Atomistry » Manganese » PDB 5ekw-5fxv » 5fcf
Atomistry »
  Manganese »
    PDB 5ekw-5fxv »
      5fcf »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy