Atomistry » Manganese » PDB 2ypq-3au8 » 2z86
Atomistry »
  Manganese »
    PDB 2ypq-3au8 »
      2z86 »

Manganese in PDB 2z86: Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp

Enzymatic activity of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp

All present enzymatic activity of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp:
2.4.1.175; 2.4.1.226;

Protein crystallography data

The structure of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp, PDB code: 2z86 was solved by T.Osawa, N.Sugiura, H.Shimada, R.Hirooka, A.Tsuji, M.Kimura, K.Kimata, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.092, 219.829, 85.856, 90.00, 103.07, 90.00
R / Rfree (%) 22.5 / 28.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp (pdb code 2z86). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp, PDB code: 2z86:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 1 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


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 Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1

b:58.2
occ:1.00
 O1B A:UGA683 2.2 64.7 1.0
O1A A:UGA683 2.2 58.5 1.0
NE2 A:HIS386 2.2 61.9 1.0
OD2 A:ASP241 2.5 57.0 1.0
CE1 A:HIS386 2.9 63.0 1.0
O A:HOH790 3.0 60.1 1.0
NH2 A:ARG161 3.1 76.1 1.0
CG A:ASP241 3.1 54.3 1.0
OD1 A:ASP241 3.3 54.7 1.0
CD2 A:HIS386 3.3 61.3 1.0
PA A:UGA683 3.4 63.2 1.0
PB A:UGA683 3.4 69.3 1.0
O3A A:UGA683 3.7 64.5 1.0
ND1 A:HIS386 4.0 62.7 1.0
CZ A:ARG161 4.2 78.2 1.0
O2A A:UGA683 4.3 60.6 1.0
O3B A:UGA683 4.3 68.1 1.0
CG A:HIS386 4.3 60.7 1.0
NH1 A:ARG161 4.4 78.5 1.0
CB A:ASP241 4.4 55.3 1.0
OD2 A:ASP239 4.5 54.7 1.0
O5D A:UGA683 4.6 59.6 1.0
O2B A:UGA683 4.7 67.2 1.0
C1' A:UGA683 4.8 69.4 1.0
C5D A:UGA683 4.8 56.2 1.0

Manganese binding site 2 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 2 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


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 Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2

b:60.8
occ:1.00
 O1A A:UGA684 2.1 64.8 1.0
OD2 A:ASP521 2.5 56.1 1.0
O1B A:UGA684 2.6 64.2 1.0
OD1 A:ASP521 2.7 50.1 1.0
CG A:ASP521 2.9 51.0 1.0
PA A:UGA684 3.6 62.4 1.0
PB A:UGA684 4.0 66.4 1.0
CE1 A:HIS631 4.0 67.2 1.0
OD1 A:ASP522 4.1 42.5 1.0
O A:VAL629 4.1 52.4 1.0
O3A A:UGA684 4.2 65.0 1.0
O2A A:UGA684 4.3 56.7 1.0
CB A:ASP521 4.3 50.6 1.0
OD2 A:ASP522 4.5 36.7 1.0
NE2 A:HIS631 4.7 67.9 1.0
CG A:ASP522 4.7 42.5 1.0
O5D A:UGA684 4.7 60.9 1.0
O3B A:UGA684 4.8 64.0 1.0
C5D A:UGA684 5.0 62.5 1.0

Manganese binding site 3 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 3 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


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 Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3

b:47.2
occ:1.00
 O2A B:UDP1 2.0 49.5 1.0
O B:HOH820 2.1 24.2 1.0
NE2 B:HIS386 2.2 47.9 1.0
O1B B:UDP1 2.2 58.3 1.0
OD2 B:ASP241 2.3 45.0 1.0
CG B:ASP241 2.9 42.4 1.0
CE1 B:HIS386 3.0 46.8 1.0
OD1 B:ASP241 3.0 42.4 1.0
CD2 B:HIS386 3.2 45.6 1.0
PA B:UDP1 3.3 47.6 1.0
PB B:UDP1 3.5 60.2 1.0
O3A B:UDP1 3.6 51.5 1.0
NH2 B:ARG161 3.7 58.1 1.0
ND1 B:HIS386 4.1 49.0 1.0
CG B:HIS386 4.2 46.5 1.0
O1A B:UDP1 4.2 50.6 1.0
CB B:ASP241 4.2 40.0 1.0
O3B B:UDP1 4.4 61.0 1.0
O5' B:UDP1 4.5 45.7 1.0
O2B B:UDP1 4.5 56.6 1.0
C5' B:UDP1 4.8 45.6 1.0
O B:HOH798 4.8 39.4 1.0
OD2 B:ASP239 4.9 41.0 1.0

