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Chlorine in PDB 3i7u: Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5

Protein crystallography data

The structure of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5, PDB code: 3i7u was solved by J.Jeyakanthan, S.P.Kanaujia, N.Nakagawa, K.Sekar, S.Kuramitsu, A.Shinkai, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.73 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.589, 38.049, 87.592, 90.00, 93.10, 90.00
R / Rfree (%) 20.3 / 23.9

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 (pdb code 3i7u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5, PDB code: 3i7u:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 3i7u

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Chlorine binding site 1 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl141

b:35.3
occ:1.00
 NZ A:LYS78 2.9 34.0 1.0
O A:HOH235 3.4 35.3 1.0
OG A:SER6 3.4 21.6 1.0
CA A:GLY32 3.4 21.4 1.0
CE A:LYS78 3.5 31.1 1.0
NZ A:LYS31 3.5 38.8 1.0
N A:GLY32 3.7 21.9 1.0
C A:GLY32 3.8 22.2 1.0
ND2 A:ASN33 3.9 27.5 1.0
O A:LYS31 3.9 24.2 1.0
C A:LYS31 3.9 23.3 1.0
CG A:LYS31 4.0 28.1 1.0
CB A:SER6 4.0 20.4 1.0
N A:ASN33 4.0 22.8 1.0
CD A:LYS31 4.4 32.1 1.0
OE2 A:GLU4 4.5 30.8 1.0
O A:GLY32 4.5 19.9 1.0
O A:HOH381 4.5 33.9 1.0
CE A:LYS31 4.5 36.5 1.0
CB A:LYS31 4.6 24.3 1.0
O A:HOH294 4.7 37.4 1.0
CG A:ASN33 4.7 26.8 1.0
CA A:LYS31 4.9 23.0 1.0
O A:HOH236 4.9 33.0 1.0
CD A:LYS78 5.0 29.7 1.0
CA A:ASN33 5.0 23.2 1.0

Chlorine binding site 2 out of 11 in 3i7u

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Chlorine binding site 2 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl148

b:37.1
occ:1.00
 O A:HOH552 3.0 40.2 1.0
O C:HOH662 3.0 29.4 1.0
O A:HOH202 3.1 28.7 1.0
N A:PHE5 3.2 18.8 1.0
CA A:GLU4 3.8 20.6 1.0
O A:PHE5 3.8 18.7 1.0
CG2 A:ILE34 3.8 21.9 1.0
CG A:GLU4 3.8 26.0 1.0
C A:GLU4 4.0 20.0 1.0
CA A:PHE5 4.1 19.6 1.0
CB A:PHE5 4.3 21.2 1.0
CB A:GLU4 4.3 22.5 1.0
C A:PHE5 4.4 19.6 1.0
CG A:ASN33 4.4 26.8 1.0
O A:LYS3 4.4 22.7 1.0
CB A:ASN33 4.5 23.7 1.0
ND2 A:ASN33 4.6 27.5 1.0
OD1 A:ASN33 4.7 32.2 1.0
N A:ILE34 4.7 21.4 1.0
CD2 A:PHE5 4.8 25.1 1.0
O C:HOH566 4.9 56.4 1.0
N A:GLU4 4.9 21.4 1.0
O A:ILE34 5.0 22.4 1.0
O C:HOH661 5.0 42.4 1.0

Chlorine binding site 3 out of 11 in 3i7u

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Chlorine binding site 3 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl151

b:34.5
occ:1.00
 O A:HOH560 3.1 50.0 1.0
N A:MET1 3.2 33.4 1.0
N A:ARG75 3.3 31.4 1.0
NE A:ARG75 3.3 35.3 1.0
CG A:GLU74 3.5 35.9 1.0
NH2 A:ARG75 3.6 37.0 1.0
CA A:MET1 3.6 32.1 1.0
CB A:MET1 3.7 35.3 1.0
CA A:GLU74 3.8 35.2 1.0
CZ A:ARG75 3.9 36.1 1.0
CB A:ARG75 4.0 30.1 1.0
C A:GLU74 4.0 33.7 1.0
OE2 C:GLU64 4.0 35.0 1.0
CA A:ARG75 4.2 29.6 1.0
CB A:GLU74 4.2 37.0 1.0
CG A:ARG75 4.2 30.2 1.0
CD A:ARG75 4.3 32.2 1.0
O A:GLY73 4.4 38.2 1.0
O A:ARG75 4.5 27.6 1.0
CD A:GLU74 4.7 37.7 1.0
CG A:MET1 4.7 37.3 1.0
OE1 A:GLU74 4.8 37.7 1.0
O A:HOH512 4.8 45.0 1.0
C A:ARG75 4.9 29.3 1.0
CD C:GLU64 5.0 31.2 1.0
N A:GLU74 5.0 36.3 1.0

