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Iron in PDB 6xi9: X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine

Enzymatic activity of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine

All present enzymatic activity of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine:
2.5.1.120;

Protein crystallography data

The structure of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine, PDB code: 6xi9 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) 19.96 / 2.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.512, 75.079, 83.269, 90.00, 107.13, 90.00
R / Rfree (%) 15.1 / 19.8

Other elements in 6xi9:

The structure of X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine (pdb code 6xi9). 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 in Complex with Aminofutalosine and Methionine, PDB code: 6xi9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6xi9

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Iron binding site 1 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:22.4
occ:1.00
 FE1 A:SF4401 0.0 22.4 1.0
O A:MET402 2.1 20.2 1.0
S2 A:SF4401 2.2 24.3 1.0
S4 A:SF4401 2.2 22.0 1.0
S3 A:SF4401 2.2 25.1 1.0
N A:MET402 2.3 21.9 1.0
SD A:MET402 2.7 25.4 1.0
C A:MET402 2.9 22.7 1.0
FE3 A:SF4401 3.0 23.1 1.0
FE2 A:SF4401 3.0 23.4 1.0
FE4 A:SF4401 3.0 23.4 1.0
CA A:MET402 3.1 22.1 1.0
CG A:MET402 3.7 26.3 1.0
CB A:MET402 3.8 24.0 1.0
CE A:MET402 3.8 23.8 1.0
S1 A:SF4401 3.9 28.4 1.0
NZ A:LYS207 4.0 22.4 1.0
OXT A:MET402 4.1 23.2 1.0
O A:GLY126 4.5 21.7 1.0
SG A:CYS80 4.9 24.6 1.0
CG1 A:VAL159 5.0 17.6 1.0
SG A:CYS84 5.0 21.9 1.0
CD A:LYS207 5.0 23.3 1.0
SG A:CYS87 5.0 22.2 1.0

Iron binding site 2 out of 8 in 6xi9

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Iron binding site 2 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.4
occ:1.00
 FE2 A:SF4401 0.0 23.4 1.0
S3 A:SF4401 2.1 25.1 1.0
S1 A:SF4401 2.1 28.4 1.0
S4 A:SF4401 2.2 22.0 1.0
SG A:CYS80 2.2 24.6 1.0
FE4 A:SF4401 2.9 23.4 1.0
FE3 A:SF4401 2.9 23.1 1.0
FE1 A:SF4401 3.0 22.4 1.0
CB A:CYS80 3.1 24.2 1.0
S2 A:SF4401 3.7 24.3 1.0
N A:MET402 4.1 21.9 1.0
CB A:TYR82 4.1 24.9 1.0
CA A:GLY127 4.5 22.2 1.0
CA A:CYS80 4.5 25.4 1.0
CD2 A:TYR82 4.7 26.5 1.0
N A:TYR82 4.7 26.2 1.0
N A:VAL128 4.7 24.2 1.0
CA A:TYR82 4.8 26.0 1.0
O A:MET402 4.8 20.2 1.0
O A:TYR82 4.8 24.3 1.0
CB A:TYR89 4.8 29.9 1.0
SG A:CYS87 4.9 22.2 1.0
CG A:TYR82 4.9 26.6 1.0
C A:TYR82 4.9 26.3 1.0
SG A:CYS84 5.0 21.9 1.0

