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Manganese in PDB 7o5r: Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1

Protein crystallography data

The structure of Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1, PDB code: 7o5r was solved by J.Laustsen, I.Justo, S.R.Marsden, U.Hanefeld, I.Bento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.13 / 1.65
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 71.54, 71.54, 225.394, 90, 90, 120
R / Rfree (%) 16 / 19.3

Other elements in 7o5r:

The structure of Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 also contains other interesting chemical elements:

Bromine (Br) 1 atom
Potassium (K) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 (pdb code 7o5r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1, PDB code: 7o5r:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7o5r

Go back to Manganese Binding Sites List in 7o5r
Manganese binding site 1 out of 3 in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1


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 Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:11.4
occ:0.61
OD2 A:ASP171 1.8 14.9 1.0
O A:HOH403 1.8 16.5 1.0
OE1 A:GLU145 1.8 20.6 1.0
MN A:MN302 2.3 13.8 0.4
CD A:GLU145 2.7 15.3 1.0
CG A:ASP171 2.8 13.1 1.0
HE22 A:GLN43 3.1 9.4 0.0
OE2 A:GLU145 3.3 19.1 1.0
HE2 A:HIS44 3.3 9.4 0.0
O A:HOH432 3.3 22.4 1.0
OD1 A:ASP171 3.5 14.2 1.0
HB2 A:ASP171 3.7 13.4 1.0
CB A:ASP171 3.7 14.3 1.0
HB3 A:ASP171 3.8 13.4 1.0
HG3 A:GLU145 3.8 15.4 1.0
NE2 A:GLN43 3.9 9.4 1.0
CG A:GLU145 3.9 16.2 1.0
O A:HOH481 3.9 17.4 0.6
HG2 A:MET93 4.1 22.2 1.0
NE2 A:HIS44 4.2 9.5 1.0
OE1 A:GLN43 4.2 9.1 1.0
HE21 A:GLN43 4.4 9.4 0.0
CD A:GLN43 4.5 8.1 1.0
HG2 A:GLU145 4.5 15.4 1.0
HE1 A:MET143 4.5 14.9 1.0
O A:HOH463 4.5 40.3 1.0
SD A:MET93 4.6 23.1 1.0
HB2 A:GLU145 4.6 13.8 1.0
HB3 A:PRO92 4.6 13.7 1.0
HB2 A:PRO92 4.7 13.7 1.0
CG A:MET93 4.8 22.9 1.0
CB A:GLU145 4.9 13.6 1.0
HD2 A:HIS44 4.9 10.7 1.0
HH12 A:ARG69 4.9 7.0 0.0
CD2 A:HIS44 5.0 11.2 1.0

Manganese binding site 2 out of 3 in 7o5r

Go back to Manganese Binding Sites List in 7o5r
Manganese binding site 2 out of 3 in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1


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 Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:13.8
occ:0.36
O A:HOH403 1.8 16.5 1.0
O A:HOH481 1.8 17.4 0.6
OD2 A:ASP171 1.8 14.9 1.0
O A:HOH432 1.9 22.4 1.0
OE1 A:GLU145 2.0 20.6 1.0
MN A:MN301 2.3 11.4 0.6
HB2 A:ASP171 2.8 13.4 1.0
CG A:ASP171 2.9 13.1 1.0
CD A:GLU145 3.3 15.3 1.0
CB A:ASP171 3.4 14.3 1.0
HH12 A:ARG69 3.5 7.0 0.0
HE3 A:MET143 3.6 14.9 1.0
HE1 A:MET143 3.6 14.9 1.0
HB3 A:ASP171 3.9 13.4 1.0
H A:ASP171 4.0 13.7 1.0
O A:HOH585 4.0 13.1 1.0
HE2 A:HIS44 4.0 9.4 0.0
HA3 A:GLY168 4.0 10.6 1.0
OD1 A:ASP171 4.0 14.2 1.0
CE A:MET143 4.1 14.2 1.0
HB2 A:GLU145 4.1 13.8 1.0
OE2 A:GLU145 4.1 19.1 1.0
NH1 A:ARG69 4.2 7.0 1.0
O A:HOH481 4.3 15.2 0.4
CG A:GLU145 4.4 16.2 1.0
HD2 A:HIS44 4.4 10.7 1.0
HH11 A:ARG69 4.5 7.0 0.0
HG3 A:GLU145 4.5 15.4 1.0
OE1 A:GLN43 4.5 9.1 1.0
CA A:ASP171 4.6 12.1 1.0
NE2 A:HIS44 4.6 9.5 1.0
N A:ASP171 4.6 13.7 1.0
CB A:GLU145 4.6 13.6 1.0
HG1 A:THR170 4.6 19.0 0.0
HB3 A:GLU145 4.7 13.8 1.0
HE22 A:GLN43 4.7 9.4 0.0
HH21 A:ARG69 4.7 8.2 1.0
HE2 A:MET143 4.8 14.9 1.0
CD2 A:HIS44 4.8 11.2 1.0
CA A:GLY168 4.8 10.4 1.0
O A:HOH569 5.0 16.3 1.0
OG1 A:THR170 5.0 19.1 1.0
HA A:ASP171 5.0 12.5 1.0
HA2 A:GLY168 5.0 10.7 1.0

