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Manganese in PDB 5fcf: Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound

Enzymatic activity of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound

All present enzymatic activity of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound, PDB code: 5fcf was solved by A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.962, 104.284, 112.324, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound (pdb code 5fcf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound, PDB code: 5fcf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5fcf

Go back to Manganese Binding Sites List in 5fcf
Manganese binding site 1 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound


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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:18.7
occ:1.00
 OE2 A:GLU374 2.0 17.4 1.0
OD2 A:ASP262 2.1 19.6 1.0
O1 A:PO4403 2.2 17.3 1.0
NE2 A:HIS331 2.2 18.1 1.0
OE2 A:GLU360 2.2 20.6 1.0
P A:PO4403 2.9 23.3 1.0
CD A:GLU374 3.0 16.9 1.0
CG A:ASP262 3.1 20.2 1.0
CE1 A:HIS331 3.1 18.7 1.0
CD A:GLU360 3.1 19.9 1.0
O3 A:PO4403 3.2 21.7 1.0
CD2 A:HIS331 3.2 18.9 1.0
MN A:MN402 3.4 18.6 1.0
OD1 A:ASP262 3.5 19.2 1.0
OE1 A:GLU360 3.5 19.0 1.0
OE1 A:GLU374 3.5 17.0 1.0
O4 A:PO4403 3.7 22.7 1.0
CB A:SER358 4.0 17.8 1.0
OG A:SER358 4.0 18.3 1.0
NE2 A:HIS376 4.1 18.8 1.0
O2 A:PO4403 4.3 18.7 1.0
ND1 A:HIS331 4.3 16.6 1.0
CG A:GLU374 4.3 17.1 1.0
CG A:HIS331 4.4 17.2 1.0
CB A:ASP262 4.4 19.4 1.0
NE2 A:HIS338 4.4 19.1 1.0
CG A:GLU360 4.4 19.4 1.0
O A:HOH501 4.5 30.5 1.0
O A:HOH522 4.5 20.5 1.0
CE1 A:HIS376 4.7 17.9 1.0
CD2 A:HIS338 4.8 20.6 1.0
O A:ASP262 4.9 18.2 1.0

Manganese binding site 2 out of 4 in 5fcf

Go back to Manganese Binding Sites List in 5fcf
Manganese binding site 2 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound


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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:18.6
occ:1.00
 O1 A:PO4403 1.8 17.3 1.0
OD1 A:ASP262 2.1 19.2 1.0
OD1 A:ASP251 2.2 17.6 1.0
OE1 A:GLU374 2.2 17.0 1.0
OD2 A:ASP251 2.3 14.9 1.0
O A:HOH522 2.4 20.5 1.0
CG A:ASP251 2.6 16.8 1.0
CD A:GLU374 3.1 16.9 1.0
CG A:ASP262 3.1 20.2 1.0
P A:PO4403 3.3 23.3 1.0
MN A:MN401 3.4 18.7 1.0
OE2 A:GLU374 3.4 17.4 1.0
OD2 A:ASP262 3.5 19.6 1.0
O2 A:PO4403 3.6 18.7 1.0
OG1 A:THR264 3.7 19.2 1.0
O4 A:PO4403 4.0 22.7 1.0
CB A:ASP251 4.1 16.6 1.0
CE2 A:PHE221 4.1 21.9 1.0
CZ A:PHE221 4.1 22.4 1.0
C A:ASP262 4.3 19.3 1.0
CB A:ASP262 4.4 19.4 1.0
OE1 A:GLU360 4.5 19.0 1.0
CG A:GLU374 4.5 17.1 1.0
N A:ILE263 4.5 18.5 1.0
O3 A:PO4403 4.6 21.7 1.0
CA A:ASP262 4.6 19.7 1.0
O A:ASP262 4.7 18.2 1.0
NE A:ARG372 4.9 17.7 1.0
NH2 A:ARG372 4.9 19.4 1.0
OE2 A:GLU360 4.9 20.6 1.0
C A:ILE263 4.9 19.1 1.0
CA A:ASP251 4.9 18.7 1.0
O A:ILE263 5.0 17.6 1.0

Manganese binding site 3 out of 4 in 5fcf

Go back to Manganese Binding Sites List in 5fcf
Manganese binding site 3 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound


