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Barium in PDB 2efx: The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide

Protein crystallography data

The structure of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide, PDB code: 2efx was solved by S.Okazaki, A.Suzuki, T.Mizushima, 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) 19.82 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.711, 123.396, 115.477, 90.00, 104.36, 90.00
R / Rfree (%) 18.7 / 25.6

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Barium atom in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide (pdb code 2efx). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 22 binding sites of Barium where determined in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide, PDB code: 2efx:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 22 in 2efx

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Barium binding site 1 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

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

b:19.7
occ:0.50
O A:HOH3045 1.8 18.4 1.0
O A:SER121 2.6 32.2 1.0
O A:GLU232 2.7 26.3 1.0
OD1 A:ASP122 2.7 36.8 1.0
O A:TRP233 3.0 23.0 1.0
O A:HOH3169 3.1 35.4 1.0
O A:HOH3139 3.2 27.0 1.0
C A:SER121 3.7 32.1 1.0
CG A:ASP122 3.7 36.6 1.0
C A:TRP233 3.7 23.5 1.0
C A:GLU232 3.9 25.6 1.0
OD2 A:ASP122 4.2 39.5 1.0
CA A:TRP233 4.2 24.0 1.0
N A:SER121 4.3 30.1 1.0
N A:ASP122 4.4 33.0 1.0
CA A:ASP122 4.5 33.9 1.0
N A:TRP233 4.5 24.8 1.0
CA A:SER121 4.6 30.9 1.0
CB A:ASP122 4.7 34.7 1.0
N A:PHE234 4.7 23.2 1.0
O A:HOH3198 4.7 39.3 1.0
CG A:PRO235 4.8 22.2 1.0
CD A:PRO235 4.9 21.9 1.0
CA A:GLU232 5.0 26.4 1.0

Barium binding site 2 out of 22 in 2efx

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Barium binding site 2 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

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

b:42.4
occ:0.40
O A:HOH3195 2.2 28.4 1.0
O D:HOH3211 2.8 30.0 1.0
O A:GLU211 2.9 26.5 1.0
OD2 D:ASP53 3.7 21.1 1.0
CG D:ASP53 3.9 18.6 1.0
OD1 D:ASP53 4.1 19.2 1.0
C A:GLU211 4.1 26.4 1.0
CD A:PRO213 4.6 25.8 1.0
ND2 A:ASN212 4.8 29.5 1.0
CB D:ASP53 4.8 16.8 1.0
O D:HOH3161 4.9 39.0 1.0
CA A:GLU211 4.9 25.8 1.0
O D:HOH3172 4.9 32.1 1.0

Barium binding site 3 out of 22 in 2efx

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Barium binding site 3 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3008

b:32.8
occ:0.20
O A:HOH3087 2.1 33.3 1.0
OE1 B:GLU323 2.7 47.8 1.0
BA B:BA3009 2.7 37.1 0.2
O A:SER301 3.1 27.3 1.0
OE1 A:GLU323 3.2 40.1 1.0
OE2 A:GLU323 3.7 42.0 1.0
CD A:GLU323 3.9 38.6 1.0
O A:HOH3217 3.9 32.2 1.0
CD B:GLU323 3.9 46.8 1.0
C A:SER301 4.1 27.0 1.0
CB A:SER301 4.4 26.7 1.0
NZ A:LYS359 4.5 40.7 1.0
CA A:SER301 4.6 27.0 1.0
OE2 B:GLU323 4.6 49.0 1.0
BA B:BA3007 4.7 64.4 0.4
CG B:GLU323 5.0 43.9 1.0

Barium binding site 4 out of 22 in 2efx

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Barium binding site 4 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3017

b:69.1
occ:0.30
OG A:SER363 2.8 50.8 1.0
O A:ASN360 3.0 43.4 1.0
O B:SER363 3.5 59.2 1.0
O A:SER363 3.6 51.0 1.0
C A:ASN360 4.0 43.1 1.0
CB A:SER363 4.2 50.5 1.0
C A:SER363 4.4 50.6 1.0
CA A:ASN360 4.5 42.2 1.0
C B:SER363 4.6 59.2 1.0
CA A:SER363 4.7 50.3 1.0
CB A:ASN360 4.8 42.4 1.0
N A:SER363 4.8 49.8 1.0

Barium binding site 5 out of 22 in 2efx

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Barium binding site 5 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

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

b:31.1
occ:0.80
O B:HOH3130 1.9 19.1 1.0
O B:HOH3088 2.6 22.7 1.0
O B:GLU232 2.7 18.6 1.0
O B:SER121 2.9 20.0 1.0
OD1 B:ASP122 3.0 23.8 1.0
O B:TRP233 3.0 19.8 1.0
O B:HOH3079 3.1 28.5 1.0
O B:HOH3252 3.2 36.6 1.0
C B:SER121 3.7 20.0 1.0
C B:TRP233 3.8 19.1 1.0
C B:GLU232 3.8 19.1 1.0
CG B:ASP122 3.9 23.3 1.0
O B:HOH3113 4.0 29.9 1.0
CA B:TRP233 4.2 18.2 1.0
N B:SER121 4.3 20.4 1.0
N B:ASP122 4.4 20.2 1.0
CA B:ASP122 4.4 20.1 1.0
N B:TRP233 4.5 18.8 1.0
OD2 B:ASP122 4.6 28.4 1.0
CA B:SER121 4.7 20.2 1.0
O B:HOH3102 4.7 25.4 1.0
N B:PHE234 4.7 18.9 1.0
CB B:ASP122 4.8 21.2 1.0

