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Zinc in PDB 1jdi: Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase

Enzymatic activity of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase

All present enzymatic activity of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase:
5.1.3.4;

Protein crystallography data

The structure of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase, PDB code: 1jdi was solved by Y.Luo, J.Samuel, S.C.Mosimann, J.E.Lee, M.E.Tanner, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.900, 105.900, 274.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase (pdb code 1jdi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase, PDB code: 1jdi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1jdi

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Zinc binding site 1 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase


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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:31.3
occ:1.00
NE2 A:HIS171 1.9 25.1 1.0
NE2 A:HIS97 2.1 27.3 1.0
NE2 A:HIS95 2.1 28.6 1.0
O A:HOH308 2.5 31.9 1.0
CE1 A:HIS171 2.8 25.0 1.0
CE1 A:HIS97 3.0 27.2 1.0
CD2 A:HIS171 3.0 24.1 1.0
CE1 A:HIS95 3.1 28.4 1.0
CD2 A:HIS97 3.1 26.5 1.0
CD2 A:HIS95 3.1 28.2 1.0
ND1 A:HIS171 3.9 24.6 1.0
CG A:HIS171 4.1 24.1 1.0
OD1 A:ASP76 4.1 33.8 1.0
ND1 A:HIS97 4.2 27.0 1.0
ND1 A:HIS95 4.2 28.8 1.0
CG A:HIS97 4.2 26.0 1.0
CG A:HIS95 4.3 28.7 1.0
OD2 A:ASP76 4.7 33.6 1.0
CG A:ASP76 4.8 33.2 1.0

Zinc binding site 2 out of 6 in 1jdi

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Zinc binding site 2 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase


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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:32.7
occ:1.00
NE2 B:HIS97 2.0 28.8 1.0
NE2 B:HIS171 2.1 25.2 1.0
NE2 B:HIS95 2.1 26.3 1.0
CE1 B:HIS97 2.9 28.7 1.0
CE1 B:HIS171 3.0 25.1 1.0
CD2 B:HIS171 3.0 24.6 1.0
CE1 B:HIS95 3.1 25.5 1.0
CD2 B:HIS97 3.1 27.8 1.0
CD2 B:HIS95 3.2 26.6 1.0
O B:HOH325 3.6 32.9 1.0
ND1 B:HIS97 4.0 28.6 1.0
ND1 B:HIS171 4.1 25.1 1.0
CG B:HIS97 4.2 26.9 1.0
CG B:HIS171 4.2 24.9 1.0
ND1 B:HIS95 4.2 26.3 1.0
OD1 B:ASP76 4.2 29.4 1.0
CG B:HIS95 4.3 26.3 1.0
OD2 B:ASP76 4.7 30.2 1.0
CG B:ASP76 4.9 29.4 1.0

Zinc binding site 3 out of 6 in 1jdi

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Zinc binding site 3 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase


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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:29.0
occ:1.00
NE2 C:HIS97 1.9 22.6 1.0
NE2 C:HIS171 2.1 19.1 1.0
NE2 C:HIS95 2.2 22.2 1.0
CE1 C:HIS97 2.7 23.3 1.0
O C:HOH312 2.9 24.4 1.0
CE1 C:HIS171 3.1 20.7 1.0
CD2 C:HIS171 3.1 20.9 1.0
CD2 C:HIS97 3.1 23.0 1.0
CE1 C:HIS95 3.1 20.2 1.0
CD2 C:HIS95 3.2 20.9 1.0
ND1 C:HIS97 3.9 23.5 1.0
CG C:HIS97 4.1 22.9 1.0
ND1 C:HIS171 4.2 20.6 1.0
OD1 C:ASP76 4.2 27.0 1.0
CG C:HIS171 4.2 20.1 1.0
ND1 C:HIS95 4.2 20.9 1.0
CG C:HIS95 4.3 21.0 1.0
OD2 C:ASP76 4.9 27.1 1.0
CG C:ASP76 5.0 27.7 1.0

