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Manganese in PDB 2a8t: 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A

Protein crystallography data

The structure of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A, PDB code: 2a8t was solved by J.N.Scarsdale, B.A.Peculis, H.T.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.17 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.702, 81.710, 111.706, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 26.4

Manganese Binding Sites:

The binding sites of Manganese atom in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A (pdb code 2a8t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A, PDB code: 2a8t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 2a8t

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Manganese binding site 1 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:60.2
occ:1.00
 O3G A:MGT251 2.1 55.0 0.8
OE2 A:GLU93 2.1 63.0 1.0
O A:GLY72 2.2 58.7 1.0
O2B A:MGT251 2.2 52.9 0.8
O A:HOH633 2.2 48.3 1.0
CD A:GLU93 3.0 62.6 1.0
MN A:MN301 3.2 62.9 1.0
OE1 A:GLU93 3.3 57.5 1.0
PG A:MGT251 3.3 60.3 0.8
C A:GLY72 3.4 56.1 1.0
PB A:MGT251 3.5 50.9 0.8
O3B A:MGT251 3.7 57.3 0.8
OE1 A:GLU150 3.9 56.0 1.0
CA A:GLY73 3.9 53.7 1.0
N A:GLY73 4.1 55.8 1.0
O2G A:MGT251 4.2 65.6 0.8
NE2 A:HIS37 4.2 56.4 1.0
NH1 A:ARG63 4.3 57.2 1.0
OE2 A:GLU89 4.3 58.2 1.0
O A:HOH639 4.3 55.8 1.0
N A:GLY72 4.4 52.0 1.0
CG A:GLU93 4.4 51.8 1.0
O3A A:MGT251 4.4 60.7 0.8
O5' A:ADN252 4.5 61.7 0.8
CA A:GLY72 4.5 54.3 1.0
O2A A:MGT251 4.6 82.3 0.8
O1B A:MGT251 4.6 53.5 0.8
CD2 A:HIS37 4.7 54.1 1.0
CD A:GLU150 4.9 53.9 1.0

Manganese binding site 2 out of 9 in 2a8t

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Manganese binding site 2 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:62.9
occ:1.00
 O A:HOH505 2.1 50.7 1.0
OE2 A:GLU93 2.2 63.0 1.0
O2B A:MGT251 2.2 52.9 0.8
OE2 A:GLU89 2.2 58.2 1.0
OE1 A:GLU150 2.4 56.0 1.0
MN A:MN300 3.2 60.2 1.0
CD A:GLU93 3.2 62.6 1.0
PB A:MGT251 3.2 50.9 0.8
CD A:GLU89 3.3 54.0 1.0
CD A:GLU150 3.4 53.9 1.0
CG A:GLU93 3.6 51.8 1.0
MN A:MN303 3.6 56.9 0.5
OE1 A:GLU89 3.7 59.5 1.0
O3A A:MGT251 3.7 60.7 0.8
MN A:MN302 3.7 74.4 1.0
O1B A:MGT251 3.7 53.5 0.8
OE2 A:GLU150 3.8 54.5 1.0
O A:GLY72 3.8 58.7 1.0
OE2 A:GLU92 4.2 57.8 1.0
OE1 A:GLU93 4.4 57.5 1.0
OD2 A:ASP146 4.5 67.8 1.0
CG A:GLU89 4.6 53.3 1.0
O3B A:MGT251 4.6 57.3 0.8
C A:GLY72 4.7 56.1 1.0
O3G A:MGT251 4.7 55.0 0.8
CG A:GLU150 4.7 55.2 1.0
CB A:GLU89 4.9 54.7 1.0
CA A:GLY73 4.9 53.7 1.0
CB A:GLU150 4.9 51.5 1.0