Chlorine binding site 4 out of 11 in 3i7u

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Chlorine binding site 4 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl142

b:18.3
occ:1.00
 OG B:SER6 3.0 11.1 1.0
NZ B:LYS31 3.2 24.5 1.0
NZ B:LYS78 3.2 20.7 1.0
O B:HOH679 3.3 39.6 1.0
O4 B:PEG172 3.3 45.9 1.0
C4 B:PEG172 3.4 47.4 1.0
CB B:SER6 3.7 10.5 1.0
CE B:LYS78 3.7 21.0 1.0
CA B:GLY32 3.8 10.3 1.0
CG B:LYS31 3.9 15.7 1.0
CD B:LYS31 4.0 17.1 1.0
C B:GLY32 4.0 9.7 1.0
N B:GLY32 4.1 11.9 1.0
CE B:LYS31 4.1 21.4 1.0
O B:HOH678 4.2 33.2 1.0
N B:ASN33 4.2 10.4 1.0
C3 B:PEG172 4.3 46.5 1.0
C B:LYS31 4.3 11.6 1.0
O B:LYS31 4.4 11.8 1.0
O B:HOH232 4.6 23.4 1.0
O B:GLY32 4.6 9.5 1.0
CB B:LYS31 4.7 11.6 1.0
O B:HOH540 4.8 47.9 1.0
O2 B:PEG172 4.8 46.9 1.0
O B:HOH253 4.9 14.7 1.0
O B:HOH680 4.9 27.6 1.0
CL B:CL145 4.9 27.3 1.0

Chlorine binding site 5 out of 11 in 3i7u

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Chlorine binding site 5 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl145

b:27.3
occ:1.00
 OH B:TYR67 2.9 25.5 1.0
O B:HOH540 3.0 47.9 1.0
NZ B:LYS78 3.1 20.7 1.0
NZ B:LYS31 3.1 24.5 1.0
CE C:LYS72 3.7 32.6 1.0
CE B:LYS78 3.7 21.0 1.0
CD2 C:LEU71 3.8 24.5 1.0
CZ B:TYR67 3.8 22.8 1.0
CE1 B:TYR67 3.9 21.4 1.0
CE B:LYS31 3.9 21.4 1.0
NZ C:LYS72 4.0 35.2 1.0
CD B:LYS78 4.1 19.2 1.0
O C:HOH338 4.2 40.8 1.0
CG C:LEU71 4.2 20.8 1.0
CD C:LYS72 4.2 28.9 1.0
CD1 C:LEU71 4.4 21.6 1.0
CG C:LYS72 4.7 26.6 1.0
O B:HOH372 4.9 45.3 1.0
CL B:CL142 4.9 18.3 1.0

Chlorine binding site 6 out of 11 in 3i7u

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Chlorine binding site 6 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl143

b:20.2
occ:1.00
 NZ C:LYS78 3.1 18.8 1.0
OG C:SER6 3.1 16.5 1.0
NZ C:LYS31 3.4 20.5 1.0
CE C:LYS78 3.6 20.7 1.0
CB C:SER6 3.7 15.5 1.0
CA C:GLY32 3.8 15.0 1.0
CG C:LYS31 3.9 14.2 1.0
CD C:LYS31 4.0 16.7 1.0
O C:HOH508 4.0 57.7 1.0
C C:GLY32 4.0 14.1 1.0
N C:GLY32 4.0 14.7 1.0
CE C:LYS31 4.2 19.4 1.0
N C:ASN33 4.2 15.7 1.0
O C:HOH267 4.3 32.6 1.0
C C:LYS31 4.3 14.7 1.0
O C:LYS31 4.3 15.1 1.0
O C:HOH316 4.4 22.3 1.0
O C:GLY32 4.6 14.7 1.0
CB C:LYS31 4.7 13.7 1.0
O C:HOH238 4.7 17.6 1.0
CL C:CL146 5.0 26.5 1.0

Chlorine binding site 7 out of 11 in 3i7u

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Chlorine binding site 7 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl146

b:26.5
occ:1.00
 OH C:TYR67 3.0 26.6 1.0
NZ C:LYS78 3.1 18.8 1.0
NZ C:LYS31 3.4 20.5 1.0
CD2 B:LEU71 3.7 19.0 1.0
CE B:LYS72 3.7 26.8 1.0
CE C:LYS78 3.7 20.7 1.0
O B:HOH551 3.8 48.7 1.0
CZ C:TYR67 3.8 26.2 1.0
CE1 C:TYR67 3.9 25.3 1.0
NZ B:LYS72 3.9 29.6 1.0
CD C:LYS78 4.0 19.2 1.0
CE C:LYS31 4.0 19.4 1.0
CD B:LYS72 4.0 25.7 1.0
CG B:LEU71 4.1 18.3 1.0
CD1 B:LEU71 4.3 18.7 1.0
CG B:LYS72 4.7 23.6 1.0
O C:HOH376 4.8 42.2 1.0
O C:HOH357 5.0 29.8 1.0
CL C:CL143 5.0 20.2 1.0

