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Manganese in PDB 2z87: Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Galnac and Udp

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

All present enzymatic activity of Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Galnac 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-Galnac and Udp, PDB code: 2z87 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) 19.96 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.371, 109.285, 85.575, 90.00, 103.47, 90.00
R / Rfree (%) 19.9 / 28.3

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-Galnac and Udp (pdb code 2z87). 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 Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Galnac and Udp, PDB code: 2z87:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2z87

Go back to Manganese Binding Sites List in 2z87
Manganese binding site 1 out of 4 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Galnac 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-Galnac and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1

b:47.2
occ:1.00
 O1A A:UD2683 1.8 42.0 1.0
OD2 A:ASP241 2.3 46.0 1.0
NE2 A:HIS386 2.4 44.2 1.0
O A:HOH690 2.4 9.0 1.0
O1B A:UD2683 2.6 62.6 1.0
CE1 A:HIS386 3.0 45.5 1.0
PA A:UD2683 3.0 54.9 1.0
CG A:ASP241 3.3 37.1 1.0
CD2 A:HIS386 3.5 41.0 1.0
O3A A:UD2683 3.5 61.9 1.0
PB A:UD2683 3.7 67.4 1.0
OD1 A:ASP241 3.7 46.3 1.0
NH1 A:ARG161 3.8 54.0 1.0
O2A A:UD2683 3.9 38.8 1.0
NH2 A:ARG161 4.0 70.4 1.0
ND1 A:HIS386 4.1 42.7 1.0
O5B A:UD2683 4.2 62.0 1.0
CZ A:ARG161 4.3 67.8 1.0
CG A:HIS386 4.4 46.6 1.0
CB A:ASP241 4.4 37.5 1.0
O1' A:UD2683 4.6 66.4 1.0
O2B A:UD2683 4.9 69.6 1.0
O A:GLN387 5.0 62.3 1.0

Manganese binding site 2 out of 4 in 2z87

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Manganese binding site 2 out of 4 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Galnac 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-Galnac and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2

b:62.9
occ:1.00
 OD2 A:ASP521 2.2 41.7 1.0
NE2 A:HIS631 2.3 0.3 1.0
CE1 A:HIS631 2.7 0.5 1.0
OD1 A:ASP521 2.8 43.3 1.0
CG A:ASP521 2.9 38.8 1.0
O1B A:UDP684 3.3 1.0 1.0
O2A A:UDP684 3.3 95.0 1.0
CD2 A:HIS631 3.5 0.9 1.0
OD1 A:ASP522 3.6 48.5 1.0
ND1 A:HIS631 3.9 0.9 1.0
CG A:HIS631 4.2 0.5 1.0
CB A:ASP521 4.4 42.0 1.0
CG A:ASP522 4.5 49.2 1.0
PB A:UDP684 4.5 0.9 1.0
OD2 A:ASP522 4.6 43.0 1.0
O A:VAL629 4.6 70.6 1.0
PA A:UDP684 4.6 99.9 1.0
O3B A:UDP684 4.6 0.4 1.0
O3A A:UDP684 4.7 0.7 1.0
CB A:ASP519 4.8 36.6 1.0
NE A:ARG628 4.8 78.3 1.0
CB A:VAL629 4.9 69.8 1.0

Manganese binding site 3 out of 4 in 2z87

Go back to Manganese Binding Sites List in 2z87
Manganese binding site 3 out of 4 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Galnac 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-Galnac and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3

b:48.6
occ:1.00
 O1B B:UD2683 1.9 50.9 1.0
O1A B:UD2683 2.0 35.9 1.0
O B:HOH746 2.2 25.6 1.0
O B:HOH712 2.2 16.6 1.0
NE2 B:HIS386 2.4 54.0 1.0
OD2 B:ASP241 2.9 42.4 1.0
CE1 B:HIS386 3.1 54.3 1.0
PB B:UD2683 3.2 55.7 1.0
PA B:UD2683 3.2 54.3 1.0
CD2 B:HIS386 3.4 56.1 1.0
OD1 B:ASP241 3.6 48.2 1.0
CG B:ASP241 3.6 43.9 1.0
O3A B:UD2683 3.7 54.5 1.0
O1' B:UD2683 3.8 55.2 1.0
NH1 B:ARG161 3.9 66.0 1.0
O2A B:UD2683 4.0 55.5 1.0
ND1 B:HIS386 4.2 53.2 1.0
CG B:HIS386 4.3 53.7 1.0
O2B B:UD2683 4.5 59.5 1.0
O5B B:UD2683 4.5 56.0 1.0
OD2 B:ASP239 4.6 48.1 1.0
C5B B:UD2683 4.8 55.0 1.0
C7' B:UD2683 4.8 68.4 1.0
C8' B:UD2683 4.9 74.8 1.0
CZ B:ARG161 4.9 67.8 1.0
NH2 B:ARG161 5.0 73.8 1.0

Manganese binding site 4 out of 4 in 2z87

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Manganese binding site 4 out of 4 in the Crystal Structure of Chondroitin Polymerase From Escherichia Coli Strain K4 (K4CP) Complexed with Udp-Galnac 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-Galnac and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn4

b:65.5
occ:1.00
 OD2 B:ASP521 2.0 50.0 1.0
O1B B:UDP1 2.1 0.5 1.0
OD1 B:ASP521 2.5 41.2 1.0
CG B:ASP521 2.6 40.8 1.0
NE2 B:HIS631 3.1 0.2 1.0
O B:HOH689 3.3 61.3 1.0
PB B:UDP1 3.5 0.6 1.0
O2A B:UDP1 3.5 93.7 1.0
CE1 B:HIS631 3.5 0.6 1.0
CD2 B:HIS631 3.9 0.6 1.0
CB B:ASP521 4.1 45.6 1.0
OD1 B:ASP522 4.1 46.1 1.0
O3B B:UDP1 4.3 0.2 1.0
OD2 B:ASP522 4.3 54.0 1.0
O2B B:UDP1 4.3 0.6 1.0
ND1 B:HIS631 4.4 0.9 1.0
CG B:ASP522 4.5 58.2 1.0
O3A B:UDP1 4.5 0.7 1.0
CB B:VAL629 4.5 61.9 1.0
CG B:HIS631 4.6 0.3 1.0
O B:VAL629 4.7 78.7 1.0
PA B:UDP1 4.7 95.3 1.0
CG B:ARG628 4.9 75.3 1.0
CB B:ASP519 5.0 62.3 1.0
CA B:ASP521 5.0 51.1 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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