Zinc binding site 4 out of 6 in 1jdi

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Zinc binding site 4 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn304

b:28.3
occ:1.00
NE2 D:HIS171 2.0 20.3 1.0
NE2 D:HIS97 2.1 21.1 1.0
NE2 D:HIS95 2.1 20.3 1.0
CE1 D:HIS171 3.0 20.4 1.0
CE1 D:HIS97 3.0 20.7 1.0
CD2 D:HIS171 3.0 20.4 1.0
CE1 D:HIS95 3.1 20.7 1.0
CD2 D:HIS97 3.1 21.1 1.0
CD2 D:HIS95 3.2 20.8 1.0
O D:HOH359 3.8 38.3 1.0
ND1 D:HIS171 4.1 19.3 1.0
ND1 D:HIS97 4.1 20.0 1.0
O D:HOH400 4.1 35.6 1.0
CG D:HIS171 4.1 19.3 1.0
OD1 D:ASP76 4.2 25.9 1.0
ND1 D:HIS95 4.2 20.4 1.0
CG D:HIS97 4.2 21.4 1.0
CG D:HIS95 4.3 20.2 1.0
OD2 D:ASP76 4.7 26.8 1.0
CG D:ASP76 4.8 24.8 1.0

Zinc binding site 5 out of 6 in 1jdi

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Zinc binding site 5 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn305

b:41.1
occ:1.00
NE2 E:HIS171 2.0 38.4 1.0
NE2 E:HIS95 2.1 41.0 1.0
NE2 E:HIS97 2.3 37.4 1.0
CE1 E:HIS171 2.8 39.7 1.0
CE1 E:HIS95 3.1 42.3 1.0
CD2 E:HIS171 3.1 37.5 1.0
CD2 E:HIS95 3.1 42.7 1.0
O E:HOH354 3.1 31.5 1.0
CE1 E:HIS97 3.2 38.1 1.0
CD2 E:HIS97 3.3 37.8 1.0
ND1 E:HIS171 4.0 37.5 1.0
OD1 E:ASP76 4.1 46.7 1.0
CG E:HIS171 4.1 36.8 1.0
ND1 E:HIS95 4.2 42.5 1.0
CG E:HIS95 4.3 41.9 1.0
ND1 E:HIS97 4.3 37.4 1.0
CG E:HIS97 4.4 37.0 1.0
OD2 E:ASP76 4.6 46.5 1.0
CG E:ASP76 4.8 46.3 1.0

Zinc binding site 6 out of 6 in 1jdi

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Zinc binding site 6 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn306

b:69.2
occ:1.00
NE2 F:HIS171 2.1 63.7 1.0
NE2 F:HIS95 2.2 58.8 1.0
NE2 F:HIS97 2.2 55.2 1.0
CE1 F:HIS171 3.0 63.4 1.0
CE1 F:HIS95 3.0 58.8 1.0
CD2 F:HIS171 3.0 62.9 1.0
CE1 F:HIS97 3.1 55.0 1.0
CD2 F:HIS97 3.2 55.6 1.0
CD2 F:HIS95 3.3 59.4 1.0
OD1 F:ASP76 4.0 76.8 1.0
ND1 F:HIS171 4.0 62.9 1.0
CG F:HIS171 4.1 62.3 1.0
ND1 F:HIS95 4.2 59.5 1.0
ND1 F:HIS97 4.3 55.2 1.0
CG F:HIS95 4.3 59.9 1.0
CG F:HIS97 4.4 54.9 1.0
OD2 F:ASP76 4.8 76.8 1.0
CG F:ASP76 4.9 76.7 1.0

Reference:

Y.Luo, J.Samuel, S.C.Mosimann, J.E.Lee, M.E.Tanner, N.C.Strynadka. The Structure of L-Ribulose-5-Phosphate 4-Epimerase: An Aldolase-Like Platform For Epimerization. Biochemistry V. 40 14763 2001.
ISSN: ISSN 0006-2960
PubMed: 11732895
DOI: 10.1021/BI0112513
Page generated: Wed Dec 16 02:53:52 2020

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