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Chlorine in PDB 4pig: Crystal Structure of the Ubiquitin K11S Mutant

Protein crystallography data

The structure of Crystal Structure of the Ubiquitin K11S Mutant, PDB code: 4pig was solved by P.J.Loll, P.J.Xu, J.Schmidt, S.L.Melideo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.76 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.700, 61.820, 91.500, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.8

Other elements in 4pig:

The structure of Crystal Structure of the Ubiquitin K11S Mutant also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Ubiquitin K11S Mutant (pdb code 4pig). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the Ubiquitin K11S Mutant, PDB code: 4pig:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4pig

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Chlorine binding site 1 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:4.9
occ:1.00
 O C:HOH231 3.2 6.6 1.0
N A:LEU71 3.2 3.5 1.0
O A:HOH238 3.2 8.3 1.0
N C:LEU71 3.4 7.6 1.0
O A:HOH235 3.4 2.7 1.0
CB C:LEU71 3.7 5.5 1.0
CA A:VAL70 3.8 4.7 1.0
CB A:LEU71 3.8 2.7 1.0
C A:VAL70 4.0 5.0 1.0
CA C:VAL70 4.1 4.6 1.0
CA A:LEU71 4.1 3.0 1.0
CG A:LEU71 4.1 4.8 1.0
CB A:VAL70 4.1 2.6 1.0
CG1 C:VAL70 4.2 9.1 1.0
CA C:LEU71 4.2 4.6 1.0
C C:VAL70 4.2 5.5 1.0
CD1 A:LEU8 4.5 15.2 1.0
CD1 A:LEU71 4.5 5.3 1.0
CG1 A:VAL70 4.6 3.7 1.0
O C:LEU69 4.6 3.4 1.0
CB C:VAL70 4.7 6.8 1.0
O A:LEU71 4.8 4.5 1.0
C A:LEU71 5.0 4.8 1.0
O A:LEU69 5.0 5.4 1.0

Chlorine binding site 2 out of 8 in 4pig

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Chlorine binding site 2 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:18.5
occ:1.00
 N A:GLU16 3.2 5.0 1.0
O A:HOH237 3.2 2.3 0.6
CA A:LEU15 3.7 7.0 1.0
CD2 A:LEU15 3.7 5.4 1.0
CB A:LEU15 3.9 5.0 1.0
O A:GLU16 3.9 6.6 1.0
C A:LEU15 4.0 7.6 1.0
CE A:LYS33 4.0 24.9 1.0
CD A:LYS29 4.1 14.4 1.0
CA A:GLU16 4.2 5.9 1.0
CB A:LYS29 4.3 4.3 1.0
CB A:GLU16 4.3 11.3 1.0
CG A:LYS29 4.4 7.9 1.0
CG A:LEU15 4.5 7.1 1.0
C A:GLU16 4.5 8.1 1.0
O A:HOH237 4.5 7.6 0.4
NZ A:LYS33 4.6 16.4 1.0
O A:THR14 4.7 9.4 1.0
NZ A:LYS29 4.7 17.4 1.0
CD A:LYS33 4.9 14.7 1.0
N A:LEU15 5.0 7.0 1.0

Chlorine binding site 3 out of 8 in 4pig

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Chlorine binding site 3 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl101

b:19.1
occ:1.00
 O C:HOH245 3.0 19.4 1.0
N C:GLU16 3.2 9.8 1.0
CA C:LEU15 3.7 12.1 1.0
O C:GLU16 3.8 11.2 1.0
CB C:LEU15 3.9 13.8 1.0
C C:LEU15 4.0 11.7 1.0
CD C:LYS29 4.0 12.3 1.0
CD2 C:LEU15 4.2 8.7 1.0
CA C:GLU16 4.2 12.5 1.0
CB C:LYS29 4.2 5.5 1.0
CG C:LYS29 4.3 11.8 1.0
CB C:GLU16 4.3 16.6 1.0
C C:GLU16 4.4 12.2 1.0
CD C:LYS33 4.4 18.1 1.0
O C:HOH247 4.5 21.0 1.0
CG C:LEU15 4.6 11.7 1.0
O C:THR14 4.7 8.9 1.0
NZ C:LYS29 4.7 10.0 1.0
N C:LEU15 4.9 6.3 1.0
CE C:LYS29 5.0 15.5 1.0

Chlorine binding site 4 out of 8 in 4pig

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Chlorine binding site 4 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl102

b:21.6
occ:1.00
 O C:HOH226 2.6 17.6 1.0
N C:GLN49 3.1 6.6 1.0
O C:HOH217 3.5 15.2 1.0
O C:HOH204 3.7 17.1 1.0
CB C:GLN49 3.8 14.6 1.0
O C:GLN49 3.8 14.5 1.0
CA C:GLN49 3.8 9.4 1.0
C C:LYS48 4.0 11.8 1.0
CA C:LYS48 4.0 8.8 1.0
C C:GLN49 4.3 11.6 1.0
CB C:LYS48 4.6 12.0 1.0
O C:GLY47 4.8 10.4 1.0
CG C:GLN49 5.0 26.8 1.0

