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Chlorine in PDB 7cd4: Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.

Protein crystallography data

The structure of Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein., PDB code: 7cd4 was solved by Z.Fujimoto, N.Kishine, K.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.68 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.101, 85.506, 106.537, 90, 90, 90
R / Rfree (%) 18.5 / 22.5

Other elements in 7cd4:

The structure of Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. (pdb code 7cd4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein., PDB code: 7cd4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 7cd4

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Chlorine binding site 1 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:34.9
occ:1.00
 NE2 A:HIS51 3.1 21.7 1.0
O A:HOH343 3.3 39.3 1.0
NE2 A:GLN93 3.3 29.2 1.0
CD2 A:HIS51 4.0 23.7 1.0
ND1 A:HIS6 4.0 26.2 1.0
CE1 A:HIS51 4.0 23.4 1.0
CG2 A:VAL90 4.1 27.7 1.0
CD A:LYS47 4.2 34.6 1.0
CD A:GLN93 4.2 29.0 1.0
OE1 A:GLN93 4.2 28.9 1.0
CB A:LYS47 4.5 28.7 1.0
CE A:LYS47 4.6 41.4 1.0
CG A:HIS6 4.6 26.0 1.0
CE1 A:HIS6 4.6 26.6 1.0
CB A:HIS6 4.8 27.1 1.0
NZ A:LYS47 4.8 47.0 1.0
O A:HOH367 4.9 35.0 1.0
CG A:LYS47 4.9 32.0 1.0

Chlorine binding site 2 out of 10 in 7cd4

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Chlorine binding site 2 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:32.3
occ:1.00
 O D:HOH323 3.1 28.0 1.0
NH1 A:ARG102 3.2 28.9 1.0
NH1 D:ARG102 3.4 30.8 1.0
NZ D:LYS73 3.4 26.9 1.0
NZ A:LYS73 3.5 27.9 1.0
CD A:ARG102 3.7 26.4 1.0
CD A:LYS73 4.0 27.1 1.0
CD D:LYS73 4.1 25.4 1.0
CD1 D:ILE121 4.2 24.8 1.0
CZ A:ARG102 4.2 27.5 1.0
CE A:LYS73 4.2 27.7 1.0
CZ D:ARG102 4.2 31.6 1.0
NH2 D:ARG102 4.2 30.3 1.0
CE D:LYS73 4.2 26.6 1.0
NE A:ARG102 4.3 25.6 1.0
CG A:ARG102 4.9 25.6 1.0
OE2 B:GLU106 5.0 41.0 1.0

Chlorine binding site 3 out of 10 in 7cd4

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Chlorine binding site 3 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:26.3
occ:1.00
 O A:HOH327 2.7 34.5 1.0
O D:HOH304 3.0 25.7 1.0
N A:ALA101 3.3 24.2 1.0
ND2 D:ASN24 3.4 35.6 1.0
CE1 A:HIS98 3.4 31.4 1.0
CB D:ASN24 3.6 36.9 1.0
CB A:ALA101 3.6 25.2 1.0
O A:VAL71 3.7 23.8 1.0
CA A:VAL72 3.8 24.4 1.0
CG D:ASN24 4.0 38.4 1.0
CA A:ALA101 4.0 23.9 1.0
CA A:PRO100 4.0 27.3 1.0
CG1 A:VAL72 4.0 25.2 1.0
NE2 A:HIS98 4.1 29.4 1.0
C A:PRO100 4.1 26.0 1.0
CB A:VAL72 4.1 24.7 1.0
CG1 D:VAL23 4.2 28.1 1.0
O A:LYS99 4.3 30.4 1.0
O A:VAL72 4.4 24.5 1.0
ND1 A:HIS98 4.4 31.2 1.0
C A:VAL71 4.5 24.8 1.0
C A:VAL72 4.6 24.9 1.0
N A:VAL72 4.6 23.4 1.0
O D:VAL23 4.8 29.4 1.0
N A:PRO100 5.0 27.0 1.0
OH D:TYR28 5.0 23.5 1.0
CA D:ASN24 5.0 34.7 1.0
CB D:VAL23 5.0 29.5 1.0

