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Chlorine in PDB 2nv1: Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis

Protein crystallography data

The structure of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis, PDB code: 2nv1 was solved by M.Strohmeier, I.Tews, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.68 / 2.08
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.055, 106.202, 182.332, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 19.1

Other elements in 2nv1:

The structure of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis (pdb code 2nv1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis, PDB code: 2nv1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 2nv1

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Chlorine binding site 1 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3001

b:56.3
occ:1.00
 O A:HOH4103 2.5 47.1 1.0
O A:HOH4328 2.6 77.9 1.0
O A:HOH4214 3.0 64.0 1.0
O A:HOH4315 3.1 76.4 1.0
NE A:ARG137 3.2 29.8 1.0
NH2 A:ARG137 3.2 32.7 1.0
NH1 A:ARG138 3.3 31.8 1.0
NH2 A:ARG138 3.6 30.7 1.0
CZ A:ARG137 3.7 32.8 1.0
CZ A:ARG138 3.9 28.6 1.0
CG A:GLU134 4.3 36.0 1.0
CD A:ARG137 4.4 30.0 1.0
OE2 A:GLU134 4.6 49.7 1.0
O A:HOH4237 4.6 67.0 1.0
NH1 A:ARG137 5.0 31.4 1.0
CD A:GLU134 5.0 41.2 1.0

Chlorine binding site 2 out of 12 in 2nv1

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Chlorine binding site 2 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3002

b:58.3
occ:1.00
 O A:HOH4186 2.7 60.9 1.0
O A:HOH4073 3.1 40.4 1.0
N A:GLY214 3.3 37.7 1.0
O A:HOH4301 3.6 74.8 1.0
O A:HOH4038 3.6 32.3 1.0
N A:GLY153 3.7 50.4 1.0
CA A:GLY213 3.9 36.8 1.0
O A:HOH4205 3.9 62.7 1.0
O A:HOH4264 4.1 70.1 1.0
C A:GLY213 4.1 37.9 1.0
CA A:PRO152 4.1 50.0 1.0
CA A:GLY214 4.2 37.4 1.0
N A:GLY213 4.4 35.6 1.0
C A:PRO152 4.4 50.4 1.0
N A:GLY235 4.6 38.5 1.0
CA A:GLY153 4.7 50.0 1.0
CA A:GLY235 4.7 39.3 1.0
CB A:PRO152 4.8 50.7 1.0
N A:VAL215 4.8 35.7 1.0
O A:GLU151 4.9 46.4 1.0
C A:GLY214 4.9 37.0 1.0

Chlorine binding site 3 out of 12 in 2nv1

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Chlorine binding site 3 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl3007

b:50.9
occ:1.00
 O B:HOH4100 2.4 42.6 1.0
O B:HOH4327 2.8 73.1 1.0
NH1 B:ARG138 3.1 32.5 1.0
NE B:ARG137 3.3 29.9 1.0
NH2 B:ARG137 3.3 35.6 1.0
NH2 B:ARG138 3.4 31.4 1.0
CZ B:ARG138 3.7 31.6 1.0
CZ B:ARG137 3.8 32.7 1.0
O B:HOH4286 3.9 68.2 1.0
O B:HOH4338 4.1 74.5 1.0
CG B:GLU134 4.3 38.3 1.0
CD B:ARG137 4.4 30.3 1.0
OE2 B:GLU134 4.5 47.3 1.0
CE1 B:HIS115 4.9 28.8 1.0
CD B:GLU134 4.9 42.9 1.0
CB B:ARG137 4.9 27.3 1.0

Chlorine binding site 4 out of 12 in 2nv1

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Chlorine binding site 4 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl3008

b:54.4
occ:1.00
 O B:HOH4177 2.8 56.0 1.0
O B:HOH4080 3.1 39.1 1.0
N B:GLY214 3.2 37.5 1.0
O B:HOH4270 3.5 66.9 1.0
N B:GLY153 3.7 48.3 1.0
O B:HOH4269 3.7 66.7 1.0
O B:HOH4045 3.7 32.2 1.0
CA B:GLY213 3.9 35.8 1.0
CA B:GLY214 4.0 37.3 1.0
C B:GLY213 4.0 37.0 1.0
O B:HOH4247 4.0 64.3 1.0
CA B:PRO152 4.1 47.7 1.0
O B:HOH4238 4.3 63.3 1.0
C B:PRO152 4.4 48.0 1.0
N B:GLY213 4.5 34.2 1.0
O B:HOH4162 4.5 52.5 1.0
CA B:GLY153 4.6 48.4 1.0
N B:GLY235 4.7 37.0 1.0
N B:VAL215 4.7 37.6 1.0
C B:GLY214 4.8 37.6 1.0
CA B:GLY235 4.8 38.4 1.0
O B:GLU151 4.9 44.8 1.0
CB B:PRO152 4.9 48.0 1.0

Chlorine binding site 5 out of 12 in 2nv1

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Chlorine binding site 5 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3013

b:46.6
occ:1.00
 O C:HOH4107 2.5 42.3 1.0
O C:HOH4312 3.0 73.2 1.0
NE C:ARG137 3.1 28.1 1.0
NH2 C:ARG137 3.2 30.3 1.0
NH1 C:ARG138 3.2 30.3 1.0
NH2 C:ARG138 3.4 30.7 1.0
CZ C:ARG137 3.6 30.5 1.0
CZ C:ARG138 3.8 29.7 1.0
O C:HOH4253 4.1 65.3 1.0
CD C:ARG137 4.3 29.6 1.0
CG C:GLU134 4.5 38.2 1.0
OE2 C:GLU134 4.7 51.8 1.0
O C:HOH4168 4.7 53.3 1.0
NH1 C:ARG137 4.9 28.1 1.0
CE1 C:HIS115 4.9 31.9 1.0
CB C:ARG137 4.9 30.0 1.0

Chlorine binding site 6 out of 12 in 2nv1

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Chlorine binding site 6 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3014

b:54.7
occ:1.00
 N C:GLY214 3.2 37.5 1.0
O C:HOH4108 3.2 42.3 1.0
O C:HOH4190 3.2 56.5 1.0
O C:HOH4216 3.3 59.8 1.0
O C:HOH4056 3.5 32.1 1.0
CA C:GLY213 3.8 36.2 1.0
N C:GLY153 3.9 50.9 1.0
O C:HOH4179 3.9 55.0 1.0
C C:GLY213 4.0 37.3 1.0
CA C:GLY214 4.0 37.8 1.0
CA C:PRO152 4.1 50.7 1.0
O C:HOH4185 4.3 55.9 1.0
N C:GLY213 4.4 34.5 1.0
C C:PRO152 4.5 50.8 1.0
N C:VAL215 4.6 38.1 1.0
N C:GLY235 4.7 36.9 1.0
C C:GLY214 4.7 38.2 1.0
CA C:GLY235 4.8 38.9 1.0
O C:GLU151 4.8 49.0 1.0
CB C:PRO152 4.8 50.7 1.0
CA C:GLY153 4.9 50.9 1.0

Chlorine binding site 7 out of 12 in 2nv1

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Chlorine binding site 7 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3020

b:51.0
occ:1.00
 O D:HOH4113 2.5 42.0 1.0
O D:HOH4411 2.9 88.3 1.0
NH2 D:ARG137 3.2 30.4 1.0
NE D:ARG137 3.2 28.6 1.0
NH1 D:ARG138 3.3 35.6 1.0
NH2 D:ARG138 3.6 33.8 1.0
CZ D:ARG137 3.6 30.9 1.0
CZ D:ARG138 3.9 32.0 1.0
O D:HOH4254 3.9 63.5 1.0
O D:HOH4403 4.1 85.6 1.0
CD D:ARG137 4.4 30.9 1.0
CG D:GLU134 4.5 37.5 1.0
OE2 D:GLU134 4.7 49.4 1.0
O D:HOH4273 4.7 66.2 1.0
NH1 D:ARG137 4.9 32.6 1.0
CE1 D:HIS115 5.0 32.5 1.0
CB D:ARG137 5.0 30.1 1.0

Chlorine binding site 8 out of 12 in 2nv1

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Chlorine binding site 8 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3021

b:53.1
occ:1.00
 O D:HOH4171 2.6 52.8 1.0
O D:HOH4128 3.0 45.0 1.0
N D:GLY214 3.1 35.6 1.0
O D:HOH4164 3.4 50.3 1.0
N D:GLY153 3.6 51.8 1.0
O D:HOH4066 3.6 30.8 1.0
CA D:GLY213 3.9 34.8 1.0
CA D:GLY214 3.9 35.3 1.0
C D:GLY213 4.0 35.7 1.0
O D:HOH4149 4.1 48.3 1.0
CA D:PRO152 4.2 51.8 1.0
C D:PRO152 4.4 51.9 1.0
CA D:GLY153 4.5 51.6 1.0
N D:VAL215 4.5 36.4 1.0
N D:GLY213 4.5 33.9 1.0
C D:GLY214 4.6 35.8 1.0
N D:GLY235 4.7 35.9 1.0
O D:HOH4226 4.7 61.1 1.0
CB D:PRO152 4.8 52.2 1.0
CA D:GLY235 4.8 38.1 1.0
O D:GLU151 4.9 49.1 1.0

Chlorine binding site 9 out of 12 in 2nv1

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Chlorine binding site 9 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl3025

b:51.1
occ:1.00
 O E:HOH4141 2.4 44.2 1.0
NH1 E:ARG138 3.2 35.7 1.0
NE E:ARG137 3.3 29.1 1.0
NH2 E:ARG137 3.3 28.8 1.0
NH2 E:ARG138 3.3 30.8 1.0
O E:HOH4308 3.3 66.0 1.0
CZ E:ARG138 3.7 32.0 1.0
CZ E:ARG137 3.7 31.6 1.0
O E:HOH4298 4.0 64.7 1.0
CG E:GLU134 4.3 38.2 1.0
CD E:ARG137 4.4 28.3 1.0
OE2 E:GLU134 4.7 49.7 1.0
O E:HOH4239 4.8 58.7 1.0
CE1 E:HIS115 4.8 33.9 1.0
CB E:ARG137 5.0 26.7 1.0

Chlorine binding site 10 out of 12 in 2nv1

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Chlorine binding site 10 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl3026

b:51.1
occ:1.00
 O E:HOH4428 2.4 82.8 1.0
O E:HOH4190 3.0 53.2 1.0
N E:GLY214 3.1 36.2 1.0
O E:HOH4143 3.3 44.4 1.0
O E:HOH4249 3.3 59.5 1.0
N E:GLY153 3.6 47.0 1.0
O E:HOH4086 3.6 32.4 1.0
CA E:GLY213 3.7 35.3 1.0
CA E:PRO152 3.9 46.2 1.0
C E:GLY213 3.9 36.2 1.0
CA E:GLY214 4.1 36.5 1.0
O E:HOH4282 4.3 63.0 1.0
C E:PRO152 4.3 46.9 1.0
N E:GLY213 4.4 34.4 1.0
CB E:PRO152 4.5 46.4 1.0
O E:HOH4216 4.6 56.8 1.0
CA E:GLY153 4.6 47.0 1.0
N E:VAL215 4.7 36.6 1.0
N E:GLY235 4.8 36.0 1.0
C E:GLY214 4.8 36.7 1.0
O E:GLU151 4.8 41.8 1.0
CA E:GLY235 4.9 38.1 1.0

Reference:

M.Strohmeier, T.Raschle, J.Mazurkiewicz, K.Rippe, I.Sinning, T.B.Fitzpatrick, I.Tews. Structure of A Bacterial Pyridoxal 5'-Phosphate Synthase Complex Proc.Natl.Acad.Sci.Usa V. 103 19284 2006.
ISSN: ISSN 0027-8424
PubMed: 17159152
DOI: 10.1073/PNAS.0604950103
Page generated: Thu Jul 10 23:20:35 2025

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