Manganese binding site 3 out of 3 in 7o5r

Go back to Manganese Binding Sites List in 7o5r
Manganese binding site 3 out of 3 in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1


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 Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:11.4
occ:0.76
OD2 B:ASP171 1.7 13.2 0.8
O B:HOH454 1.8 20.0 1.0
O B:HOH466 1.8 16.8 1.0
O B:HOH458 1.9 12.3 1.0
OE1 B:GLU145 2.2 17.1 1.0
CG B:ASP171 2.7 13.7 0.8
OD1 B:ASP171 2.8 8.3 0.2
CD B:GLU145 3.1 18.1 1.0
HE22 B:GLN43 3.3 10.6 0.0
CG B:ASP171 3.3 8.8 0.2
HE2 B:HIS44 3.4 12.7 0.0
OE2 B:GLU145 3.5 17.2 1.0
OD1 B:ASP171 3.6 11.9 0.8
HB2 B:ASP171 3.6 13.2 0.8
CB B:ASP171 3.6 13.6 0.8
HB3 B:ASP171 3.6 13.2 0.8
HB3 B:ASP171 3.6 9.3 0.2
O B:HOH423 3.9 23.3 1.0
NE2 B:GLN43 3.9 10.5 1.0
OD2 B:ASP171 4.0 9.1 0.2
CB B:ASP171 4.1 9.3 0.2
NE2 B:HIS44 4.2 12.7 1.0
OE1 B:GLN43 4.3 9.1 1.0
CG B:GLU145 4.3 18.0 1.0
HG3 B:GLU145 4.3 17.7 1.0
O B:HOH410 4.4 22.2 1.0
HB2 B:GLU145 4.5 16.4 1.0
HE21 B:GLN43 4.5 10.6 0.0
CD B:GLN43 4.5 8.3 1.0
HE1 B:MET143 4.5 15.9 1.0
HG2 B:MET93 4.5 23.2 1.0
O B:HOH498 4.5 21.6 1.0
HB2 B:ASP171 4.6 9.3 0.2
HB3 B:PRO92 4.7 12.1 1.0
HD2 B:HIS44 4.8 12.7 1.0
HE3 B:MET143 4.8 15.9 1.0
O B:HOH583 4.8 20.9 1.0
CB B:GLU145 4.9 16.7 1.0
HB2 B:PRO92 4.9 12.1 1.0
CD2 B:HIS44 5.0 13.0 1.0

Reference:

S.R.Marsden, H.J.Wijma, M.K.F.Mohr, I.Justo, P.L.Hagedoorn, J.Laustsen, C.M.Jeffries, D.Svergun, L.Mestrom, D.G.G.Mcmillan, I.Bento, U.Hanefeld. Substrate Induced Movement of the Metal Cofactor Between Active and Resting State. Angew.Chem.Int.Ed.Engl. V. 61 13338 2022.
ISSN: ESSN 1521-3773
PubMed: 36214476
DOI: 10.1002/ANIE.202213338
Page generated: Sun Oct 6 10:18:45 2024

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