Manganese binding site 3 out of 9 in 2a8t

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Manganese binding site 3 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:74.4
occ:1.00
 O1B A:MGT251 2.1 53.5 0.8
OE1 A:GLU89 2.2 59.5 1.0
MN A:MN303 3.0 56.9 0.5
PB A:MGT251 3.1 50.9 0.8
CD A:GLU89 3.2 54.0 1.0
O3A A:MGT251 3.4 60.7 0.8
OE2 A:GLU89 3.6 58.2 1.0
NH1 A:ARG88 3.6 79.2 1.0
O2B A:MGT251 3.7 52.9 0.8
MN A:MN301 3.7 62.9 1.0
N A:PHE74 4.3 58.7 1.0
O A:PHE74 4.3 63.4 1.0
CB A:PHE74 4.4 63.6 1.0
O3B A:MGT251 4.5 57.3 0.8
CG A:GLU89 4.5 53.3 1.0
OE2 A:GLU92 4.6 57.8 1.0
O A:HOH505 4.6 50.7 1.0
CZ A:ARG88 4.7 76.8 1.0
CA A:PHE74 4.8 62.1 1.0
CD2 A:PHE74 4.8 66.2 1.0
OE2 A:GLU150 4.8 54.5 1.0
PA A:MGT251 5.0 79.8 0.8

Manganese binding site 4 out of 9 in 2a8t

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Manganese binding site 4 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:56.9
occ:0.50
 OE2 A:GLU150 2.0 54.5 1.0
O3A A:MGT251 2.1 60.7 0.8
MN A:MN302 3.0 74.4 1.0
CD A:GLU150 3.0 53.9 1.0
O5' A:MGT251 3.1 80.0 0.8
O4' A:MGT251 3.1 84.1 0.8
PB A:MGT251 3.2 50.9 0.8
PA A:MGT251 3.2 79.8 0.8
OE1 A:GLU150 3.3 56.0 1.0
O1B A:MGT251 3.5 53.5 0.8
MN A:MN301 3.6 62.9 1.0
O2B A:MGT251 3.7 52.9 0.8
C5' A:MGT251 3.9 80.2 0.8
C4' A:MGT251 4.0 82.2 0.8
O2A A:MGT251 4.1 82.3 0.8
O1A A:MGT251 4.2 84.0 0.8
C1' A:MGT251 4.3 89.0 0.8
O A:HOH505 4.3 50.7 1.0
CG A:GLU150 4.4 55.2 1.0
N9 A:MGT251 4.5 90.2 0.8
O3B A:MGT251 4.6 57.3 0.8
OE1 A:GLU89 4.7 59.5 1.0
OE2 A:GLU92 4.9 57.8 1.0
C4 A:MGT251 4.9 89.9 0.8
OE2 A:GLU89 5.0 58.2 1.0
C8 A:MGT251 5.0 89.8 0.8

Manganese binding site 5 out of 9 in 2a8t

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Manganese binding site 5 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn304

b:64.1
occ:0.80
 O B:HOH635 2.0 57.8 1.0
OE2 B:GLU93 2.1 61.3 1.0
O3G B:MGT251 2.1 55.0 0.5
O B:GLY72 2.1 58.2 1.0
O2B B:MGT251 2.2 47.9 0.5
CD B:GLU93 3.0 55.8 1.0
MN B:MN305 3.0 64.7 0.8
OE1 B:GLU93 3.2 57.7 1.0
C B:GLY72 3.3 56.9 1.0
PG B:MGT251 3.3 57.0 0.5
PB B:MGT251 3.5 60.7 0.5
O3B B:MGT251 3.8 55.7 0.5
CA B:GLY73 3.9 52.9 1.0
OE1 B:GLU150 3.9 63.8 1.0
O B:HOH636 3.9 52.4 1.0
N B:GLY73 4.1 55.0 1.0
O2G B:MGT251 4.1 56.4 0.5
N B:GLY72 4.2 53.2 1.0
O2A B:MGT251 4.3 80.0 0.5
CG B:GLU93 4.3 57.4 1.0
CA B:GLY72 4.4 54.9 1.0
OE2 B:GLU89 4.4 74.2 1.0
O3A B:MGT251 4.4 67.2 0.5
NE2 B:HIS37 4.4 60.7 1.0
CG B:GLU89 4.5 66.7 1.0
O5' B:ADN252 4.5 55.6 0.5
O1B B:MGT251 4.6 53.9 0.5
CE B:MET61 4.6 64.0 1.0
NH1 B:ARG63 4.7 54.1 1.0
CD B:GLU89 4.8 63.2 1.0
CD2 B:HIS37 4.8 56.3 1.0
CD B:GLU150 5.0 65.4 1.0
MN B:MN305 5.0 45.5 0.2

Manganese binding site 6 out of 9 in 2a8t

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Manganese binding site 6 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn305

b:64.7
occ:0.80
 MN B:MN305 0.0 64.7 0.8
OE2 B:GLU89 2.0 74.2 1.0
OE2 B:GLU93 2.1 61.3 1.0
O2B B:MGT251 2.2 47.9 0.5
MN B:MN305 2.3 45.5 0.2
OE1 B:GLU150 2.4 63.8 1.0
MN B:MN304 3.0 64.1 0.8
CD B:GLU89 3.0 63.2 1.0
CD B:GLU93 3.2 55.8 1.0
PB B:MGT251 3.4 60.7 0.5
MN B:MN306 3.5 65.6 0.3
CD B:GLU150 3.5 65.4 1.0
CG B:GLU89 3.6 66.7 1.0
MN B:MN306 3.6 85.8 0.6
CG B:GLU93 3.6 57.4 1.0
O B:GLY72 3.7 58.2 1.0
O3A B:MGT251 3.8 67.2 0.5
OE2 B:GLU150 3.9 67.2 1.0
OE1 B:GLU89 4.0 65.9 1.0
O1B B:MGT251 4.0 53.9 0.5
OE1 B:GLU93 4.3 57.7 1.0
OD2 B:ASP146 4.4 67.3 1.0
O3G B:MGT251 4.5 55.0 0.5
O B:HOH629 4.6 71.1 1.0
O2A B:MGT251 4.6 80.0 0.5
O B:HOH635 4.6 57.8 1.0
C B:GLY72 4.7 56.9 1.0
O3B B:MGT251 4.7 55.7 0.5
CA B:GLY73 4.8 52.9 1.0
CG B:GLU150 4.8 60.9 1.0
O B:HOH628 4.9 66.4 1.0
PA B:MGT251 4.9 77.6 0.5
O B:GLU89 5.0 58.6 1.0

Manganese binding site 7 out of 9 in 2a8t

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Manganese binding site 7 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn305

b:45.5
occ:0.20
 MN B:MN305 0.0 45.5 0.2
MN B:MN305 2.3 64.7 0.8
OE2 B:GLU89 2.5 74.2 1.0
OD2 B:ASP146 2.5 67.3 1.0
OE1 B:GLU150 3.0 63.8 1.0
CG B:GLU93 3.3 57.4 1.0
OE2 B:GLU93 3.4 61.3 1.0
CB B:GLU92 3.5 56.9 1.0
CD B:GLU92 3.6 69.5 1.0
OE1 B:GLU92 3.6 80.9 1.0
CD B:GLU89 3.7 63.2 1.0
CG B:ASP146 3.7 66.6 1.0
O B:HOH629 3.7 71.1 1.0
OE2 B:GLU92 3.7 79.8 1.0
CD B:GLU150 3.8 65.4 1.0
CD B:GLU93 3.8 55.8 1.0
CG B:GLU92 4.2 66.3 1.0
MN B:MN306 4.2 65.6 0.3
OE2 B:GLU150 4.3 67.2 1.0
O B:HOH628 4.3 66.4 1.0
O2B B:MGT251 4.5 47.9 0.5
O B:GLU89 4.5 58.6 1.0
CB B:ASP146 4.5 57.1 1.0
CG B:GLU89 4.5 66.7 1.0
OE1 B:GLU89 4.5 65.9 1.0
OD1 B:ASP146 4.5 68.9 1.0
N B:GLU93 4.6 56.3 1.0
MN B:MN306 4.6 85.8 0.6
CB B:GLU93 4.6 55.8 1.0
C B:GLU92 4.6 55.8 1.0
CA B:GLU92 4.7 59.0 1.0
CG B:GLU150 4.8 60.9 1.0
CB B:GLU150 4.9 58.3 1.0
CA B:GLU93 4.9 56.2 1.0
MN B:MN304 5.0 64.1 0.8

