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Manganese in PDB 6omq: Crystal Structure of PTMU3 Complexed with Ptm Substrate

Protein crystallography data

The structure of Crystal Structure of PTMU3 Complexed with Ptm Substrate, PDB code: 6omq was solved by Y.C.Liu, L.B.Dong, B.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.73 / 1.86
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 112.564, 122.864, 139.936, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of PTMU3 Complexed with Ptm Substrate (pdb code 6omq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of PTMU3 Complexed with Ptm Substrate, PDB code: 6omq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 6omq

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Manganese binding site 1 out of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:10.2
occ:1.00
 OD1 A:ASP308 1.9 11.4 1.0
NE2 A:HIS12 2.2 10.5 1.0
OE1 A:GLU241 2.2 13.0 1.0
NE2 A:HIS189 2.3 13.5 1.0
OD1 A:ASP10 2.3 10.8 1.0
OD2 A:ASP10 2.3 10.4 1.0
CG A:ASP10 2.6 10.5 1.0
CG A:ASP308 3.1 10.7 1.0
CD2 A:HIS12 3.2 11.2 1.0
CE1 A:HIS12 3.2 10.7 1.0
CE1 A:HIS189 3.2 12.5 1.0
CD2 A:HIS189 3.3 12.2 1.0
CD A:GLU241 3.3 13.1 1.0
MN A:MN407 3.8 11.5 1.0
CG A:GLU241 3.8 12.3 1.0
OD2 A:ASP308 3.8 11.9 1.0
CB A:GLU241 3.9 12.3 1.0
CB A:ASP308 4.1 9.7 1.0
CB A:ASP10 4.1 9.9 1.0
ND1 A:HIS12 4.3 12.2 1.0
CG A:HIS12 4.3 10.5 1.0
ND1 A:HIS189 4.4 11.7 1.0
OE2 A:GLU241 4.4 12.6 1.0
ND1 A:HIS311 4.4 9.7 1.0
CG A:HIS189 4.5 12.9 1.0
CA A:ASP308 4.5 9.2 1.0
O A:HOH757 4.6 12.9 1.0
CE1 A:HIS311 4.6 11.1 1.0
N A:SER11 4.7 8.9 1.0
C A:ASP10 4.9 8.4 1.0
CD2 A:PHE88 4.9 10.9 1.0
CA A:ASP10 4.9 9.7 1.0

Manganese binding site 2 out of 7 in 6omq

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Manganese binding site 2 out of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:11.5
occ:1.00
 OE2 A:GLU313 2.1 11.8 1.0
OD2 A:ASP308 2.2 11.9 1.0
OE1 A:GLU241 2.2 13.0 1.0
ND1 A:HIS311 2.2 9.7 1.0
O A:HOH757 2.3 12.9 1.0
OE2 A:GLU241 2.4 12.6 1.0
CD A:GLU241 2.6 13.1 1.0
CG A:ASP308 3.0 10.7 1.0
OD1 A:ASP308 3.1 11.4 1.0
CE1 A:HIS311 3.2 11.1 1.0
CD A:GLU313 3.2 10.6 1.0
CG A:HIS311 3.2 10.9 1.0
CB A:HIS311 3.5 10.7 1.0
CG A:GLU313 3.6 11.4 1.0
MN A:MN406 3.8 10.2 1.0
CG A:GLU241 4.1 12.3 1.0
O A:HOH753 4.1 39.0 1.0
OE1 A:GLU313 4.2 10.7 1.0
NE2 A:HIS12 4.2 10.5 1.0
NE2 A:HIS311 4.3 10.4 1.0
CD2 A:HIS311 4.4 10.6 1.0
CB A:ASP308 4.4 9.7 1.0
O A:HOH801 4.6 35.3 1.0
CD2 A:HIS12 4.6 11.2 1.0
CE1 A:HIS189 4.7 12.5 1.0
O A:HOH553 4.8 31.1 1.0
NE2 A:HIS189 4.9 13.5 1.0
O A:HOH815 5.0 38.9 1.0
CA A:HIS311 5.0 11.9 1.0