Chlorine binding site 4 out of 10 in 7cd4

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Chlorine binding site 4 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:52.5
occ:1.00
 O A:HOH373 2.8 45.6 1.0
O A:HOH372 3.2 36.2 1.0
NZ A:LYS58 3.4 45.3 1.0
CE2 A:TYR94 3.5 27.8 1.0
CD2 A:TYR94 3.8 26.8 1.0
CD A:LYS58 4.0 39.2 1.0
CD A:LYS8 4.1 53.4 1.0
CG A:LYS8 4.1 45.3 1.0
CE A:LYS58 4.2 42.6 1.0
O A:HOH368 4.4 52.3 1.0
CE2 A:PHE68 4.5 26.3 1.0
O A:HOH355 4.6 43.9 1.0
NZ A:LYS8 4.7 63.9 1.0
CZ A:TYR94 4.7 26.1 1.0
CE A:LYS8 4.8 57.1 1.0
O A:HOH337 4.9 25.8 1.0
CB A:LYS8 4.9 37.4 1.0

Chlorine binding site 5 out of 10 in 7cd4

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Chlorine binding site 5 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:38.8
occ:1.00
 NE2 B:HIS51 3.1 27.8 1.0
NE2 B:GLN93 3.5 30.4 1.0
CD2 B:HIS51 4.0 26.5 1.0
CE1 B:HIS51 4.0 28.1 1.0
CD B:LYS47 4.1 33.2 1.0
CG2 B:VAL90 4.3 25.8 1.0
CD B:GLN93 4.5 29.6 1.0
OE1 B:GLN93 4.5 32.2 1.0
CB B:LYS47 4.6 29.0 1.0
NZ B:LYS47 4.8 42.0 1.0
CG B:LYS47 4.9 31.0 1.0

Chlorine binding site 6 out of 10 in 7cd4

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Chlorine binding site 6 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:29.2
occ:1.00
 O C:HOH301 3.1 33.4 1.0
O B:HOH302 3.1 31.4 1.0
ND2 B:ASN24 3.2 45.2 1.0
N C:ALA101 3.3 25.9 1.0
CE1 C:HIS98 3.5 38.8 1.0
CB C:ALA101 3.6 28.0 1.0
CB B:ASN24 3.6 38.8 1.0
CA C:VAL72 3.7 26.3 1.0
O C:VAL71 3.8 23.7 1.0
CG B:ASN24 3.9 44.0 1.0
CG1 C:VAL72 3.9 27.8 1.0
CA C:PRO100 4.0 29.7 1.0
CA C:ALA101 4.0 27.5 1.0
C C:PRO100 4.1 28.1 1.0
CB C:VAL72 4.1 27.9 1.0
NE2 C:HIS98 4.2 34.4 1.0
O C:LYS99 4.3 33.1 1.0
O C:VAL72 4.3 26.3 1.0
C C:VAL72 4.5 26.6 1.0
CG1 B:VAL23 4.5 36.9 1.0
ND1 C:HIS98 4.6 40.0 1.0
C C:VAL71 4.6 25.8 1.0
N C:VAL72 4.6 25.5 1.0
N C:PRO100 4.9 29.9 1.0
O B:VAL23 4.9 32.8 1.0
C C:LYS99 4.9 33.3 1.0
OH B:TYR28 4.9 25.8 1.0

Chlorine binding site 7 out of 10 in 7cd4

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Chlorine binding site 7 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:41.5
occ:1.00
 NE2 C:HIS51 3.0 26.5 1.0
NE2 C:GLN93 3.5 33.4 1.0
CD2 C:HIS51 3.9 28.6 1.0
ND1 C:HIS6 4.0 34.6 1.0
CE1 C:HIS51 4.0 27.8 1.0
CD C:LYS47 4.0 47.3 1.0
CG2 C:VAL90 4.1 29.3 1.0
CE C:LYS47 4.3 49.4 1.0
CB C:LYS47 4.4 37.8 1.0
CD C:GLN93 4.4 34.8 1.0
CE1 C:HIS6 4.4 34.2 1.0
OE1 C:GLN93 4.5 36.4 1.0
CG C:HIS6 4.7 38.0 1.0
CG C:LYS47 4.8 43.5 1.0
NZ C:LYS47 4.8 52.5 1.0

