Atomistry » Manganese » PDB 4qsh-4u3o » 4r60
Atomistry »
  Manganese »
    PDB 4qsh-4u3o »
      4r60 »

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: Sat Oct 5 21:05:48 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy