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Chlorine in PDB 7dvc: Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein

Protein crystallography data

The structure of Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein, PDB code: 7dvc was solved by S.Yagi, S.Tagami, A.K.Padhi, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.30 / 1.71
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 98.151, 98.151, 177.324, 90, 90, 90
R / Rfree (%) 16.6 / 17.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein (pdb code 7dvc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein, PDB code: 7dvc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 7dvc

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Chlorine binding site 1 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl101

b:18.8
occ:0.74
 O A:HOH288 2.8 38.1 1.0
O A:HOH256 2.9 26.6 1.0
N A:LYS23 3.3 16.6 1.0
NH1 A:ARG26 3.4 16.2 1.0
O A:HOH243 3.5 25.2 1.0
CA A:ASP22 3.5 12.9 1.0
O A:HOH329 3.6 47.7 1.0
C A:ASP22 3.8 17.2 1.0
CG A:GLU52 3.9 17.7 1.0
CB A:ALA53 3.9 17.1 1.0
CB A:ASP22 3.9 17.7 1.0
CG2 A:VAL58 4.0 23.2 1.0
CB A:LYS23 4.1 17.3 1.0
N A:ALA53 4.1 16.8 1.0
CA A:LYS23 4.1 15.0 1.0
O A:MET21 4.2 16.5 1.0
NH2 A:ARG26 4.2 16.1 1.0
CZ A:ARG26 4.3 16.7 1.0
O A:ALA53 4.3 15.7 1.0
O A:HOH260 4.4 42.0 1.0
CA A:ALA53 4.5 15.5 1.0
CD A:GLU52 4.7 23.2 1.0
N A:ASP22 4.7 16.0 1.0
C A:ALA53 4.7 16.3 1.0
O A:HOH312 4.8 49.7 1.0
OE2 A:GLU52 4.8 28.9 1.0
O A:ASP22 4.9 16.5 1.0
C A:MET21 4.9 14.9 1.0
C A:GLU52 4.9 17.4 1.0

Chlorine binding site 2 out of 9 in 7dvc

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Chlorine binding site 2 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:32.1
occ:0.67
 NZ A:LYS43 2.9 40.5 1.0
O A:HOH311 3.0 49.9 1.0
CE A:LYS43 3.5 41.6 1.0
CD A:LYS43 4.6 48.8 1.0
O A:HOH283 4.7 23.9 1.0
O A:ASP71 5.0 26.7 1.0

Chlorine binding site 3 out of 9 in 7dvc

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Chlorine binding site 3 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


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 the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:32.1
occ:0.65
 O A:HOH302 2.7 54.4 1.0
NZ C:LYS43 2.8 40.1 1.0
SD A:MET51 3.0 18.9 0.3
NH2 A:ARG49 3.2 48.8 1.0
NH1 A:ARG49 3.4 46.3 1.0
CE A:MET51 3.4 20.6 0.3
O A:HOH279 3.5 27.0 1.0
CE A:MET51 3.7 21.4 0.7
CZ A:ARG49 3.8 46.9 1.0
CG2 A:ILE18 4.1 18.2 1.0
SD A:MET51 4.1 24.0 0.7
CE C:LYS43 4.1 47.0 1.0
CD A:LYS16 4.1 19.3 0.4
CD A:LYS16 4.2 19.6 0.6
CG A:MET51 4.4 18.1 0.3
CG A:MET51 4.5 17.5 0.7
CD C:LYS43 4.5 54.1 1.0
O C:HOH295 4.7 27.6 1.0
CE A:LYS16 4.8 20.4 0.6
CE A:LYS16 4.8 20.9 0.4
CB A:LYS16 4.8 17.5 0.4
CB A:LYS16 4.8 17.4 0.6
CG A:LYS16 4.8 19.1 0.4
CG A:LYS16 4.9 19.5 0.6
O C:ASP71 5.0 22.2 1.0

Chlorine binding site 4 out of 9 in 7dvc

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Chlorine binding site 4 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