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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:14.6
occ:1.00
 O2 B:PO4403 2.1 14.8 1.0
OE2 B:GLU374 2.1 13.4 1.0
OD2 B:ASP262 2.2 14.4 1.0
OE2 B:GLU360 2.2 14.2 1.0
NE2 B:HIS331 2.3 13.3 1.0
O4 B:PO4403 2.9 18.1 1.0
P B:PO4403 3.1 19.7 1.0
CD B:GLU374 3.1 14.4 1.0
CG B:ASP262 3.1 15.8 1.0
CD2 B:HIS331 3.2 13.3 1.0
CD B:GLU360 3.2 15.5 1.0
CE1 B:HIS331 3.2 12.8 1.0
MN B:MN402 3.4 15.8 1.0
OD1 B:ASP262 3.4 15.4 1.0
OE1 B:GLU374 3.5 12.9 1.0
OE1 B:GLU360 3.6 16.6 1.0
O1 B:PO4403 3.7 15.9 1.0
CB B:SER358 4.1 12.7 1.0
OG B:SER358 4.1 12.2 1.0
NE2 B:HIS376 4.1 14.3 1.0
O3 B:PO4403 4.3 16.9 1.0
CG B:GLU374 4.3 13.3 1.0
ND1 B:HIS331 4.4 13.2 1.0
CB B:ASP262 4.4 15.1 1.0
CG B:HIS331 4.4 13.7 1.0
O B:HOH507 4.4 17.3 1.0
NE2 B:HIS338 4.4 20.2 1.0
CG B:GLU360 4.5 14.8 1.0
O B:HOH519 4.6 20.2 1.0
CE1 B:HIS376 4.7 15.1 1.0
CD2 B:HIS338 4.8 18.6 1.0
O B:ASP262 4.9 13.1 1.0

Manganese binding site 4 out of 4 in 5fcf

Go back to Manganese Binding Sites List in 5fcf
Manganese binding site 4 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound


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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Mn Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:15.8
occ:1.00
 OD1 B:ASP262 2.0 15.4 1.0
O2 B:PO4403 2.2 14.8 1.0
OE1 B:GLU374 2.2 12.9 1.0
OD2 B:ASP251 2.3 14.1 1.0
OD1 B:ASP251 2.4 16.1 1.0
O B:HOH507 2.4 17.3 1.0
CG B:ASP251 2.6 15.3 1.0
CD B:GLU374 3.0 14.4 1.0
CG B:ASP262 3.1 15.8 1.0
OE2 B:GLU374 3.3 13.4 1.0
MN B:MN401 3.4 14.6 1.0
P B:PO4403 3.4 19.7 1.0
OD2 B:ASP262 3.5 14.4 1.0
O3 B:PO4403 3.6 16.9 1.0
OG1 B:THR264 3.7 15.6 1.0
O1 B:PO4403 4.1 15.9 1.0
CB B:ASP251 4.2 15.8 1.0
CE2 B:PHE221 4.2 18.0 1.0
CZ B:PHE221 4.2 17.2 1.0
C B:ASP262 4.4 14.5 1.0
CB B:ASP262 4.4 15.1 1.0
O4 B:PO4403 4.4 18.1 1.0
CG B:GLU374 4.5 13.3 1.0
N B:ILE263 4.5 15.7 1.0
OE1 B:GLU360 4.6 16.6 1.0
CA B:ASP262 4.6 14.9 1.0
O B:ASP262 4.6 13.1 1.0
NE B:ARG372 4.8 16.6 1.0
OE2 B:GLU360 4.8 14.2 1.0
C B:ILE263 4.9 15.6 1.0
O B:ILE263 4.9 14.3 1.0
CA B:ASP251 5.0 16.4 1.0
NH2 B:ARG372 5.0 18.6 1.0

Reference:

V.N.Are, A.Kumar, S.Kumar, V.D.Goyal, B.Ghosh, D.Bhatnagar, S.N.Jamdar, R.D.Makde. Crystal Structure and Biochemical Investigations Reveal Novel Mode of Substrate Selectivity and Illuminate Substrate Inhibition and Allostericity in A Subfamily of Xaa-Pro Dipeptidases. Biochim. Biophys. Acta V.1865 153 2017.
ISSN: ISSN 0006-3002
PubMed: 27816563
DOI: 10.1016/J.BBAPAP.2016.10.016
Page generated: Sun Oct 6 00:11:56 2024

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