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Zinc in PDB 7vpf: Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4

Protein crystallography data

The structure of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4, PDB code: 7vpf was solved by H.H.Park, J.H.Lee, S.Kwon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.82 / 2.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 141.932, 141.932, 76.701, 90, 90, 120
R / Rfree (%) 21.4 / 27.1

Other elements in 7vpf:

The structure of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 (pdb code 7vpf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4, PDB code: 7vpf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7vpf

Go back to Zinc Binding Sites List in 7vpf
Zinc binding site 1 out of 2 in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4


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 A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:200.5
occ:1.00
ND1 A:HIS203 2.1 116.2 1.0
OE1 A:GLU247 2.1 128.8 1.0
OD2 A:ASP178 2.2 103.7 1.0
OE1 A:GLU142 2.8 114.7 1.0
CG A:HIS203 2.8 86.0 1.0
CB A:HIS203 2.8 69.5 1.0
CG A:ASP178 2.8 90.9 1.0
CB A:ASP178 3.2 67.9 1.0
CE1 A:HIS203 3.2 105.3 1.0
CD A:GLU247 3.3 110.0 1.0
CA A:CA301 3.8 126.7 1.0
OD1 A:ASP178 3.8 83.0 1.0
CB A:GLU247 3.8 95.1 1.0
CD A:GLU142 3.9 93.7 1.0
NH1 A:ARG218 3.9 80.7 1.0
CD2 A:HIS203 4.0 74.4 1.0
CG A:GLU247 4.1 97.7 1.0
NE2 A:HIS203 4.2 76.1 1.0
OE2 A:GLU247 4.3 119.1 1.0
CA A:ASP178 4.3 55.5 1.0
CA A:HIS203 4.3 69.3 1.0
OE2 A:GLU142 4.4 90.7 1.0
C A:HIS203 4.9 70.3 1.0
CD2 A:HIS181 4.9 73.3 1.0
N A:HIS203 5.0 79.8 1.0
CG A:GLU142 5.0 67.9 1.0
NE2 A:HIS181 5.0 82.6 1.0

Zinc binding site 2 out of 2 in 7vpf

Go back to Zinc Binding Sites List in 7vpf
Zinc binding site 2 out of 2 in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4


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 A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:175.0
occ:1.00
OE1 B:GLU142 2.3 125.5 1.0
OE2 B:GLU247 2.3 119.2 1.0
CD B:GLU142 2.7 101.4 1.0
OE2 B:GLU142 2.7 99.3 1.0
OD2 B:ASP178 2.9 92.9 1.0
CA B:CA302 2.9 133.5 1.0
ND1 B:HIS203 3.2 99.1 1.0
CD B:GLU247 3.2 107.1 1.0
OE1 B:GLU247 3.7 115.5 1.0
NH1 B:ARG218 3.7 85.3 1.0
NE2 B:HIS181 3.8 87.8 1.0
CG B:ASP178 3.8 93.9 1.0
CE1 B:HIS203 3.9 102.9 1.0
CB B:ASP178 4.0 67.8 1.0
CD2 B:HIS181 4.0 75.8 1.0
CG B:GLU142 4.0 68.5 1.0
CG B:HIS203 4.3 84.2 1.0
CG B:GLU247 4.4 94.7 1.0
CB B:HIS203 4.6 67.0 1.0
CZ B:ARG218 4.7 96.9 1.0
NH2 B:ARG218 4.7 85.4 1.0
CB B:GLU247 4.7 93.8 1.0
OD1 B:ASP178 5.0 87.1 1.0

Reference:

S.Kwon, H.J.Ha, Y.J.Kang, J.H.Sung, J.Hwang, M.J.Lee, J.H.Lee, H.H.Park. Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4. Biochem.Biophys.Res.Commun. V. 585 48 2021.
ISSN: ESSN 1090-2104
PubMed: 34784551
DOI: 10.1016/J.BBRC.2021.11.026
Page generated: Thu Mar 31 05:24:37 2022

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