Barium binding site 6 out of 22 in 2efx

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Barium binding site 6 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3007

b:64.4
occ:0.40
O A:HOH3217 3.1 32.2 1.0
BA B:BA3009 3.5 37.1 0.2
O A:HOH3087 4.1 33.3 1.0
OE2 F:GLU323 4.1 59.0 1.0
OE2 A:GLU323 4.4 42.0 1.0
OE1 F:GLU323 4.7 58.2 1.0
BA A:BA3008 4.7 32.8 0.2
OE1 B:GLU323 4.7 47.8 1.0
CD F:GLU323 4.8 59.0 1.0
OE2 B:GLU323 4.9 49.0 1.0
O B:HOH3189 5.0 40.2 1.0
O B:SER301 5.0 34.8 1.0

Barium binding site 7 out of 22 in 2efx

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Barium binding site 7 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3009

b:37.1
occ:0.20
OE1 B:GLU323 2.7 47.8 1.0
BA A:BA3008 2.7 32.8 0.2
O B:SER301 2.9 34.8 1.0
OE2 B:GLU323 3.1 49.0 1.0
CD B:GLU323 3.3 46.8 1.0
BA B:BA3007 3.5 64.4 0.4
O A:HOH3217 3.7 32.2 1.0
O A:HOH3087 3.9 33.3 1.0
C B:SER301 4.0 34.3 1.0
OE1 F:GLU323 4.3 58.2 1.0
CA B:SER301 4.5 34.0 1.0
CB B:SER301 4.7 34.1 1.0
CG B:GLU323 4.8 43.9 1.0
OE2 A:GLU323 5.0 42.0 1.0

Barium binding site 8 out of 22 in 2efx

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Barium binding site 8 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3021

b:65.6
occ:0.30
O B:THR190 4.0 16.9 1.0
O B:GLU192 4.1 18.6 1.0
C B:GLU192 4.1 19.4 1.0
OG1 B:THR193 4.2 23.9 1.0
N B:GLU192 4.2 18.0 1.0
C B:HIS191 4.3 17.5 1.0
N B:THR193 4.4 20.6 1.0
CA B:GLU192 4.6 18.6 1.0
C B:THR190 4.6 16.3 1.0
O B:GLY189 4.6 14.4 1.0
O B:HOH3148 4.7 27.1 1.0
O B:HIS191 4.7 17.6 1.0
CA B:HIS191 4.7 16.6 1.0
N B:HIS191 4.8 16.3 1.0
CA B:THR193 4.9 22.1 1.0

Barium binding site 9 out of 22 in 2efx

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Barium binding site 9 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3001

b:20.3
occ:0.80
O C:HOH3035 1.9 28.9 1.0
O C:SER121 2.8 27.5 1.0
O C:GLU232 2.8 21.7 1.0
OD1 C:ASP122 2.9 29.7 1.0
O C:HOH3118 2.9 18.7 1.0
O C:HOH3221 2.9 34.4 1.0
O C:TRP233 3.0 22.8 1.0
O C:HOH3093 3.0 23.4 1.0
O C:HOH3107 3.3 33.7 1.0
C C:TRP233 3.7 22.2 1.0
C C:SER121 3.7 27.9 1.0
CG C:ASP122 3.8 29.9 1.0
C C:GLU232 4.0 22.2 1.0
CA C:TRP233 4.2 22.2 1.0
N C:SER121 4.3 27.9 1.0
OD2 C:ASP122 4.3 33.7 1.0
N C:ASP122 4.4 28.3 1.0
CA C:ASP122 4.5 28.4 1.0
N C:TRP233 4.6 22.4 1.0
N C:PHE234 4.7 21.1 1.0
CA C:SER121 4.7 28.0 1.0
O C:HOH3126 4.7 28.6 1.0
CB C:ASP122 4.7 29.0 1.0
O C:HOH3113 4.8 23.2 1.0
CD C:PRO235 4.9 19.2 1.0

Barium binding site 10 out of 22 in 2efx

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Barium binding site 10 out of 22 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with L-Phenylalanine Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3005

b:36.9
occ:0.50
O B:HOH3067 3.1 21.9 1.0
O C:ALA206 3.2 35.1 1.0
C C:ALA206 4.3 34.3 1.0
CA C:ALA206 4.6 33.8 1.0
O B:HOH3100 4.7 29.9 1.0
O B:LEU36 4.8 23.9 1.0
N C:ASP210 4.9 46.4 1.0
CB C:ALA206 5.0 34.0 1.0

Reference:

S.Okazaki, A.Suzuki, T.Mizushima, H.Komeda, Y.Asano, T.Yamane. Structures of D-Amino-Acid Amidase Complexed with L-Phenylalanine and with L-Phenylalanine Amide: Insight Into the D-Stereospecificity of D-Amino-Acid Amidase From Ochrobactrum Anthropi SV3. Acta Crystallogr.,Sect.D V. 64 331 2008.
ISSN: ISSN 0907-4449
PubMed: 18323628
DOI: 10.1107/S0907444907067479
Page generated: Wed Jul 10 15:02:59 2024

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