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Iron in PDB 6xig: X-Ray Crystal Structure of Mqne From Pedobacter Heparinus

Enzymatic activity of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus

All present enzymatic activity of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus:
2.5.1.120;

Protein crystallography data

The structure of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus, PDB code: 6xig was solved by T.L.Grove, J.B.Bonanno, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.968, 75.403, 83.921, 90.00, 107.69, 90.00
R / Rfree (%) 15.6 / 18.3

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus (pdb code 6xig). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus, PDB code: 6xig:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6xig

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Iron binding site 1 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.4
occ:1.00
 FE1 A:SF4401 0.0 18.4 1.0
S4 A:SF4401 2.2 17.9 1.0
S2 A:SF4401 2.2 17.7 1.0
S3 A:SF4401 2.3 19.3 1.0
SG A:CYS84 2.3 20.1 1.0
FE4 A:SF4401 2.6 19.5 1.0
FE2 A:SF4401 2.7 18.6 1.0
FE3 A:SF4401 2.8 19.3 1.0
CB A:CYS84 3.2 20.3 1.0
NZ A:LYS207 3.6 16.9 1.0
S1 A:SF4401 3.7 17.9 1.0
CD A:LYS207 4.1 18.0 1.0
O41 A:TAR402 4.1 19.1 1.0
N A:CYS84 4.1 20.9 1.0
CA A:CYS84 4.2 21.1 1.0
CB A:TYR82 4.3 19.3 1.0
CB A:CYS87 4.4 23.1 1.0
CE A:LYS207 4.4 16.9 1.0
SG A:CYS87 4.6 21.4 1.0
SG A:CYS80 4.7 18.6 1.0
O3 A:TAR402 4.8 24.8 1.0
O A:HOH599 4.8 21.2 1.0
N A:ASP83 5.0 19.7 1.0

Iron binding site 2 out of 8 in 6xig

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Iron binding site 2 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.6
occ:1.00
 FE2 A:SF4401 0.0 18.6 1.0
S4 A:SF4401 2.2 17.9 1.0
S1 A:SF4401 2.2 17.9 1.0
S3 A:SF4401 2.2 19.3 1.0
SG A:CYS80 2.3 18.6 1.0
FE1 A:SF4401 2.7 18.4 1.0
FE4 A:SF4401 2.7 19.5 1.0
FE3 A:SF4401 2.8 19.3 1.0
CB A:CYS80 3.2 18.9 1.0
S2 A:SF4401 3.8 17.7 1.0
O3 A:TAR402 4.0 24.8 1.0
CB A:TYR82 4.1 19.3 1.0
CA A:CYS80 4.7 18.9 1.0
CA A:GLY127 4.7 19.2 1.0
CD2 A:TYR82 4.7 18.8 1.0
N A:TYR82 4.7 22.1 1.0
O41 A:TAR402 4.8 19.1 1.0
SG A:CYS87 4.8 21.4 1.0
CB A:TYR89 4.8 23.7 1.0
CA A:TYR82 4.8 20.8 1.0
SG A:CYS84 4.8 20.1 1.0
N A:VAL128 4.9 19.4 1.0
C A:TYR82 5.0 18.7 1.0
CG A:TYR82 5.0 17.3 1.0

Iron binding site 3 out of 8 in 6xig

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Iron binding site 3 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:19.3
occ:1.00
 FE3 A:SF4401 0.0 19.3 1.0
O3 A:TAR402 2.2 24.8 1.0
S2 A:SF4401 2.2 17.7 1.0
S1 A:SF4401 2.2 17.9 1.0
S4 A:SF4401 2.2 17.9 1.0
O41 A:TAR402 2.2 19.1 1.0
FE4 A:SF4401 2.8 19.5 1.0
FE1 A:SF4401 2.8 18.4 1.0
O11 A:TAR402 2.8 41.5 1.0
FE2 A:SF4401 2.8 18.6 1.0
C4 A:TAR402 3.1 23.5 1.0
C3 A:TAR402 3.2 27.7 1.0
C1 A:TAR402 3.7 42.4 1.0
C2 A:TAR402 3.8 37.5 1.0
NZ A:LYS207 3.9 16.9 1.0
S3 A:SF4401 4.0 19.3 1.0
O4 A:TAR402 4.2 19.9 1.0
O A:GLY126 4.6 18.3 1.0
O1 A:TAR402 4.7 50.2 1.0
SG A:CYS84 4.8 20.1 1.0
SG A:CYS80 4.8 18.6 1.0
SG A:CYS87 4.8 21.4 1.0
CG1 A:VAL159 4.9 15.8 1.0
CD A:LYS207 5.0 18.0 1.0