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 the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl102

b:18.4
occ:0.62
 O A:HOH273 2.7 33.9 1.0
O C:HOH296 3.0 25.4 1.0
NH2 C:ARG70 3.1 15.0 1.0
CD C:GLU8 3.2 19.1 1.0
OE1 C:GLU8 3.5 16.2 1.0
OE2 C:GLU8 3.5 18.5 1.0
CG C:GLU8 3.6 15.8 1.0
CG B:GLU56 3.7 15.6 1.0
CG A:PRO55 3.8 15.0 1.0
CB C:LYS67 4.0 14.0 1.0
CB C:GLU8 4.1 15.5 1.0
CD C:LYS67 4.1 16.5 1.0
O A:HOH312 4.1 49.7 1.0
CZ C:ARG70 4.3 16.4 1.0
OE2 B:GLU56 4.3 16.0 1.0
CD B:GLU56 4.3 19.2 1.0
CD A:PRO55 4.4 15.4 1.0
CG C:LYS67 4.5 13.8 1.0
CB B:GLU56 4.6 15.3 1.0
NH1 C:ARG70 4.6 18.3 1.0
OE1 A:GLU52 4.6 25.8 1.0
CA B:GLU56 4.6 14.9 1.0
CA C:LYS67 4.9 12.6 1.0
O C:HOH319 4.9 48.7 1.0
O A:HOH256 5.0 26.6 1.0

Chlorine binding site 5 out of 9 in 7dvc

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Chlorine binding site 5 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


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 the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl103

b:30.8
occ:0.62
 O A:HOH230 2.9 35.7 1.0
NH2 C:ARG5 3.1 31.2 1.0
O A:HOH205 3.2 59.4 1.0
NZ A:LYS23 3.5 36.8 1.0
CD A:LYS23 3.8 26.7 1.0
CE A:LYS23 3.8 35.4 1.0
CZ C:ARG5 4.3 31.3 1.0
NH1 C:ARG5 4.8 28.1 1.0
O A:HOH234 4.8 41.3 1.0
CG A:LYS23 4.9 22.6 1.0
OD2 A:ASP27 5.0 23.5 1.0

Chlorine binding site 6 out of 9 in 7dvc

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Chlorine binding site 6 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


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 the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl104

b:25.3
occ:0.64
 N C:LEU80 3.2 17.9 1.0
O C:HOH219 3.3 43.2 1.0
O C:HOH322 3.4 53.9 1.0
CA C:ASP79 3.6 18.6 1.0
CB C:ASP79 3.8 16.4 1.0
C C:ASP79 3.9 18.1 1.0
OD1 C:ASP79 4.1 21.0 1.0
CB C:LEU80 4.1 18.6 1.0
CG C:ASP79 4.2 22.4 1.0
CA C:LEU80 4.2 17.0 1.0
CG C:LEU80 4.4 24.9 1.0
O C:LEU80 4.4 23.2 1.0
O A:HOH226 4.4 75.7 1.0
O C:HOH210 4.5 56.4 1.0
C C:LEU80 4.8 20.3 1.0
CD1 C:LEU80 4.8 26.8 1.0
N C:ASP79 4.9 16.8 1.0
O C:GLY78 4.9 19.3 1.0
OD2 C:ASP79 5.0 21.8 1.0

Chlorine binding site 7 out of 9 in 7dvc

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Chlorine binding site 7 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


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 the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl102