Manganese binding site 4 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 4 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


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 Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn4

b:62.7
occ:1.00
 O B:HOH822 2.1 32.7 1.0
O1A B:UGA683 2.1 51.6 1.0
O1B B:UGA683 2.2 49.8 1.0
O B:HOH821 2.2 34.4 1.0
OD2 B:ASP521 2.3 51.3 1.0
NE2 B:HIS631 2.9 77.9 1.0
OD1 B:ASP521 2.9 46.5 1.0
CG B:ASP521 2.9 50.8 1.0
PA B:UGA683 3.5 53.7 1.0
PB B:UGA683 3.5 48.9 1.0
CD2 B:HIS631 3.5 78.1 1.0
CE1 B:HIS631 3.9 77.1 1.0
O3A B:UGA683 3.9 51.8 1.0
O B:VAL629 4.1 58.3 1.0
O3B B:UGA683 4.3 53.2 1.0
CB B:ASP521 4.3 45.2 1.0
OD1 B:ASP522 4.4 53.9 1.0
O5D B:UGA683 4.5 52.6 1.0
O2A B:UGA683 4.5 57.9 1.0
NE B:ARG628 4.6 61.9 1.0
OD2 B:ASP522 4.7 51.7 1.0
CG B:HIS631 4.7 78.0 1.0
C5D B:UGA683 4.7 52.5 1.0
O2B B:UGA683 4.7 54.8 1.0
ND1 B:HIS631 4.8 78.3 1.0
C3D B:UGA683 4.9 50.0 1.0
CG B:ASP522 4.9 49.6 1.0
O2' B:UGA683 5.0 56.6 1.0

Manganese binding site 5 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 5 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn5

b:44.3
occ:1.00
 O1B C:UDP1 1.9 46.6 1.0
OD2 C:ASP241 2.3 37.7 1.0
O2A C:UDP1 2.4 49.7 1.0
NE2 C:HIS386 2.5 41.1 1.0
O C:HOH853 2.5 38.1 1.0
CD2 C:HIS386 3.3 38.5 1.0
CG C:ASP241 3.3 31.4 1.0
PB C:UDP1 3.3 53.0 1.0
CE1 C:HIS386 3.3 40.8 1.0
PA C:UDP1 3.6 44.2 1.0
OD1 C:ASP241 3.6 29.7 1.0
O3A C:UDP1 3.9 45.4 1.0
O2B C:UDP1 4.0 53.1 1.0
O C:HOH819 4.0 40.4 1.0
NH1 C:ARG161 4.2 23.2 1.0
CG C:HIS386 4.3 35.2 1.0
ND1 C:HIS386 4.3 37.8 1.0
O1A C:UDP1 4.4 48.8 1.0
O3B C:UDP1 4.5 49.4 1.0
CB C:ASP241 4.6 32.1 1.0
NH2 C:ARG161 4.7 21.4 1.0
O5' C:UDP1 4.8 46.3 1.0
CZ C:ARG161 4.8 22.9 1.0

Manganese binding site 6 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 6 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn6

b:49.5
occ:1.00
 O1B C:UGA683 2.2 40.1 1.0
O1A C:UGA683 2.2 43.6 1.0
O C:HOH795 2.5 37.3 1.0
OD2 C:ASP521 2.5 55.2 1.0
NE2 C:HIS631 2.8 84.6 1.0
CE1 C:HIS631 3.0 85.0 1.0
OD1 C:ASP521 3.0 55.2 1.0
CG C:ASP521 3.1 51.8 1.0
PB C:UGA683 3.6 43.5 1.0
PA C:UGA683 3.7 48.9 1.0
OD1 C:ASP522 4.0 44.8 1.0
CD2 C:HIS631 4.0 83.0 1.0
O3A C:UGA683 4.1 44.9 1.0
ND1 C:HIS631 4.1 83.1 1.0
O3B C:UGA683 4.2 43.5 1.0
OD2 C:ASP522 4.4 42.8 1.0
O C:VAL629 4.5 51.6 1.0
C5D C:UGA683 4.6 46.1 1.0
CB C:ASP521 4.6 47.7 1.0
O5D C:UGA683 4.6 48.4 1.0
CG C:ASP522 4.6 42.9 1.0
CG C:HIS631 4.7 80.5 1.0
CB C:ASP519 4.7 36.5 1.0
O2' C:UGA683 4.7 44.7 1.0
O2A C:UGA683 4.7 47.9 1.0
CD C:ARG628 4.7 50.8 1.0
O2B C:UGA683 4.8 45.3 1.0
CG C:ARG628 4.8 48.0 1.0
OD2 C:ASP519 4.9 44.5 1.0
C3D C:UGA683 4.9 42.0 1.0

Manganese binding site 7 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 7 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn7

b:46.5
occ:1.00
 O1B D:UGA683 2.1 60.7 1.0
O1A D:UGA683 2.1 55.1 1.0
O D:HOH807 2.2 32.5 1.0
OD2 D:ASP241 2.5 38.9 1.0
CE1 D:HIS386 2.7 53.9 1.0
NE2 D:HIS386 2.7 49.9 1.0
CG D:ASP241 3.3 38.0 1.0
PA D:UGA683 3.4 53.4 1.0
OD1 D:ASP241 3.4 36.6 1.0
PB D:UGA683 3.5 60.5 1.0
O3A D:UGA683 3.8 59.3 1.0
ND1 D:HIS386 3.9 53.0 1.0
CD2 D:HIS386 3.9 52.2 1.0
O2A D:UGA683 4.2 57.7 1.0
NH2 D:ARG161 4.3 59.0 1.0
O3B D:UGA683 4.3 60.0 1.0
OD2 D:ASP239 4.4 41.5 1.0
C1' D:UGA683 4.4 63.7 1.0
CG D:HIS386 4.5 50.8 1.0
O5D D:UGA683 4.6 52.6 1.0
O2B D:UGA683 4.7 59.2 1.0
CB D:ASP241 4.8 36.3 1.0
C5D D:UGA683 4.8 51.4 1.0
NH1 D:ARG161 4.8 61.8 1.0
O D:HOH796 4.9 45.4 1.0
O5' D:UGA683 5.0 68.4 1.0

Manganese binding site 8 out of 8 in 2z86

Go back to Manganese Binding Sites List in 2z86
Manganese binding site 8 out of 8 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Glcua and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn8

b:64.4
occ:1.00
 O1A D:UGA684 2.2 55.9 1.0
O1B D:UGA684 2.3 60.9 1.0
OD2 D:ASP521 2.4 60.3 1.0
OD1 D:ASP521 2.8 59.3 1.0
CG D:ASP521 2.9 58.0 1.0
CE1 D:HIS631 3.3 78.1 1.0
PA D:UGA684 3.6 60.2 1.0
PB D:UGA684 3.7 58.6 1.0
NE2 D:HIS631 3.8 80.2 1.0
O3A D:UGA684 4.1 58.9 1.0
OD2 D:ASP522 4.2 51.0 1.0
O D:HOH756 4.2 57.1 1.0
NE D:ARG628 4.2 53.6 1.0
O D:VAL629 4.2 54.1 1.0
OD1 D:ASP522 4.3 51.5 1.0
CB D:ASP521 4.3 56.6 1.0
O3B D:UGA684 4.4 55.2 1.0
C5D D:UGA684 4.5 56.8 1.0
O5D D:UGA684 4.5 57.3 1.0
ND1 D:HIS631 4.6 79.5 1.0
CG D:ASP522 4.6 47.9 1.0
CD D:ARG628 4.6 56.5 1.0
OD2 D:ASP519 4.7 46.5 1.0
CB D:ASP519 4.7 42.9 1.0
C3D D:UGA684 4.8 52.7 1.0
O2A D:UGA684 4.8 59.0 1.0
O2B D:UGA684 4.8 60.8 1.0

Reference:

T.Osawa, N.Sugiura, H.Shimada, R.Hirooka, A.Tsuji, T.Shirakawa, K.Fukuyama, M.Kimura, K.Kimata, Y.Kakuta. Crystal Structure of Chondroitin Polymerase From Escherichia Coli K4. Biochem. Biophys. Res. V. 378 10 2009COMMUN..
ISSN: ESSN 1090-2104
PubMed: 18771653
DOI: 10.1016/J.BBRC.2008.08.121
Page generated: Sat Oct 5 15:34:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy