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Barium in PDB 2drw: The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3

Protein crystallography data

The structure of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3, PDB code: 2drw was solved by S.Okazaki, A.Suzuki, H.Komeda, Y.Asano, T.Yamane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.57 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.205, 123.219, 115.706, 90.00, 104.36, 90.00
R / Rfree (%) 18.2 / 24.3

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Barium atom in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 (pdb code 2drw). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 23 binding sites of Barium where determined in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3, PDB code: 2drw:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 23 in 2drw

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Barium binding site 1 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3003

b:37.4
occ:0.50
 O A:SER121 2.7 36.8 1.0
OD1 A:ASP122 2.9 40.3 1.0
O A:GLU232 3.0 34.3 1.0
O A:TRP233 3.1 34.3 1.0
O A:HOH3230 3.1 41.5 1.0
O A:HOH3357 3.1 44.4 1.0
C A:SER121 3.6 36.6 1.0
C A:TRP233 3.8 34.3 1.0
CG A:ASP122 4.0 39.3 1.0
C A:GLU232 4.1 33.5 1.0
N A:SER121 4.3 35.3 1.0
N A:ASP122 4.3 37.3 1.0
CA A:TRP233 4.3 34.2 1.0
CA A:ASP122 4.3 37.7 1.0
O A:HOH3316 4.4 39.5 1.0
CA A:SER121 4.5 36.1 1.0
N A:TRP233 4.7 34.2 1.0
OD2 A:ASP122 4.7 41.4 1.0
N A:PHE234 4.7 34.4 1.0
O A:HOH3351 4.7 40.1 1.0
CB A:ASP122 4.8 38.3 1.0

Barium binding site 2 out of 23 in 2drw

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Barium binding site 2 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3004

b:34.9
occ:0.40
 O D:HOH3371 2.1 29.3 1.0
O A:HOH3196 2.6 40.2 1.0
O A:HOH3204 2.7 27.6 1.0
O D:HOH3134 2.8 28.7 1.0
O A:GLU211 2.8 23.3 1.0
OD2 D:ASP53 3.7 15.6 1.0
CG D:ASP53 4.0 14.8 1.0
C A:GLU211 4.0 22.9 1.0
OD1 D:ASP53 4.2 15.4 1.0
O D:HOH3373 4.2 27.3 1.0
CD A:PRO213 4.4 22.0 1.0
O A:HOH3212 4.7 26.9 1.0
ND2 A:ASN212 4.9 24.4 1.0
CA A:GLU211 4.9 22.7 1.0
CB D:ASP53 5.0 13.7 1.0
N A:ASN212 5.0 22.5 1.0
CA A:ASN212 5.0 22.5 1.0

Barium binding site 3 out of 23 in 2drw

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Barium binding site 3 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3009

b:47.6
occ:0.20
 BA B:BA3010 2.5 47.0 0.2
O A:HOH3378 2.7 36.3 1.0
O A:SER301 2.8 22.9 1.0
OE2 A:GLU323 3.2 39.5 1.0
OE1 A:GLU323 3.3 39.2 1.0
OE1 B:GLU323 3.3 39.1 1.0
O B:HOH3217 3.5 40.5 1.0
CD A:GLU323 3.6 37.5 1.0
O A:HOH3280 3.8 44.7 1.0
C A:SER301 3.9 23.1 1.0
CD B:GLU323 4.0 36.6 1.0
OE2 B:GLU323 4.0 38.9 1.0
BA F:BA3008 4.3 44.9 0.2
CA A:SER301 4.4 23.1 1.0
CB A:SER301 4.4 23.4 1.0
NZ A:LYS359 4.5 38.4 1.0
O A:HOH3257 4.8 43.9 1.0
BA F:BA3007 4.9 52.4 0.5
O F:HOH3206 4.9 29.7 1.0