Chlorine binding site 8 out of 11 in 3i7u

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Chlorine binding site 8 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl144

b:19.6
occ:1.00
 O D:HOH666 3.0 32.1 1.0
NZ D:LYS78 3.1 15.1 1.0
OG D:SER6 3.1 9.1 1.0
C1 D:PEG173 3.6 60.7 1.0
CE D:LYS78 3.7 13.4 1.0
CB D:SER6 3.7 9.4 1.0
CA D:GLY32 3.8 8.7 1.0
C2 D:PEG173 3.9 61.1 1.0
C D:GLY32 4.0 7.0 1.0
ND2 D:ASN33 4.1 14.1 1.0
N D:GLY32 4.1 7.0 1.0
CG D:LYS31 4.2 14.1 1.0
N D:ASN33 4.3 7.1 1.0
O D:LYS31 4.3 7.9 1.0
O1 D:PEG173 4.3 62.1 1.0
O D:HOH665 4.3 16.5 1.0
C D:LYS31 4.3 8.9 1.0
O D:HOH659 4.6 20.7 1.0
O D:GLY32 4.6 7.3 1.0
O D:HOH485 4.7 33.2 1.0
CD D:LYS31 4.7 19.1 1.0
OE2 D:GLU4 4.7 12.9 1.0
CG D:ASN33 4.8 15.1 1.0
CB D:LYS31 4.9 9.2 1.0
CE D:LYS31 4.9 19.9 1.0

Chlorine binding site 9 out of 11 in 3i7u

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Chlorine binding site 9 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl147

b:22.1
occ:1.00
 O D:HOH292 2.9 25.8 1.0
O2 B:EDO163 3.0 34.0 1.0
N D:PHE5 3.2 7.1 1.0
O D:HOH365 3.3 24.2 1.0
C2 B:EDO163 3.4 37.3 1.0
CA D:GLU4 3.6 9.7 1.0
CG D:GLU4 3.7 12.0 1.0
CG2 D:ILE34 3.8 11.3 1.0
O D:PHE5 3.8 7.4 1.0
C D:GLU4 3.9 9.0 1.0
CB D:GLU4 4.2 10.1 1.0
CA D:PHE5 4.2 8.1 1.0
O D:LYS3 4.3 11.0 1.0
C D:PHE5 4.5 7.5 1.0
ND2 D:ASN33 4.5 14.1 1.0
CB D:PHE5 4.5 9.8 1.0
CG D:ASN33 4.6 15.1 1.0
C1 B:EDO163 4.7 36.1 1.0
N D:GLU4 4.8 10.2 1.0
O D:HOH544 4.8 40.1 1.0
CB D:ASN33 4.8 12.4 1.0
CD D:GLU4 4.9 13.8 1.0
CD2 D:PHE5 4.9 15.8 1.0
C D:LYS3 5.0 11.4 1.0
N D:ILE34 5.0 7.8 1.0

Chlorine binding site 10 out of 11 in 3i7u

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Chlorine binding site 10 out of 11 in the Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of AP4A Hydrolase (AQ_158) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl149

b:22.7
occ:1.00
 O D:HOH538 2.9 11.5 1.0
NZ D:LYS55 3.1 11.8 1.0
O D:HOH720 3.1 47.2 1.0
CE D:LYS55 4.1 9.2 1.0
O D:GLY56 4.4 10.0 1.0
CG1 D:VAL45 4.5 12.7 1.0
CG2 D:VAL45 4.6 12.3 1.0
C2 D:EDO161 4.6 32.4 1.0
O2 D:EDO161 4.6 27.3 1.0
O D:HOH537 4.7 12.4 1.0
CA D:GLU57 4.8 10.7 1.0
C1 D:EDO161 4.9 33.0 1.0

Reference:

J.Jeyakanthan, S.P.Kanaujia, Y.Nishida, N.Nakagawa, S.Praveen, A.Shinkai, S.Kuramitsu, S.Yokoyama, K.Sekar. Free and Atp-Bound Structures of Ap(4)A Hydrolase From Aquifex Aeolicus V5 Acta Crystallogr.,Sect.D V. 66 116 2010.
ISSN: ISSN 0907-4449
PubMed: 20124691
DOI: 10.1107/S0907444909047064
Page generated: Sat Jul 20 21:23:19 2024

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