Iron binding site 3 out of 8 in 6xi9

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Iron binding site 3 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.1
occ:1.00
 FE3 A:SF4401 0.0 23.1 1.0
S4 A:SF4401 2.1 22.0 1.0
S2 A:SF4401 2.1 24.3 1.0
S1 A:SF4401 2.2 28.4 1.0
SG A:CYS87 2.2 22.2 1.0
FE4 A:SF4401 2.8 23.4 1.0
FE2 A:SF4401 2.9 23.4 1.0
FE1 A:SF4401 3.0 22.4 1.0
CB A:CYS87 3.0 22.9 1.0
S3 A:SF4401 3.7 25.1 1.0
CB A:TYR89 4.0 29.9 1.0
SD A:MET402 4.1 25.4 1.0
CA A:CYS87 4.5 24.3 1.0
CB A:CYS84 4.5 23.6 1.0
CE A:MET402 4.6 23.8 1.0
N A:TYR89 4.8 29.6 1.0
CA A:TYR89 4.8 29.6 1.0
CG A:TYR89 4.8 31.1 1.0
SG A:CYS84 4.8 21.9 1.0
C A:TYR89 4.8 29.8 1.0
O A:MET402 4.9 20.2 1.0
CD2 A:TYR89 4.9 32.7 1.0
N A:SER90 4.9 29.9 1.0
N A:MET402 5.0 21.9 1.0
SG A:CYS80 5.0 24.6 1.0

Iron binding site 4 out of 8 in 6xi9

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Iron binding site 4 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.4
occ:1.00
 FE4 A:SF4401 0.0 23.4 1.0
S3 A:SF4401 2.1 25.1 1.0
S1 A:SF4401 2.1 28.4 1.0
S2 A:SF4401 2.2 24.3 1.0
SG A:CYS84 2.3 21.9 1.0
FE3 A:SF4401 2.8 23.1 1.0
FE2 A:SF4401 2.9 23.4 1.0
CB A:CYS84 2.9 23.6 1.0
FE1 A:SF4401 3.0 22.4 1.0
NZ A:LYS207 3.5 22.4 1.0
S4 A:SF4401 3.7 22.0 1.0
CD A:LYS207 4.0 23.3 1.0
O A:MET402 4.0 20.2 1.0
N A:CYS84 4.1 29.3 1.0
CA A:CYS84 4.1 25.4 1.0
CE A:LYS207 4.3 23.1 1.0
CB A:CYS87 4.4 22.9 1.0
CB A:TYR82 4.4 24.9 1.0
SG A:CYS87 4.7 22.2 1.0
O A:HOH557 4.8 27.0 1.0
SG A:CYS80 4.8 24.6 1.0
CZ A:PHE86 4.9 20.5 1.0
CE1 A:PHE86 5.0 20.3 1.0

Iron binding site 5 out of 8 in 6xi9

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Iron binding site 5 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:21.2
occ:1.00
 FE1 B:SF4401 0.0 21.2 1.0
S4 B:SF4401 2.1 22.3 1.0
S2 B:SF4401 2.2 23.4 1.0
S3 B:SF4401 2.2 22.7 1.0
SG B:CYS87 2.3 22.2 1.0
FE3 B:SF4401 2.8 20.5 1.0
FE4 B:SF4401 2.8 22.9 1.0
FE2 B:SF4401 2.9 18.6 1.0
CB B:CYS87 3.0 23.1 1.0
S1 B:SF4401 3.6 24.3 1.0
SD B:MET402 4.2 27.6 1.0
CB B:TYR89 4.2 23.4 1.0
CA B:CYS87 4.5 23.7 1.0
CB B:CYS84 4.5 21.4 1.0
CE B:MET402 4.6 31.0 1.0
SG B:CYS84 4.7 19.9 1.0
N B:MET402 4.7 23.2 1.0
C B:TYR89 4.8 23.2 1.0
N B:TYR89 4.8 24.7 1.0
CA B:TYR89 4.8 22.9 1.0
N B:SER90 4.8 21.6 1.0
CG B:TYR89 4.9 24.6 1.0
CD2 B:TYR89 4.9 24.9 1.0
SG B:CYS80 4.9 22.4 1.0
OXT B:MET402 4.9 20.6 1.0

