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Zinc in PDB 7u5y: Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa

Enzymatic activity of Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa:
5.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa, PDB code: 7u5y was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.03 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.01, 110.13, 126.76, 90, 90, 90
R / Rfree (%) 20.3 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa (pdb code 7u5y). 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 Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa, PDB code: 7u5y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7u5y

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Zinc binding site 1 out of 6 in the Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa


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 Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:55.0
occ:0.50
 OD1 A:ASP36 2.1 49.2 1.0
ND1 A:HIS68 2.3 46.3 1.0
NE2 A:HIS34 2.3 48.0 1.0
OD2 A:ASP177 2.8 54.9 1.0
CG A:ASP36 3.2 52.4 1.0
CD2 A:HIS34 3.2 48.0 1.0
CE1 A:HIS68 3.3 48.2 1.0
CG A:HIS68 3.3 46.4 1.0
CE1 A:HIS34 3.3 47.0 1.0
O A:HOH405 3.3 49.6 1.0
CB A:HIS68 3.5 44.8 1.0
OD2 A:ASP36 3.6 55.4 1.0
CG A:ASP177 4.0 53.2 1.0
CE A:MET70 4.3 48.7 1.0
NE2 A:HIS68 4.4 46.5 1.0
CG A:HIS34 4.4 51.1 1.0
ND1 A:HIS34 4.4 48.5 1.0
CD2 A:HIS68 4.4 46.7 1.0
CD2 A:LEU137 4.4 42.7 1.0
CB A:ASP36 4.5 50.4 1.0
CB A:ASP177 4.7 50.4 1.0
CA A:ASP36 4.8 48.3 1.0
SD A:MET139 4.9 55.0 1.0
OD1 A:ASP177 4.9 52.9 1.0

Zinc binding site 2 out of 6 in 7u5y

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Zinc binding site 2 out of 6 in the Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa


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 Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:81.0
occ:0.57
 OD1 B:ASP36 2.2 69.8 1.0
NE2 B:HIS34 2.3 63.0 1.0
ND1 B:HIS68 2.3 62.3 1.0
OD2 B:ASP177 2.8 69.2 1.0
CE1 B:HIS34 3.2 61.9 1.0
CE1 B:HIS68 3.2 57.9 1.0
CG B:ASP36 3.3 67.7 1.0
CG B:HIS68 3.3 57.9 1.0
CD2 B:HIS34 3.3 61.6 1.0
O B:HOH418 3.5 63.9 1.0
CB B:HIS68 3.6 60.5 1.0
OD2 B:ASP36 3.7 70.6 1.0
CG B:ASP177 3.9 71.0 1.0
CD2 B:LEU137 4.2 58.7 1.0
ND1 B:HIS34 4.4 62.0 1.0
NE2 B:HIS68 4.4 59.7 1.0
CE B:MET70 4.4 61.1 1.0
CD2 B:HIS68 4.4 58.1 1.0
CG B:HIS34 4.5 64.6 1.0
CB B:ASP177 4.5 67.7 1.0
CB B:ASP36 4.5 64.1 1.0
SD B:MET139 4.6 63.8 1.0
CA B:ASP36 4.9 63.0 1.0
OD1 B:ASP177 4.9 73.0 1.0

Zinc binding site 3 out of 6 in 7u5y

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Zinc binding site 3 out of 6 in the Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa


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 Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:116.1
occ:0.45
 OD1 C:ASP36 2.1 63.2 1.0
NE2 C:HIS34 2.3 64.5 1.0
ND1 C:HIS68 2.3 61.2 1.0
OD2 C:ASP177 3.0 72.5 1.0
CG C:HIS68 3.1 53.8 1.0
CB C:HIS68 3.2 52.2 1.0
CE1 C:HIS34 3.2 63.0 1.0
CG C:ASP36 3.2 66.1 1.0
CD2 C:HIS34 3.3 62.6 1.0
CE1 C:HIS68 3.4 54.6 1.0
OD2 C:ASP36 3.8 68.8 1.0
CG C:ASP177 4.1 73.0 1.0
CE C:MET70 4.2 51.0 1.0
CD2 C:LEU137 4.2 57.7 1.0
CD2 C:HIS68 4.3 55.0 1.0
ND1 C:HIS34 4.4 60.2 1.0
CB C:ASP36 4.4 61.9 1.0
NE2 C:HIS68 4.5 54.5 1.0
CG C:HIS34 4.5 60.1 1.0
CA C:ASP36 4.7 56.5 1.0
CA C:HIS68 4.7 53.2 1.0
CB C:ASP177 4.9 64.5 1.0
OD1 C:ASP177 4.9 70.9 1.0