Barium binding site 4 out of 23 in 2drw

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Barium binding site 4 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3020

b:52.9
occ:0.30
 OG A:SER363 2.6 44.5 1.0
O A:ASN360 2.8 39.0 1.0
C A:ASN360 3.9 39.0 1.0
CB A:SER363 4.0 44.5 1.0
CA A:ASN360 4.5 38.4 1.0
O A:SER363 4.6 45.3 1.0
CB A:ASN360 4.7 38.6 1.0
N A:SER363 4.8 44.0 1.0
CA A:SER363 4.9 44.5 1.0
ND2 A:ASN360 4.9 43.2 1.0
N A:SER361 4.9 39.7 1.0

Barium binding site 5 out of 23 in 2drw

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Barium binding site 5 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3002

b:43.8
occ:0.80
 O B:HOH3068 2.6 19.3 1.0
O B:GLU232 2.7 19.3 1.0
OD1 B:ASP122 2.8 21.4 1.0
O B:SER121 3.1 19.2 1.0
O B:HOH3156 3.3 29.5 1.0
O B:HOH3205 3.3 34.2 1.0
O B:TRP233 3.4 19.0 1.0
C B:SER121 3.8 19.3 1.0
C B:GLU232 3.8 20.3 1.0
O B:HOH3109 3.9 22.8 1.0
CG B:ASP122 4.0 23.1 1.0
C B:TRP233 4.0 19.0 1.0
O B:HOH3225 4.0 36.0 1.0
CA B:TRP233 4.3 18.7 1.0
N B:ASP122 4.3 19.4 1.0
CA B:ASP122 4.3 19.5 1.0
O B:HOH3416 4.4 37.0 1.0
N B:SER121 4.5 19.3 1.0
N B:TRP233 4.5 19.2 1.0
O B:HOH3321 4.6 34.3 1.0
O B:HOH3339 4.6 33.1 1.0
OD2 B:ASP122 4.8 27.3 1.0
CA B:SER121 4.8 19.3 1.0
CB B:ASP122 4.8 20.2 1.0
O B:HOH3204 4.8 30.5 1.0
N B:PHE234 4.8 19.1 1.0
CB B:GLU232 4.9 22.3 1.0
CA B:GLU232 4.9 21.3 1.0

Barium binding site 6 out of 23 in 2drw

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Barium binding site 6 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3010

b:47.0
occ:0.20
 BA A:BA3009 2.5 47.6 0.2
O F:HOH3206 2.7 29.7 1.0
O B:HOH3217 2.7 40.5 1.0
OE2 B:GLU323 2.8 38.9 1.0
BA F:BA3007 2.8 52.4 0.5
O A:HOH3378 3.2 36.3 1.0
O A:HOH3280 3.2 44.7 1.0
OE1 B:GLU323 3.5 39.1 1.0
CD B:GLU323 3.5 36.6 1.0
BA F:BA3008 3.5 44.9 0.2
OE2 A:GLU323 4.4 39.5 1.0
O B:HOH3368 4.4 43.1 1.0
OE2 F:GLU323 4.7 44.2 1.0
O A:HOH3257 4.8 43.9 1.0
O A:SER301 4.8 22.9 1.0
O B:SER301 4.8 29.6 1.0
CG B:GLU323 4.9 35.3 1.0
OE1 A:GLU323 5.0 39.2 1.0

Barium binding site 7 out of 23 in 2drw

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Barium binding site 7 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3001

