Zinc 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:

Chlorine (Cl) 10 atoms
Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein., PDB code: 7cd4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7cd4

Go back to Zinc Binding Sites List in 7cd4
Zinc binding site 1 out of 3 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn201

b:25.4
occ:1.00
OE1 A:GLU48 1.9 27.0 1.0
NE2 A:HIS9 2.0 22.0 1.0
NE2 A:HIS6 2.0 26.7 1.0
CD A:GLU48 2.7 26.1 1.0
CE1 A:HIS9 2.9 23.2 1.0
OE2 A:GLU48 2.9 27.3 1.0
CD2 A:HIS6 2.9 27.6 1.0
CE1 A:HIS6 3.1 26.6 1.0
CD2 A:HIS9 3.1 22.4 1.0
ND1 A:HIS9 4.0 22.8 1.0
CG A:HIS6 4.1 26.0 1.0
ND1 A:HIS6 4.1 26.2 1.0
O A:HOH348 4.2 30.4 1.0
CG A:HIS9 4.2 23.5 1.0
CG A:GLU48 4.2 25.7 1.0
O A:THR7 4.2 27.0 1.0
CB A:HIS51 4.3 26.1 1.0
CD2 A:HIS51 4.5 23.7 1.0
CG A:HIS51 4.6 25.1 1.0
CA A:GLU48 4.6 24.2 1.0
CB A:GLU48 4.6 24.5 1.0
O A:GLU48 5.0 22.3 1.0

Zinc binding site 2 out of 3 in 7cd4

Go back to Zinc Binding Sites List in 7cd4
Zinc binding site 2 out of 3 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn201

b:83.3
occ:1.00
OE1 B:GLU48 2.5 52.9 1.0
CD B:GLU48 3.3 46.9 1.0
OE2 B:GLU48 3.5 54.0 1.0
CB B:HIS51 4.1 24.9 1.0
CG B:HIS51 4.1 26.5 1.0
CD2 B:HIS51 4.1 26.5 1.0
CG B:GLU48 4.7 40.6 1.0
CA B:GLU48 4.8 31.4 1.0
ND1 B:HIS51 4.9 27.2 1.0
NE2 B:HIS51 4.9 27.8 1.0
O B:GLU48 5.0 28.9 1.0

Zinc binding site 3 out of 3 in 7cd4

Go back to Zinc Binding Sites List in 7cd4
Zinc binding site 3 out of 3 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
C:Zn201

b:32.0
occ:1.00
OE1 C:GLU48 1.8 28.7 1.0
NE2 C:HIS9 2.0 29.8 1.0
NE2 C:HIS6 2.1 36.5 1.0
CD C:GLU48 2.7 32.3 1.0
CD2 C:HIS6 2.9 34.2 1.0
CE1 C:HIS9 2.9 30.5 1.0
OE2 C:GLU48 3.0 34.9 1.0
CD2 C:HIS9 3.1 30.6 1.0
CE1 C:HIS6 3.2 34.2 1.0
ND1 C:HIS9 4.1 30.1 1.0
CG C:HIS6 4.1 38.0 1.0
CG C:GLU48 4.1 31.8 1.0
O C:THR7 4.1 37.0 1.0
CG C:HIS9 4.2 31.2 1.0
ND1 C:HIS6 4.2 34.6 1.0
CB C:HIS51 4.3 29.9 1.0
CG C:HIS51 4.5 28.6 1.0
CB C:GLU48 4.5 31.6 1.0
CD2 C:HIS51 4.5 28.6 1.0
CA C:GLU48 4.6 32.1 1.0
O C:GLU48 5.0 31.8 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: Sat Apr 3 18:32:16 2021

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