ND1 B:HIS215 4.2 3.2 1.0
C3D B:HEM401 4.2 3.0 0.8
C2D B:HEM401 4.2 3.0 0.8
CG B:HIS215 4.2 3.9 1.0
C3A B:HEM401 4.2 3.1 0.8
C2A B:HEM401 4.2 3.1 0.8
C3C B:HEM401 4.2 3.1 0.2
C3C B:HEM401 4.3 3.1 0.8
C3D B:HEM401 4.3 3.0 0.2
HE1 B:MET276 4.3 3.0 1.0
C3A B:HEM401 4.3 3.1 0.2
C3B B:HEM401 4.3 3.1 0.8
C2C B:HEM401 4.3 3.0 0.2
C2B B:HEM401 4.3 3.0 0.8
NH1 B:ARG232 4.3 3.0 1.0
C2D B:HEM401 4.3 3.0 0.2
C2A B:HEM401 4.3 3.1 0.2
C2C B:HEM401 4.3 3.0 0.8
C2B B:HEM401 4.3 3.0 0.2
C3B B:HEM401 4.3 3.1 0.2
HHA B:HEM401 4.3 3.0 0.2
HD3 B:ARG232 4.4 3.0 1.0
HHC B:HEM401 4.4 3.0 0.2
HHD B:HEM401 4.4 3.0 0.2
HHB B:HEM401 4.4 3.0 0.2
HHA B:HEM401 4.4 3.0 0.8
HHD B:HEM401 4.5 3.0 0.8
HH12 B:ARG232 4.5 3.0 1.0
HHB B:HEM401 4.5 3.0 0.8
HHC B:HEM401 4.6 3.0 0.8
OD1 B:ASP143 4.6 9.0 0.5
HD2 B:ARG232 4.6 3.0 1.0
CE1 B:PHE248 4.6 3.1 1.0
HG11 B:VAL219 4.6 3.0 1.0
O B:HOH525 4.8 21.0 1.0
CG2 B:VAL219 4.8 3.0 1.0
CD B:ARG232 4.9 3.0 1.0
HG23 B:VAL219 4.9 3.0 1.0
HD1 B:HIS215 5.0 3.0 1.0
CZ B:ARG232 5.0 8.5 1.0

Reference:

V.Pfanzagl, J.H.Beale, H.Michlits, D.Schmidt, T.Gabler, C.Obinger, K.Djinovic-Carugo, S.Hofbauer. X-Ray-Induced Photoreduction of Heme Metal Centers Rapidly Induces Active-Site Perturbations in A Protein-Independent Manner. J.Biol.Chem. V. 295 13488 2020.
ISSN: ESSN 1083-351X
PubMed: 32723869
DOI: 10.1074/JBC.RA120.014087
Page generated: Wed Aug 7 09:21:01 2024

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