Manganese binding site 3 out of 7 in 6omq

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Manganese binding site 3 out of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn408

b:42.8
occ:1.00
 O A:LEU312 2.3 12.7 1.0
OE1 B:GLN260 2.4 19.3 1.0
O A:GLY314 2.5 12.3 1.0
O B:HOH783 2.5 16.4 1.0
O A:HOH746 2.5 12.9 1.0
O A:HOH645 2.5 13.4 1.0
O B:HOH587 3.2 26.0 1.0
C A:LEU312 3.4 14.1 1.0
CD B:GLN260 3.4 17.7 1.0
C A:GLY314 3.6 12.7 1.0
O A:PHE316 4.0 15.4 1.0
N A:GLY314 4.1 12.8 1.0
CG B:GLN260 4.1 16.2 1.0
CA A:LEU312 4.2 15.5 1.0
O A:HIS311 4.3 12.4 1.0
O A:HOH858 4.3 38.6 1.0
O A:HOH673 4.3 15.8 1.0
CB B:GLN260 4.4 15.0 1.0
O A:HOH755 4.4 32.5 1.0
N A:GLU313 4.4 12.9 1.0
C A:GLU313 4.4 13.4 1.0
NE2 B:GLN260 4.4 17.4 1.0
CA A:GLY314 4.4 12.0 1.0
N A:THR315 4.5 12.2 1.0
O B:HOH536 4.5 20.3 1.0
O B:HOH756 4.6 45.7 1.0
CA A:GLU313 4.6 13.2 1.0
C A:THR315 4.7 13.7 1.0
CA A:THR315 4.7 13.0 1.0
CE1 A:HIS287 4.8 12.6 1.0
O A:THR315 4.9 13.1 1.0
N A:PHE316 4.9 15.8 1.0
O A:HOH758 4.9 34.8 1.0
O A:HOH644 4.9 13.1 1.0
O A:GLU313 5.0 12.8 1.0
O A:HOH864 5.0 46.2 1.0

Manganese binding site 4 out of 7 in 6omq

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Manganese binding site 4 out of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn406

b:11.7
occ:1.00
 OD1 B:ASP10 1.9 12.3 1.0
OD1 B:ASP308 2.0 10.9 1.0
OE1 B:GLU241 2.0 16.0 1.0
NE2 B:HIS189 2.2 11.2 1.0
NE2 B:HIS12 2.2 10.8 1.0
OD2 B:ASP10 2.6 13.8 1.0
CG B:ASP10 2.6 13.9 1.0
CG B:ASP308 3.1 10.4 1.0
CE1 B:HIS189 3.1 12.7 1.0
CD2 B:HIS12 3.2 13.2 1.0
CD B:GLU241 3.2 13.3 1.0
CE1 B:HIS12 3.3 14.3 1.0
CD2 B:HIS189 3.3 11.4 1.0
OD2 B:ASP308 3.6 11.2 1.0
MN B:MN407 3.8 16.4 1.0
CG B:GLU241 3.8 13.6 1.0
CB B:GLU241 3.9 13.0 1.0
CB B:ASP10 4.1 13.4 1.0
CB B:ASP308 4.1 12.1 1.0
O B:HOH760 4.2 19.4 1.0
OE2 B:GLU241 4.3 15.0 1.0
ND1 B:HIS189 4.3 11.5 1.0
CG B:HIS12 4.3 12.9 1.0
ND1 B:HIS12 4.4 12.4 1.0
CG B:HIS189 4.4 11.5 1.0
CA B:ASP308 4.5 12.8 1.0
ND1 B:HIS311 4.6 22.2 1.0
CE1 B:HIS311 4.8 24.8 1.0
N B:SER11 4.8 12.4 1.0
C B:ASP10 4.9 13.3 1.0
CA B:ASP10 5.0 14.2 1.0