b:34.0
occ:0.80
 O C:HOH3309 2.7 40.6 1.0
O C:GLU232 2.8 30.1 1.0
O C:SER121 2.9 32.1 1.0
O C:HOH3289 3.0 34.9 1.0
O C:TRP233 3.0 29.2 1.0
O C:HOH3310 3.1 35.7 1.0
O C:HOH3146 3.1 30.1 1.0
OD1 C:ASP122 3.3 35.6 1.0
C C:TRP233 3.7 29.2 1.0
C C:SER121 3.8 32.5 1.0
O C:HOH3236 3.9 49.1 1.0
C C:GLU232 3.9 29.7 1.0
CG C:ASP122 4.0 34.6 1.0
N C:SER121 4.2 32.5 1.0
CA C:TRP233 4.3 28.9 1.0
OD2 C:ASP122 4.4 36.5 1.0
N C:ASP122 4.5 32.5 1.0
N C:TRP233 4.6 29.4 1.0
CA C:SER121 4.6 32.7 1.0
CA C:ASP122 4.6 32.7 1.0
N C:PHE234 4.6 29.2 1.0
O C:HOH3389 4.8 30.6 1.0
O C:HOH3230 4.8 35.8 1.0
CB C:ASP122 4.9 33.0 1.0
CD C:PRO235 5.0 28.4 1.0
O C:HOH3262 5.0 34.1 1.0

Barium binding site 8 out of 23 in 2drw

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Barium binding site 8 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3005

b:20.2
occ:0.50
 O C:HOH3200 2.6 37.0 1.0
O C:HOH3155 2.9 38.1 1.0
O B:HOH3267 2.9 25.9 1.0
O B:HOH3304 3.1 26.1 1.0
O C:ALA206 3.2 35.5 1.0
O B:HOH3308 4.2 40.8 1.0
C C:ALA206 4.2 34.8 1.0
O B:HOH3319 4.4 47.8 1.0
CA C:ALA206 4.7 34.2 1.0
O B:HOH3250 4.8 42.6 1.0
O B:LEU36 4.8 18.4 1.0
O C:HOH3281 4.8 27.4 1.0

Barium binding site 9 out of 23 in 2drw

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Barium binding site 9 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3011

b:46.6
occ:0.35
 O D:HOH3207 2.6 35.3 1.0
OE1 C:GLU323 2.6 31.8 1.0
O C:SER301 2.9 25.0 1.0
O D:HOH3384 3.0 51.2 1.0
O C:HOH3274 3.0 51.0 1.0
OE2 C:GLU323 3.1 33.5 1.0
CD C:GLU323 3.2 31.9 1.0
C C:SER301 4.1 25.0 1.0
O C:HOH3057 4.5 28.7 1.0
OE2 D:GLU323 4.6 33.5 1.0
BA D:BA3014 4.6 46.0 0.2
BA E:BA3012 4.7 49.3 0.3
CG C:GLU323 4.7 28.2 1.0
CA C:SER301 4.8 25.0 1.0
O E:HOH3247 4.8 34.1 1.0
CB C:SER301 4.8 25.1 1.0
OE1 D:GLU323 4.9 33.8 1.0
O C:HOH3210 5.0 35.0 1.0

Barium binding site 10 out of 23 in 2drw

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Barium binding site 10 out of 23 in the The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of The Crystal Structutre of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba3013

b:44.1
occ:0.35
 O E:HOH3220 2.4 42.3 1.0
O C:HOH3392 2.5 44.9 1.0
O D:HOH3384 2.7 51.2 1.0
O E:HOH3247 3.2 34.1 1.0
O E:HOH3037 3.8 19.4 1.0
O C:HOH3274 4.2 51.0 1.0
O D:HOH3337 4.5 36.5 1.0
O E:HOH3244 4.5 40.9 1.0
OE2 C:GLU323 4.5 33.5 1.0
BA E:BA3012 4.7 49.3 0.3
OE2 D:GLU303 4.8 34.4 1.0
OE2 D:GLU323 4.8 33.5 1.0
O D:HOH3207 4.8 35.3 1.0

Reference:

S.Okazaki, A.Suzuki, H.Komeda, S.Yamaguchi, Y.Asano, T.Yamane. Crystal Structure and Functional Characterization of A D-Stereospecific Amino Acid Amidase From Ochrobactrum Anthropi SV3, A New Member of the Penicillin-Recognizing Proteins J.Mol.Biol. V. 368 79 2007.
ISSN: ISSN 0022-2836
PubMed: 17331533
DOI: 10.1016/J.JMB.2006.10.070
Page generated: Wed Jul 10 15:02:21 2024

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