Iron binding site 4 out of 8 in 6xig

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Iron binding site 4 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:19.5
occ:1.00
 FE4 A:SF4401 0.0 19.5 1.0
S1 A:SF4401 2.2 17.9 1.0
S3 A:SF4401 2.3 19.3 1.0
S2 A:SF4401 2.3 17.7 1.0
SG A:CYS87 2.3 21.4 1.0
FE1 A:SF4401 2.6 18.4 1.0
FE2 A:SF4401 2.7 18.6 1.0
FE3 A:SF4401 2.8 19.3 1.0
CB A:CYS87 3.1 23.1 1.0
S4 A:SF4401 3.7 17.9 1.0
CB A:TYR89 4.1 23.7 1.0
O11 A:TAR402 4.3 41.5 1.0
CA A:CYS87 4.5 24.3 1.0
CB A:CYS84 4.6 20.3 1.0
O3 A:TAR402 4.6 24.8 1.0
SG A:CYS84 4.6 20.1 1.0
SG A:CYS80 4.8 18.6 1.0
CG A:TYR89 4.8 25.1 1.0
C A:TYR89 4.8 24.6 1.0
CA A:TYR89 4.8 23.2 1.0
CD2 A:TYR89 4.8 25.8 1.0
N A:TYR89 4.8 25.4 1.0
O41 A:TAR402 4.9 19.1 1.0
N A:SER90 4.9 22.9 1.0

Iron binding site 5 out of 8 in 6xig

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Iron binding site 5 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:14.9
occ:1.00
 FE1 B:SF4401 0.0 14.9 1.0
S4 B:SF4401 2.2 15.3 1.0
S3 B:SF4401 2.3 14.4 1.0
S2 B:SF4401 2.3 13.8 1.0
SG B:CYS87 2.3 15.7 1.0
FE4 B:SF4401 2.6 14.2 1.0
FE3 B:SF4401 2.7 14.4 1.0
FE2 B:SF4401 2.8 15.6 1.0
CB B:CYS87 3.2 14.4 1.0
S1 B:SF4401 3.7 13.8 1.0
O B:HOH934 4.1 39.0 1.0
CB B:TYR89 4.2 16.2 1.0
O2 B:TAR403 4.4 30.1 1.0
CB B:CYS84 4.5 14.4 1.0
O B:HOH502 4.6 30.7 1.0
CA B:CYS87 4.6 15.4 1.0
SG B:CYS84 4.6 14.1 1.0
O3 B:TAR403 4.7 24.5 1.0
N B:SER90 4.8 17.0 1.0
C B:TYR89 4.8 15.8 1.0
O41 B:TAR403 4.8 14.7 1.0
SG B:CYS80 4.8 14.1 1.0
N B:TYR89 4.8 16.4 1.0
CA B:TYR89 4.9 16.8 1.0
CG B:TYR89 4.9 18.6 1.0
CD2 B:TYR89 4.9 19.8 1.0

Iron binding site 6 out of 8 in 6xig

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Iron binding site 6 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:15.6
occ:1.00
 FE2 B:SF4401 0.0 15.6 1.0
O41 B:TAR403 2.2 14.7 1.0
S3 B:SF4401 2.2 14.4 1.0
S1 B:SF4401 2.3 13.8 1.0
S4 B:SF4401 2.3 15.3 1.0
O3 B:TAR403 2.3 24.5 1.0
FE4 B:SF4401 2.7 14.2 1.0
FE1 B:SF4401 2.8 14.9 1.0
FE3 B:SF4401 2.8 14.4 1.0
O2 B:TAR403 2.9 30.1 1.0
C4 B:TAR403 3.0 20.6 1.0
C3 B:TAR403 3.1 24.8 1.0
C2 B:TAR403 3.6 29.0 1.0
S2 B:SF4401 3.9 13.8 1.0
NZ B:LYS207 4.0 13.1 1.0
O4 B:TAR403 4.2 20.7 1.0
C1 B:TAR403 4.5 26.8 1.0
O B:HOH502 4.6 30.7 1.0
O B:GLY126 4.6 15.2 1.0
O11 B:TAR403 4.6 26.0 1.0
SG B:CYS84 4.7 14.1 1.0
SG B:CYS80 4.8 14.1 1.0
SG B:CYS87 4.8 15.7 1.0
CG1 B:VAL159 4.9 13.5 1.0
CD B:LYS207 4.9 12.7 1.0

Iron binding site 7 out of 8 in 6xig

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Iron binding site 7 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:14.4
occ:1.00
 FE3 B:SF4401 0.0 14.4 1.0
S2 B:SF4401 2.2 13.8 1.0
S1 B:SF4401 2.2 13.8 1.0
S4 B:SF4401 2.3 15.3 1.0
SG B:CYS80 2.3 14.1 1.0
FE1 B:SF4401 2.7 14.9 1.0
FE4 B:SF4401 2.7 14.2 1.0
FE2 B:SF4401 2.8 15.6 1.0
CB B:CYS80 3.2 15.7 1.0
S3 B:SF4401 3.8 14.4 1.0
O3 B:TAR403 4.2 24.5 1.0
CB B:TYR82 4.2 14.9 1.0
CA B:GLY127 4.6 15.3 1.0
CA B:CYS80 4.6 15.9 1.0
O41 B:TAR403 4.7 14.7 1.0
O B:TYR82 4.7 17.1 1.0
CD2 B:TYR82 4.7 15.2 1.0
N B:TYR82 4.8 16.0 1.0
SG B:CYS87 4.8 15.7 1.0
CA B:TYR82 4.8 15.8 1.0
SG B:CYS84 4.8 14.1 1.0
N B:VAL128 4.9 14.0 1.0
CB B:TYR89 4.9 16.2 1.0
C B:TYR82 4.9 14.8 1.0
CG B:TYR82 5.0 14.5 1.0

Iron binding site 8 out of 8 in 6xig

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Iron binding site 8 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:14.2
occ:1.00
 FE4 B:SF4401 0.0 14.2 1.0
S1 B:SF4401 2.2 13.8 1.0
S3 B:SF4401 2.3 14.4 1.0
S2 B:SF4401 2.3 13.8 1.0
SG B:CYS84 2.3 14.1 1.0
FE1 B:SF4401 2.6 14.9 1.0
FE3 B:SF4401 2.7 14.4 1.0
FE2 B:SF4401 2.7 15.6 1.0
CB B:CYS84 3.1 14.4 1.0
NZ B:LYS207 3.7 13.1 1.0
S4 B:SF4401 3.7 15.3 1.0
O41 B:TAR403 4.1 14.7 1.0
N B:CYS84 4.1 15.0 1.0
CD B:LYS207 4.1 12.7 1.0
CA B:CYS84 4.2 15.0 1.0
CB B:TYR82 4.4 14.9 1.0
CE B:LYS207 4.5 13.1 1.0
CB B:CYS87 4.5 14.4 1.0
SG B:CYS87 4.6 15.7 1.0
SG B:CYS80 4.8 14.1 1.0
O B:HOH595 4.9 15.2 1.0
O3 B:TAR403 5.0 24.5 1.0

Reference:

A.G.Carl, L.D.Harris, M.Feng, L.U.Nordstrom, G.J.Gerfen, G.B.Evans, A.Silakov, S.C.Almo, T.L.Grove. Narrow-Spectrum Antibiotic Targeting of the Radical Sam Enzyme Mqne in Menaquinone Biosynthesis. Biochemistry V. 59 2562 2020.
ISSN: ISSN 0006-2960
PubMed: 32627538
DOI: 10.1021/ACS.BIOCHEM.0C00070
Page generated: Wed Aug 7 15:22:29 2024

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