Chlorine binding site 8 out of 10 in 7cd4

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Chlorine binding site 8 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:49.5
occ:1.00
 NE2 D:HIS51 3.0 38.1 1.0
NE2 D:GLN93 3.2 42.8 1.0
CD2 D:HIS51 3.8 38.2 1.0
CD D:LYS47 4.0 56.1 1.0
CE1 D:HIS51 4.1 36.5 1.0
CG2 D:VAL90 4.1 43.0 1.0
CE D:LYS47 4.2 58.6 1.0
CD D:GLN93 4.2 43.5 1.0
OE1 D:GLN93 4.3 44.8 1.0
CB D:LYS47 4.6 51.0 1.0
CG D:LYS47 4.9 54.5 1.0

Chlorine binding site 9 out of 10 in 7cd4

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Chlorine binding site 9 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj 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 S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:32.7
occ:1.00
 O A:HOH314 3.0 28.0 1.0
N D:ALA101 3.3 26.5 1.0
ND2 A:ASN24 3.4 43.2 1.0
CE1 D:HIS98 3.5 43.8 1.0
CB A:ASN24 3.6 40.5 1.0
CB D:ALA101 3.7 27.9 1.0
O D:VAL71 3.7 31.5 1.0
CA D:VAL72 3.7 27.0 1.0
CG1 D:VAL72 3.9 27.8 1.0
CA D:PRO100 4.0 31.7 1.0
NE2 D:HIS98 4.0 45.0 1.0
CG A:ASN24 4.0 44.0 1.0
CB D:VAL72 4.1 26.4 1.0
C D:PRO100 4.1 28.2 1.0
CA D:ALA101 4.1 27.5 1.0
O D:LYS99 4.2 31.2 1.0
CG1 A:VAL23 4.3 35.3 1.0
O D:VAL72 4.4 26.5 1.0
C D:VAL71 4.5 31.2 1.0
C D:VAL72 4.5 26.1 1.0
N D:VAL72 4.5 28.9 1.0
ND1 D:HIS98 4.6 44.4 1.0
O A:VAL23 4.8 33.0 1.0
N D:PRO100 4.8 32.3 1.0
C D:LYS99 4.9 33.3 1.0
OH A:TYR28 4.9 25.8 1.0
CA A:ASN24 4.9 37.5 1.0

Chlorine binding site 10 out of 10 in 7cd4

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Chlorine binding site 10 out of 10 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.


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 the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl203

b:47.3
occ:1.00
 N D:PHE68 3.2 31.5 1.0
CD2 D:PHE68 3.4 34.8 1.0
CG D:PHE68 3.7 34.7 1.0
CB D:SER67 3.8 32.5 1.0
CE D:LYS58 3.8 44.2 1.0
CB D:PHE68 3.8 33.9 1.0
CA D:SER67 3.9 32.3 1.0
C D:SER67 4.1 31.2 1.0
CE2 D:PHE68 4.1 34.4 1.0
CA D:PHE68 4.1 33.5 1.0
OE1 D:GLU69 4.2 56.8 1.0
CG D:LYS58 4.3 40.3 1.0
CD D:LYS58 4.4 43.2 1.0
CD1 D:PHE68 4.6 33.8 1.0
NZ D:LYS58 4.8 47.9 1.0
OE2 D:GLU69 4.9 58.9 1.0
OG D:SER67 4.9 34.4 1.0
CD D:GLU69 4.9 55.0 1.0
CZ D:PHE68 4.9 36.6 1.0

Reference:

Z.Fujimoto, L.T.T.Hong, N.Kishine, N.Suzuki, K.Kimura. Tetramer Formation of Bacillus Subtilis Yabj Protein That Belongs to Yjgf/YER057C/UK114 Family. Biosci.Biotechnol.Biochem. V. 85 297 2021.
ISSN: ISSN 0916-8451
PubMed: 33590041
DOI: 10.1093/BBB/ZBAA037
Page generated: Mon Jul 29 19:39:53 2024

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