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

Protein crystallography data

The structure of The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine, PDB code: 2dns 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) 19.87 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.067, 123.702, 116.046, 90.00, 104.44, 90.00
R / Rfree (%) 19.5 / 26.9

Barium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Barium atom in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine (pdb code 2dns). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 20 binding sites of Barium where determined in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine, PDB code: 2dns:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 20 in 2dns

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Barium binding site 1 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3003

b:28.9
occ:0.70
O A:HOH3023 1.9 12.1 1.0
O A:SER121 2.7 38.8 1.0
O A:HOH3071 2.8 24.0 1.0
O A:GLU232 2.8 28.2 1.0
O A:TRP233 3.1 27.8 1.0
OD1 A:ASP122 3.3 40.2 1.0
O A:HOH3036 3.6 34.5 1.0
C A:SER121 3.7 38.5 1.0
CG A:ASP122 3.8 40.4 1.0
C A:TRP233 3.8 27.6 1.0
C A:GLU232 3.9 28.3 1.0
OD2 A:ASP122 4.0 41.5 1.0
CA A:TRP233 4.2 27.4 1.0
N A:ASP122 4.3 39.0 1.0
CA A:ASP122 4.4 39.3 1.0
N A:SER121 4.4 37.2 1.0
N A:TRP233 4.5 28.1 1.0
CA A:SER121 4.6 37.9 1.0
N A:PHE234 4.7 27.9 1.0
CB A:ASP122 4.7 39.5 1.0
CD A:PRO235 5.0 28.4 1.0

Barium binding site 2 out of 20 in 2dns

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Barium binding site 2 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3004

b:41.7
occ:0.40
O A:HOH3059 2.3 23.5 1.0
O A:GLU211 2.9 28.5 1.0
OD2 D:ASP53 3.9 19.8 1.0
C A:GLU211 4.1 28.0 1.0
CG D:ASP53 4.1 21.0 1.0
OD1 D:ASP53 4.3 22.5 1.0
CD A:PRO213 4.4 27.8 1.0
ND2 A:ASN212 4.6 30.6 1.0
O A:HOH3116 4.8 37.9 1.0
CA A:ASN212 4.9 28.2 1.0
CB D:ASP53 5.0 20.1 1.0
N A:ASN212 5.0 27.9 1.0

Barium binding site 3 out of 20 in 2dns

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Barium binding site 3 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3007

b:59.4
occ:0.40
BA F:BA3008 3.0 49.9 0.2
BA B:BA3019 4.0 59.4 0.3
BA A:BA3020 4.0 66.5 0.3
OE2 A:GLU323 4.1 45.0 1.0
OE2 F:GLU323 4.3 56.5 1.0
OE1 F:GLU303 4.4 58.8 1.0
OE2 B:GLU323 4.6 43.5 1.0
O B:HOH3164 4.8 36.0 1.0
OE1 A:GLU303 4.8 36.3 1.0

Barium binding site 4 out of 20 in 2dns

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Barium binding site 4 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3018

b:57.1
occ:0.30
OG A:SER363 2.6 55.8 1.0
O A:ASN360 2.7 50.4 1.0
C A:ASN360 3.8 50.0 1.0
CB A:SER363 4.0 55.5 1.0
C A:SER363 4.2 55.5 1.0
CA A:ASN360 4.5 49.3 1.0
CA A:SER363 4.5 55.4 1.0
N A:SER363 4.7 55.0 1.0
CB A:ASN360 4.7 49.4 1.0
N A:SER361 4.9 51.1 1.0
ND2 A:ASN360 5.0 51.6 1.0

Barium binding site 5 out of 20 in 2dns

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Barium binding site 5 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3020

b:66.5
occ:0.30
OE2 B:GLU323 2.9 43.5 1.0
O A:SER301 3.0 28.9 1.0
OE1 A:GLU323 3.0 43.1 1.0
BA B:BA3019 3.1 59.4 0.3
OE2 A:GLU323 3.3 45.0 1.0
CD A:GLU323 3.5 42.8 1.0
BA F:BA3008 3.6 49.9 0.2
CD B:GLU323 3.7 42.5 1.0
OE1 B:GLU323 3.8 44.2 1.0
BA A:BA3007 4.0 59.4 0.4
C A:SER301 4.1 28.6 1.0
CA A:SER301 4.6 28.3 1.0
CB A:SER301 4.8 28.2 1.0
CG A:GLU323 5.0 40.1 1.0

