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Manganese in PDB 4r60: Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris

Enzymatic activity of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris

All present enzymatic activity of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris:
3.4.13.9;

Protein crystallography data

The structure of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, PDB code: 4r60 was solved by A.Kumar, B.Ghosh, V.N.Are, S.N.Jamdar, R.D.Makde, S.M.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.46 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.324, 105.515, 111.352, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.6

Other elements in 4r60:

The structure of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris (pdb code 4r60). 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, PDB code: 4r60:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4r60

Go back to Manganese Binding Sites List in 4r60
Manganese binding site 1 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:21.7
occ:0.47
 OD1 A:ASP262 2.0 23.3 1.0
OE1 A:GLU374 2.3 19.6 1.0
OD2 A:ASP251 2.3 22.7 1.0
OD1 A:ASP251 2.4 20.1 1.0
CG A:ASP251 2.6 21.3 1.0
CG A:ASP262 2.8 23.5 1.0
OD2 A:ASP262 3.0 27.2 1.0
CD A:GLU374 3.2 18.8 1.0
MN A:MN403 3.3 24.8 0.6
OE2 A:GLU374 3.3 18.0 1.0
OG1 A:THR264 3.7 18.7 1.0
CE1 A:PHE221 4.1 24.7 1.0
CB A:ASP251 4.1 19.8 1.0
CZ A:PHE221 4.2 24.6 1.0
CB A:ASP262 4.3 20.4 1.0
OE1 A:GLU360 4.4 22.7 1.0
C A:ASP262 4.5 17.7 1.0
CG A:GLU374 4.6 16.9 1.0
CA A:ASP262 4.7 18.6 1.0
O A:ASP262 4.8 16.6 1.0
NH2 A:ARG372 4.8 30.9 1.0
N A:ILE263 4.8 17.8 1.0
NE A:ARG372 5.0 27.1 1.0
CA A:ASP251 5.0 19.8 1.0

Manganese binding site 2 out of 4 in 4r60

Go back to Manganese Binding Sites List in 4r60
Manganese binding site 2 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:24.8
occ:0.63
 OE2 A:GLU374 2.2 18.0 1.0
NE2 A:HIS331 2.4 19.3 1.0
OD2 A:ASP262 2.4 27.2 1.0
OE2 A:GLU360 2.6 22.2 1.0
CD A:GLU374 3.1 18.8 1.0
CE1 A:HIS331 3.1 18.9 1.0
CG A:ASP262 3.2 23.5 1.0
MN A:MN402 3.3 21.7 0.5
CD A:GLU360 3.4 21.6 1.0
OE1 A:GLU374 3.5 19.6 1.0
OE1 A:GLU360 3.5 22.7 1.0
CD2 A:HIS331 3.5 18.1 1.0
OD1 A:ASP262 3.6 23.3 1.0
CB A:SER358 4.1 17.0 1.0
NE2 A:HIS376 4.1 18.6 1.0
OG A:SER358 4.2 15.6 1.0
CB A:ASP262 4.3 20.4 1.0
CG A:GLU374 4.3 16.9 1.0
ND1 A:HIS331 4.3 18.6 1.0
CG A:HIS331 4.5 17.1 1.0
CG A:GLU360 4.7 18.7 1.0
CE1 A:HIS376 4.7 18.8 1.0
NE2 A:HIS338 4.8 25.2 1.0

Manganese binding site 3 out of 4 in 4r60

Go back to Manganese Binding Sites List in 4r60
Manganese binding site 3 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:23.7
occ:0.60
 OE2 B:GLU374 2.1 21.1 1.0
OD2 B:ASP262 2.2 25.1 1.0
NE2 B:HIS331 2.3 19.8 1.0
OE2 B:GLU360 2.7 22.8 1.0
CD B:GLU374 3.1 20.0 1.0
CE1 B:HIS331 3.1 20.0 1.0
CG B:ASP262 3.2 21.6 1.0
MN B:MN402 3.2 22.5 0.5
CD B:GLU360 3.4 21.8 1.0
OE1 B:GLU374 3.4 19.8 1.0
CD2 B:HIS331 3.4 18.7 1.0
OE1 B:GLU360 3.5 22.9 1.0
OD1 B:ASP262 3.7 21.1 1.0
CB B:SER358 4.1 15.4 1.0
OG B:SER358 4.1 17.2 1.0
O B:HOH686 4.2 43.0 1.0
NE2 B:HIS376 4.2 16.8 1.0
ND1 B:HIS331 4.3 19.9 1.0
CG B:GLU374 4.3 17.0 1.0
CB B:ASP262 4.4 19.1 1.0
CG B:HIS331 4.5 18.5 1.0
NE2 B:HIS338 4.7 20.3 1.0
CE1 B:HIS376 4.8 16.2 1.0
CG B:GLU360 4.8 19.6 1.0
CD2 B:HIS338 4.9 20.6 1.0

Manganese binding site 4 out of 4 in 4r60

Go back to Manganese Binding Sites List in 4r60
Manganese binding site 4 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:22.5
occ:0.47
 OD1 B:ASP262 2.0 21.1 1.0
OE1 B:GLU374 2.2 19.8 1.0
OD1 B:ASP251 2.4 21.1 1.0
OD2 B:ASP251 2.4 22.7 1.0
CG B:ASP251 2.7 21.9 1.0
O B:HOH686 2.7 43.0 1.0
CG B:ASP262 2.8 21.6 1.0
OD2 B:ASP262 3.0 25.1 1.0
CD B:GLU374 3.1 20.0 1.0
MN B:MN401 3.2 23.7 0.6
OE2 B:GLU374 3.3 21.1 1.0
OG1 B:THR264 3.7 17.9 1.0
CZ B:PHE221 4.1 25.0 1.0
CE2 B:PHE221 4.2 24.9 1.0
CB B:ASP251 4.2 20.1 1.0
CB B:ASP262 4.2 19.1 1.0
OE1 B:GLU360 4.3 22.9 1.0
CG B:GLU374 4.5 17.0 1.0
C B:ASP262 4.5 18.1 1.0
CA B:ASP262 4.7 18.7 1.0
NH2 B:ARG372 4.8 26.1 1.0
O B:ASP262 4.8 18.4 1.0
N B:ILE263 4.8 18.1 1.0
NE B:ARG372 5.0 24.1 1.0

Reference:

A.Kumar, B.Ghosh, V.N.Are, S.N.Jamdar, R.D.Makde, S.M.Sharma. Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris To Be Published.
Page generated: Tue Dec 15 04:28:40 2020

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