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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

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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

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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

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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

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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

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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

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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

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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

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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

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