Barium binding site 6 out of 20 in 2dns

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Barium binding site 6 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3002

b:28.8
occ:0.80
O B:HOH3103 1.7 10.8 1.0
O B:HOH3059 2.1 9.8 1.0
O B:GLU232 2.7 21.8 1.0
OD1 B:ASP122 2.7 31.0 1.0
O B:TRP233 2.9 21.0 1.0
O B:HOH3068 2.9 20.6 1.0
O B:SER121 2.9 26.4 1.0
O B:HOH3095 2.9 31.3 1.0
C B:TRP233 3.6 20.2 1.0
C B:SER121 3.8 26.0 1.0
C B:GLU232 3.9 21.2 1.0
CG B:ASP122 3.9 29.1 1.0
CA B:TRP233 4.0 20.0 1.0
N B:SER121 4.3 25.5 1.0
N B:TRP233 4.5 20.4 1.0
N B:ASP122 4.5 26.1 1.0
CA B:ASP122 4.5 26.3 1.0
OD2 B:ASP122 4.6 33.2 1.0
N B:PHE234 4.7 20.8 1.0
CA B:SER121 4.7 25.6 1.0
CB B:ASP122 4.8 27.0 1.0
O B:HOH3097 4.9 19.0 1.0
O B:HOH3057 4.9 22.4 1.0
CB B:GLU232 5.0 22.3 1.0

Barium binding site 7 out of 20 in 2dns

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Barium binding site 7 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3019

b:59.4
occ:0.30
OE1 B:GLU323 3.0 44.2 1.0
O B:SER301 3.0 30.2 1.0
BA A:BA3020 3.1 66.5 0.3
BA F:BA3008 3.1 49.9 0.2
OE2 B:GLU323 3.7 43.5 1.0
CD B:GLU323 3.7 42.5 1.0
OE2 F:GLU323 3.8 56.5 1.0
BA A:BA3007 4.0 59.4 0.4
C B:SER301 4.2 29.5 1.0
CD F:GLU323 4.5 56.1 1.0
OE1 F:GLU323 4.5 56.8 1.0
CB B:SER301 4.7 29.8 1.0
CA B:SER301 4.7 29.7 1.0

Barium binding site 8 out of 20 in 2dns

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Barium binding site 8 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3001

b:29.9
occ:1.00
O C:HOH3161 2.2 25.0 1.0
O C:GLU232 2.8 25.8 1.0
O C:SER121 2.9 28.9 1.0
O C:TRP233 2.9 24.8 1.0
OD1 C:ASP122 2.9 32.5 1.0
O C:HOH3122 3.0 27.6 1.0
O C:HOH3156 3.0 27.1 1.0
C C:TRP233 3.6 24.7 1.0
C C:SER121 3.8 29.1 1.0
C C:GLU232 3.9 25.7 1.0
CG C:ASP122 4.0 31.7 1.0
CA C:TRP233 4.1 24.5 1.0
N C:SER121 4.3 28.9 1.0
N C:TRP233 4.5 24.9 1.0
N C:ASP122 4.5 29.2 1.0
OD2 C:ASP122 4.6 33.8 1.0
N C:PHE234 4.6 24.5 1.0
CA C:ASP122 4.6 29.9 1.0
O C:HOH3107 4.7 27.3 1.0
O C:HOH3145 4.7 32.8 1.0
CA C:SER121 4.7 29.1 1.0
CB C:ASP122 4.9 30.0 1.0
CD C:PRO235 5.0 23.5 1.0

Barium binding site 9 out of 20 in 2dns

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Barium binding site 9 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3005

b:37.3
occ:0.75
O C:ALA206 2.9 40.4 1.0
O C:ALA208 3.1 45.1 1.0
O C:HOH3046 3.1 17.1 1.0
O C:HOH3043 3.2 28.3 1.0
C C:ALA208 3.8 44.9 1.0
CA C:ALA208 3.9 44.7 1.0
C C:ALA206 4.0 40.1 1.0
N C:ALA208 4.7 44.0 1.0
O B:HOH3137 4.8 37.9 1.0
CA C:ALA206 4.9 39.1 1.0
CA C:ALA207 4.9 42.5 1.0
O B:LEU36 4.9 30.5 1.0
N C:ASP209 4.9 45.0 1.0
N C:ALA207 4.9 41.3 1.0
N C:ASP210 5.0 43.5 1.0

Barium binding site 10 out of 20 in 2dns

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Barium binding site 10 out of 20 in the The Crystal Structure of D-Amino Acid Amidase From Ochrobactrum Anthropi SV3 Complexed with D-Phenylalanine


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 D-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba3009

b:71.5
occ:0.25
OE2 D:GLU323 3.1 39.7 1.0
OE2 C:GLU323 3.1 39.8 1.0
BA C:BA3011 3.2 53.7 0.3
BA D:BA3012 3.4 61.6 0.2
O C:SER301 3.6 29.1 1.0
O D:HOH3140 3.9 27.3 1.0
CD D:GLU323 4.0 37.6 1.0
CD C:GLU323 4.0 38.2 1.0
BA E:BA3010 4.1 73.1 0.3
OE1 C:GLU323 4.2 39.0 1.0
OE1 D:GLU323 4.3 38.6 1.0
C C:SER301 4.6 28.4 1.0
CA C:SER301 5.0 28.4 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: Tue Oct 27 17:00:17 2020

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