Iron binding site 6 out of 8 in 6xi9

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Iron binding site 6 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:18.6
occ:1.00
 FE2 B:SF4401 0.0 18.6 1.0
N B:MET402 2.1 23.2 1.0
S3 B:SF4401 2.1 22.7 1.0
OXT B:MET402 2.2 20.6 1.0
S1 B:SF4401 2.2 24.3 1.0
S4 B:SF4401 2.3 22.3 1.0
SD B:MET402 2.6 27.6 1.0
FE1 B:SF4401 2.9 21.2 1.0
FE4 B:SF4401 3.0 22.9 1.0
C B:MET402 3.0 23.4 1.0
FE3 B:SF4401 3.0 20.5 1.0
CA B:MET402 3.1 22.4 1.0
CG B:MET402 3.7 27.6 1.0
CB B:MET402 3.8 26.1 1.0
CE B:MET402 3.8 31.0 1.0
S2 B:SF4401 3.9 23.4 1.0
NZ B:LYS207 4.1 20.2 1.0
O B:MET402 4.2 22.3 1.0
O B:GLY126 4.6 19.6 1.0
SG B:CYS87 4.9 22.2 1.0
CG1 B:VAL159 4.9 19.8 1.0
SG B:CYS84 4.9 19.9 1.0
SG B:CYS80 5.0 22.4 1.0

Iron binding site 7 out of 8 in 6xi9

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Iron binding site 7 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:20.5
occ:1.00
 FE3 B:SF4401 0.0 20.5 1.0
S1 B:SF4401 2.1 24.3 1.0
S2 B:SF4401 2.1 23.4 1.0
S4 B:SF4401 2.2 22.3 1.0
SG B:CYS80 2.3 22.4 1.0
FE1 B:SF4401 2.8 21.2 1.0
FE4 B:SF4401 2.9 22.9 1.0
FE2 B:SF4401 3.0 18.6 1.0
CB B:CYS80 3.1 21.6 1.0
S3 B:SF4401 3.7 22.7 1.0
N B:MET402 4.0 23.2 1.0
CB B:TYR82 4.1 25.2 1.0
CA B:GLY127 4.5 21.8 1.0
CA B:CYS80 4.6 22.9 1.0
CD2 B:TYR82 4.7 24.0 1.0
N B:VAL128 4.8 19.8 1.0
O B:TYR82 4.8 25.9 1.0
N B:TYR82 4.8 25.3 1.0
CA B:TYR82 4.9 24.9 1.0
SG B:CYS87 4.9 22.2 1.0
O B:TYR89 4.9 24.1 1.0
CB B:TYR89 4.9 23.4 1.0
OXT B:MET402 4.9 20.6 1.0
SG B:CYS84 4.9 19.9 1.0
CG B:TYR82 4.9 24.6 1.0
C B:TYR82 4.9 24.0 1.0

Iron binding site 8 out of 8 in 6xi9

Go back to Iron Binding Sites List in 6xi9
Iron binding site 8 out of 8 in the X-Ray Crystal Structure of Mqne From Pedobacter Heparinus in Complex with Aminofutalosine and Methionine


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 in Complex with Aminofutalosine and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:22.9
occ:1.00
 FE4 B:SF4401 0.0 22.9 1.0
S1 B:SF4401 2.1 24.3 1.0
S3 B:SF4401 2.1 22.7 1.0
S2 B:SF4401 2.1 23.4 1.0
SG B:CYS84 2.2 19.9 1.0
FE1 B:SF4401 2.8 21.2 1.0
FE3 B:SF4401 2.9 20.5 1.0
FE2 B:SF4401 3.0 18.6 1.0
CB B:CYS84 3.0 21.4 1.0
NZ B:LYS207 3.6 20.2 1.0
S4 B:SF4401 3.7 22.3 1.0
CD B:LYS207 4.0 18.8 1.0
OXT B:MET402 4.1 20.6 1.0
N B:CYS84 4.1 23.2 1.0
CA B:CYS84 4.2 22.2 1.0
CE B:LYS207 4.3 19.8 1.0
CB B:CYS87 4.4 23.1 1.0
CB B:TYR82 4.5 25.2 1.0
SG B:CYS87 4.7 22.2 1.0
O B:HOH600 4.8 18.5 1.0
N B:MET402 4.8 23.2 1.0
SG B:CYS80 4.9 22.4 1.0
CZ B:PHE86 4.9 20.6 1.0
CE1 B:PHE86 5.0 19.3 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 15:22:28 2024

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