Chlorine binding site 5 out of 8 in 4pig

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Chlorine binding site 5 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl103

b:34.9
occ:1.00
 NE2 C:HIS68 3.3 19.2 1.0
NE2 D:HIS68 3.3 14.3 1.0
NZ D:LYS6 3.6 38.7 1.0
CE D:LYS6 3.6 38.6 1.0
CE1 C:HIS68 3.8 12.1 1.0
NZ C:LYS6 3.8 32.4 1.0
CE1 D:HIS68 4.0 11.7 1.0
CE C:LYS6 4.3 31.4 1.0
CD2 D:HIS68 4.4 6.9 1.0
CD C:LYS6 4.5 26.7 1.0
CD2 C:HIS68 4.5 11.1 1.0
CD D:LYS6 4.6 31.4 1.0
O C:HOH242 5.0 16.5 1.0

Chlorine binding site 6 out of 8 in 4pig

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Chlorine binding site 6 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl103

b:9.4
occ:1.00
 O D:HOH227 2.8 21.2 1.0
N D:LEU71 3.2 9.2 1.0
CA D:VAL70 3.7 5.0 1.0
O D:HOH212 3.7 11.2 1.0
O D:HOH210 3.8 18.0 1.0
CB D:VAL70 4.0 7.4 1.0
CG D:LEU71 4.0 17.7 1.0
C D:VAL70 4.0 7.7 1.0
CB D:LEU71 4.0 12.8 1.0
CA D:LEU71 4.2 9.3 1.0
CG1 D:VAL70 4.4 5.1 1.0
CD1 D:LEU71 4.4 18.1 1.0
O D:LEU69 4.8 5.0 1.0
N D:VAL70 5.0 6.1 1.0

Chlorine binding site 7 out of 8 in 4pig

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Chlorine binding site 7 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl104

b:17.3
occ:1.00
 O D:HOH244 3.0 14.2 1.0
O D:HOH235 3.1 7.6 0.5
N D:GLU16 3.1 6.7 1.0
CA D:LEU15 3.7 5.4 1.0
O D:GLU16 3.8 10.9 1.0
C D:LEU15 3.9 7.5 1.0
CB D:LEU15 4.0 2.5 1.0
CA D:GLU16 4.1 5.3 1.0
CD D:LYS29 4.1 13.1 1.0
CB D:LYS29 4.1 5.0 1.0
CD2 D:LEU15 4.2 5.8 1.0
CB D:GLU16 4.2 9.6 1.0
C D:GLU16 4.4 6.4 1.0
CG D:LYS29 4.4 10.9 1.0
CD D:LYS33 4.5 20.5 1.0
O D:THR14 4.5 9.2 1.0
O D:HOH254 4.6 19.6 1.0
NZ D:LYS33 4.6 30.9 1.0
CG D:LEU15 4.7 6.2 1.0
N D:LEU15 4.9 7.4 1.0
O D:HOH235 5.0 6.7 0.5

Chlorine binding site 8 out of 8 in 4pig

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Chlorine binding site 8 out of 8 in the Crystal Structure of the Ubiquitin K11S Mutant


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 Ubiquitin K11S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl105

b:27.3
occ:1.00
 O D:HOH229 2.9 3.6 1.0
NH1 D:ARG72 3.0 30.4 1.0
NE D:ARG42 3.1 11.7 1.0
NH2 D:ARG42 3.6 17.8 1.0
CZ D:ARG42 3.8 14.4 1.0
CG D:ARG42 3.9 9.1 1.0
CZ D:ARG72 4.0 35.1 1.0
CD D:ARG42 4.0 8.2 1.0
CB D:ARG42 4.1 5.1 1.0
CD D:ARG72 4.1 17.5 1.0
O D:LEU50 4.2 9.1 1.0
CA D:ARG42 4.3 5.0 1.0
NZ D:LYS27 4.4 10.2 1.0
NE D:ARG72 4.4 20.7 1.0
NE2 D:GLN49 4.5 16.6 1.0
O D:GLN41 4.6 7.4 1.0
NH2 D:ARG72 5.0 23.2 1.0

Reference:

P.J.Loll, P.Xu, J.T.Schmidt, S.L.Melideo. Enhancing Ubiquitin Crystallization Through Surface-Entropy Reduction. Acta Crystallogr.,Sect.F V. 70 1434 2014.
ISSN: ESSN 2053-230X
PubMed: 25286958
DOI: 10.1107/S2053230X14019244
Page generated: Thu Jul 25 23:59:07 2024

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