Manganese binding site 5 out of 7 in 6omq

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Manganese binding site 5 out of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn407

b:16.4
occ:1.00
 OE1 B:GLU313 1.7 13.2 1.0
OD2 B:ASP308 2.2 11.2 1.0
OE2 B:GLU241 2.2 15.0 1.0
OE1 B:GLU241 2.3 16.0 1.0
ND1 B:HIS311 2.4 22.2 1.0
O B:HOH760 2.5 19.4 1.0
CD B:GLU241 2.5 13.3 1.0
CD B:GLU313 3.0 15.8 1.0
CG B:ASP308 3.0 10.4 1.0
OD1 B:ASP308 3.3 10.9 1.0
CG B:HIS311 3.3 21.4 1.0
CE1 B:HIS311 3.4 24.8 1.0
CB B:HIS311 3.5 20.0 1.0
CG B:GLU313 3.7 18.9 1.0
MN B:MN406 3.8 11.7 1.0
OE2 B:GLU313 4.0 19.3 1.0
CG B:GLU241 4.0 13.6 1.0
C41 B:MZD405 4.2 28.3 1.0
NE2 B:HIS12 4.3 10.8 1.0
CB B:GLU313 4.3 19.6 1.0
CB B:ASP308 4.4 12.1 1.0
CD2 B:HIS311 4.5 21.5 1.0
NE2 B:HIS311 4.5 20.0 1.0
C43 B:MZD405 4.6 29.3 1.0
C42 B:MZD405 4.7 28.6 1.0
CE1 B:HIS189 4.7 12.7 1.0
CD2 B:HIS12 4.7 13.2 1.0
C16 B:MZD405 4.9 27.3 1.0
NE2 B:HIS189 4.9 11.2 1.0

Manganese binding site 6 out of 7 in 6omq

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Manganese binding site 6 out of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn408

b:28.5
occ:1.00
 O B:HOH514 2.4 33.6 1.0
O B:HOH594 2.4 29.3 1.0
O B:HOH752 4.2 29.4 1.0
OD2 B:ASP17 4.2 24.7 1.0
OE2 B:GLU21 4.4 28.6 1.0
OE1 B:GLU21 4.5 29.7 1.0
O B:HOH881 4.8 38.6 1.0
CD B:GLU21 4.9 32.0 1.0

Manganese binding site 7 out of 7 in 6omq

Go back to Manganese Binding Sites List in 6omq
Manganese binding site 7 out of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn409

b:64.0
occ:1.00
 O B:HOH782 2.4 21.8 1.0
O B:LEU312 2.4 21.5 1.0
O B:HOH517 2.5 23.2 1.0
OE1 A:GLN260 2.5 21.1 1.0
O B:GLY314 2.7 17.2 1.0
O A:HOH791 2.9 32.9 1.0
C B:LEU312 3.4 24.0 1.0
CD A:GLN260 3.4 21.2 1.0
O A:HOH594 3.5 41.9 1.0
C B:GLY314 3.8 16.4 1.0
CA B:LEU312 4.0 24.1 1.0
O B:PHE316 4.0 27.0 1.0
O B:HOH630 4.1 21.5 1.0
CG A:GLN260 4.1 21.4 1.0
N B:GLY314 4.2 19.8 1.0
NE2 A:GLN260 4.3 18.5 1.0
O A:HOH536 4.4 29.3 1.0
CB A:GLN260 4.4 22.5 1.0
O B:HOH887 4.4 45.1 1.0
O B:HIS311 4.5 19.3 1.0
N B:GLU313 4.5 21.2 1.0
C B:GLU313 4.5 20.9 1.0
CA B:GLY314 4.6 20.0 1.0
O B:HOH795 4.6 49.4 1.0
N B:THR315 4.7 18.5 1.0
CE1 B:HIS287 4.7 17.2 1.0
CA B:THR315 4.8 18.9 1.0
C B:THR315 4.8 21.8 1.0
CB B:LEU312 4.9 26.6 1.0
NE2 B:HIS287 4.9 16.6 1.0
CA B:GLU313 4.9 22.0 1.0

Reference:

L.B.Dong, Y.C.Liu, A.J.Cepeda, E.Kalkreuter, M.R.Deng, J.D.Rudolf, C.Chang, A.Joachimiak, G.N.Phillips Jr., B.Shen. Characterization and Crystal Structure of A Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis. J.Am.Chem.Soc. V. 141 12406 2019.
ISSN: ESSN 1520-5126
PubMed: 31291107
DOI: 10.1021/JACS.9B06183
Page generated: Sun Oct 6 05:43:04 2024

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