Zinc binding site 4 out of 6 in 7u5y

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Zinc binding site 4 out of 6 in the Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa


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 Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:72.2
occ:0.58
 OD1 D:ASP36 2.1 64.9 1.0
NE2 D:HIS34 2.3 61.4 1.0
ND1 D:HIS68 2.3 58.0 1.0
OD2 D:ASP177 2.9 67.1 1.0
CG D:HIS68 3.2 55.0 1.0
CE1 D:HIS34 3.3 55.1 1.0
CG D:ASP36 3.3 63.6 1.0
CD2 D:HIS34 3.3 60.2 1.0
CE1 D:HIS68 3.4 54.0 1.0
CB D:HIS68 3.4 52.5 1.0
OD2 D:ASP36 3.8 67.0 1.0
CG D:ASP177 4.1 63.8 1.0
CE D:MET70 4.4 51.6 1.0
CD2 D:LEU137 4.4 52.4 1.0
CD2 D:HIS68 4.4 50.7 1.0
ND1 D:HIS34 4.4 57.3 1.0
NE2 D:HIS68 4.4 49.6 1.0
CG D:HIS34 4.5 60.3 1.0
CB D:ASP36 4.5 57.9 1.0
CA D:ASP36 4.7 56.7 1.0
CB D:ASP177 4.8 58.6 1.0
CA D:HIS68 4.9 50.3 1.0
OD1 D:ASP177 4.9 64.8 1.0
SD D:MET139 5.0 60.8 1.0

Zinc binding site 5 out of 6 in 7u5y

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Zinc binding site 5 out of 6 in the Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa


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 Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn300

b:94.0
occ:0.53
 OD1 E:ASP36 2.2 72.8 1.0
NE2 E:HIS34 2.3 71.0 1.0
ND1 E:HIS68 2.3 70.6 1.0
OD2 E:ASP177 3.0 78.5 1.0
CG E:ASP36 3.2 73.6 1.0
CD2 E:HIS34 3.3 69.1 1.0
CE1 E:HIS68 3.3 65.3 1.0
CE1 E:HIS34 3.3 70.9 1.0
CG E:HIS68 3.3 64.0 1.0
CB E:HIS68 3.5 64.4 1.0
OD2 E:ASP36 3.6 80.7 1.0
CG E:ASP177 4.0 77.6 1.0
CD2 E:LEU137 4.1 68.7 1.0
ND1 E:HIS34 4.4 70.8 1.0
NE2 E:HIS68 4.4 63.0 1.0
CG E:HIS34 4.4 70.0 1.0
CD2 E:HIS68 4.4 61.9 1.0
CB E:ASP177 4.5 76.5 1.0
CB E:ASP36 4.5 67.6 1.0
CE E:MET70 4.6 59.7 1.0
SD E:MET139 4.8 74.9 1.0
CA E:ASP36 4.9 63.9 1.0

Zinc binding site 6 out of 6 in 7u5y

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Zinc binding site 6 out of 6 in the Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa


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 Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn300

b:77.5
occ:0.49
 OD1 F:ASP36 2.2 68.7 1.0
ND1 F:HIS68 2.3 67.0 1.0
NE2 F:HIS34 2.3 70.8 1.0
OD2 F:ASP177 2.7 75.5 1.0
CD2 F:HIS34 3.2 70.4 1.0
CG F:ASP36 3.3 68.3 1.0
CE1 F:HIS68 3.3 61.4 1.0
CG F:HIS68 3.3 61.7 1.0
CE1 F:HIS34 3.4 70.4 1.0
CB F:HIS68 3.5 61.6 1.0
OD2 F:ASP36 3.6 77.0 1.0
CG F:ASP177 3.9 73.8 1.0
CD2 F:LEU137 4.2 64.1 1.0
NE2 F:HIS68 4.4 60.7 1.0
CG F:HIS34 4.4 71.8 1.0
CD2 F:HIS68 4.4 58.3 1.0
CE F:MET70 4.4 59.6 1.0
ND1 F:HIS34 4.4 71.4 1.0
CB F:ASP177 4.5 70.0 1.0
CB F:ASP36 4.6 64.0 1.0
OD1 F:ASP177 4.8 76.0 1.0
SD F:MET139 4.9 64.8 1.0
CA F:ASP36 4.9 62.9 1.0

Reference:

J.Abendroth, D.R.Davies, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Ribulose-Phosphate 3-Epimerase From Pseudomonas Aeruginosa To Be Published.
Page generated: Fri Aug 22 05:10:30 2025

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