Manganese binding site 8 out of 9 in 2a8t

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Manganese binding site 8 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn306

b:65.6
occ:0.30
 MN B:MN306 0.0 65.6 0.3
OE2 B:GLU150 2.3 67.2 1.0
O3A B:MGT251 2.3 67.2 0.5
MN B:MN306 2.8 85.8 0.6
O B:HOH629 2.9 71.1 1.0
CD B:GLU150 3.2 65.4 1.0
PB B:MGT251 3.3 60.7 0.5
O5' B:MGT251 3.3 75.8 0.5
OE1 B:GLU150 3.4 63.8 1.0
PA B:MGT251 3.4 77.6 0.5
MN B:MN305 3.5 64.7 0.8
O1B B:MGT251 3.5 53.9 0.5
O2B B:MGT251 3.6 47.9 0.5
O B:HOH628 3.8 66.4 1.0
O2A B:MGT251 4.0 80.0 0.5
OE2 B:GLU89 4.2 74.2 1.0
MN B:MN305 4.2 45.5 0.2
O4' B:MGT251 4.5 86.1 0.5
C5' B:MGT251 4.6 79.3 0.5
CG B:GLU150 4.6 60.9 1.0
O1A B:MGT251 4.6 78.4 0.5
O3B B:MGT251 4.7 55.7 0.5
CD B:GLU89 4.9 63.2 1.0
C4' B:MGT251 4.9 82.1 0.5

Manganese binding site 9 out of 9 in 2a8t

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Manganese binding site 9 out of 9 in the 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 Snorna Decapping Nudix Hydrolase X29, Manganese and M7G-Ppp-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn306

b:85.8
occ:0.60
 MN B:MN306 0.0 85.8 0.6
O1B B:MGT251 2.3 53.9 0.5
O B:HOH615 2.6 69.5 1.0
OE1 B:GLU89 2.7 65.9 1.0
MN B:MN306 2.8 65.6 0.3
O B:HOH628 3.0 66.4 1.0
OE2 B:GLU89 3.1 74.2 1.0
CD B:GLU89 3.1 63.2 1.0
PB B:MGT251 3.2 60.7 0.5
O3A B:MGT251 3.5 67.2 0.5
O2B B:MGT251 3.6 47.9 0.5
MN B:MN305 3.6 64.7 0.8
N B:PHE74 4.2 54.7 1.0
O B:HOH629 4.2 71.1 1.0
CG B:GLU89 4.4 66.7 1.0
O B:PHE74 4.6 55.6 1.0
MN B:MN305 4.6 45.5 0.2
O3B B:MGT251 4.6 55.7 0.5
CA B:GLY73 4.7 52.9 1.0
OE1 B:GLU92 4.8 80.9 1.0
CB B:PHE74 4.8 58.7 1.0
C B:GLY73 4.9 53.6 1.0
OE2 B:GLU150 4.9 67.2 1.0
CA B:PHE74 4.9 56.2 1.0

Reference:

J.N.Scarsdale, B.A.Peculis, H.T.Wright. Crystal Structures of U8 Snorna Decapping Nudix Hydrolase, X29, and Its Metal and Cap Complexes Structure V. 14 331 2006.
ISSN: ISSN 0969-2126
PubMed: 16472752
DOI: 10.1016/J.STR.2005.11.010
Page generated: Sat Oct 5 13:22:40 2024

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