b:24.8
occ:0.58
 O E:HOH264 2.8 25.8 1.0
NH1 E:ARG26 3.1 24.5 1.0
N E:LYS23 3.2 22.6 1.0
O E:ACT101 3.3 34.7 1.0
CA E:ASP22 3.3 22.6 1.0
O E:HOH219 3.6 27.3 1.0
C E:ASP22 3.7 22.2 1.0
CG E:GLU52 3.8 19.5 1.0
CB E:ASP22 3.8 23.0 1.0
CB E:ALA53 3.8 19.1 1.0
N E:ALA53 3.9 19.4 1.0
O E:MET21 3.9 21.1 1.0
CZ E:ARG26 4.0 26.6 1.0
NH2 E:ARG26 4.0 25.0 1.0
CA E:LYS23 4.2 26.2 1.0
C E:ACT101 4.2 45.0 1.0
CB E:LYS23 4.2 29.1 1.0
O E:ALA53 4.3 19.6 1.0
CA E:ALA53 4.3 19.7 1.0
CH3 E:ACT101 4.4 41.6 1.0
N E:ASP22 4.4 23.3 1.0
CG2 E:VAL58 4.5 28.4 1.0
C E:MET21 4.6 17.8 1.0
C E:ALA53 4.7 23.3 1.0
O E:ASP22 4.7 23.7 1.0
C E:GLU52 4.8 18.1 1.0
CD E:GLU52 4.8 21.6 1.0
CA E:GLU52 4.9 18.6 1.0
CB E:GLU52 4.9 19.4 1.0

Chlorine binding site 8 out of 9 in 7dvc

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Chlorine binding site 8 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


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 the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:26.9
occ:0.55
 NZ E:LYS43 2.9 36.6 1.0
O B:HOH309 2.9 44.2 1.0
SD B:MET7 3.0 22.1 0.3
NH1 B:ARG5 3.1 40.9 1.0
CE B:MET7 3.2 20.1 0.3
CE E:LYS43 3.4 46.5 1.0
NH2 B:ARG5 3.5 45.4 1.0
O B:HOH204 3.5 25.4 1.0
CE B:MET7 3.6 24.9 0.7
CZ B:ARG5 3.7 40.5 1.0
CD B:LYS60 3.9 16.4 0.4
CD B:LYS60 4.0 15.7 0.6
SD B:MET7 4.0 22.6 0.7
CG2 B:ILE62 4.1 22.4 1.0
CG B:MET7 4.2 19.4 0.3
CG B:MET7 4.2 19.4 0.7
NZ B:LYS60 4.5 23.9 0.4
CE B:LYS60 4.5 19.3 0.4
CG B:LYS60 4.6 15.8 0.4
O E:HOH271 4.7 23.5 1.0
CD1 B:ILE62 4.7 26.3 1.0
CB B:LYS60 4.8 14.1 0.4
CE B:LYS60 4.8 16.3 0.6
CG B:LYS60 4.8 14.1 0.6
CB B:LYS60 4.9 14.6 0.6
CD E:LYS43 4.9 47.3 1.0
NZ B:LYS60 5.0 13.2 0.6
O B:HOH291 5.0 66.3 1.0
O E:ASP71 5.0 22.0 1.0

Chlorine binding site 9 out of 9 in 7dvc

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Chlorine binding site 9 out of 9 in the Crystal Structure of the Computationally Designed REDPBB_SYM1 Protein


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 the Computationally Designed REDPBB_SYM1 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl102

b:22.3
occ:0.62
 NH2 D:ARG70 3.0 20.4 1.0
O D:HOH278 3.1 27.9 1.0
CD D:GLU8 3.2 23.2 1.0
OE2 D:GLU8 3.4 25.0 1.0
OE1 D:GLU8 3.5 21.4 1.0
CG D:GLU8 3.6 21.5 1.0
CB D:LYS67 3.9 15.8 1.0
CD D:LYS67 4.0 17.5 1.0
CZ D:ARG70 4.2 21.2 1.0
CB D:GLU8 4.2 20.1 1.0
CG D:LYS67 4.2 17.2 1.0
NH1 D:ARG70 4.5 21.4 1.0
CA D:LYS67 4.8 18.2 1.0
N D:LYS67 5.0 15.1 1.0

Reference:

S.Yagi, A.K.Padhi, J.Vucinic, S.Barbe, T.Schiex, R.Nakagawa, D.Simoncini, K.Y.J.Zhang, S.Tagami. Seven Amino Acid Typessuffice to Reconstruct the Core Fold of Rna Polymerase Biorxiv 2021.
Page generated: Sun Jul 13 00:14:33 2025

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