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Zinc in PDB 3qc3: Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution

Enzymatic activity of Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution

All present enzymatic activity of Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution:
5.1.3.1;

Protein crystallography data

The structure of Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution, PDB code: 3qc3 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.13 / 2.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 47.665, 47.665, 220.774, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.1

Other elements in 3qc3:

The structure of Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution (pdb code 3qc3). 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 D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution, PDB code: 3qc3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3qc3

Go back to Zinc Binding Sites List in 3qc3
Zinc binding site 1 out of 2 in the Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution


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 D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn229

b:41.4
occ:0.45
 FE A:FE231 0.2 40.4 0.2
NI A:NI230 0.2 40.6 0.3
OD1 A:ASP37 2.0 38.6 1.0
NE2 A:HIS35 2.1 34.8 1.0
OD2 A:ASP175 2.1 36.7 1.0
ND1 A:HIS70 2.1 35.9 1.0
O1 A:GOL232 2.3 64.1 1.0
O A:HOH463 2.3 42.0 1.0
CD2 A:HIS35 3.0 33.5 1.0
CE1 A:HIS70 3.0 38.4 1.0
CG A:ASP37 3.1 38.0 1.0
CG A:ASP175 3.1 40.5 1.0
CE1 A:HIS35 3.1 36.0 1.0
CG A:HIS70 3.1 34.5 1.0
OD2 A:ASP37 3.4 45.2 1.0
C1 A:GOL232 3.5 68.0 1.0
CB A:HIS70 3.5 34.2 1.0
OD1 A:ASP175 3.5 42.7 1.0
CE A:MSE72 4.1 35.0 1.0
CG A:HIS35 4.1 35.1 1.0
NE2 A:HIS70 4.2 35.3 1.0
ND1 A:HIS35 4.2 35.7 1.0
CD2 A:HIS70 4.2 35.2 1.0
CB A:ASP37 4.3 37.3 1.0
CB A:ASP175 4.4 39.7 1.0
O2 A:GOL232 4.6 71.4 1.0
C2 A:GOL232 4.6 69.5 1.0
OG A:SER10 4.8 41.7 0.5
CA A:ASP37 4.8 36.3 1.0
CD2 A:LEU139 4.9 31.9 1.0
CG1 A:VAL195 5.0 33.9 1.0

Zinc binding site 2 out of 2 in 3qc3

Go back to Zinc Binding Sites List in 3qc3
Zinc binding site 2 out of 2 in the Crystal Structure of A D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution


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 D-Ribulose-5-Phosphate-3-Epimerase (NP_954699) From Homo Sapiens at 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn229

b:39.7
occ:0.45
 NI B:NI230 0.1 37.0 0.3
FE B:FE231 0.2 34.1 0.2
OD2 B:ASP175 2.0 38.8 1.0
OD1 B:ASP37 2.1 38.3 1.0
NE2 B:HIS35 2.1 32.8 1.0
ND1 B:HIS70 2.2 30.8 1.0
O3 B:GOL232 2.3 59.1 1.0
O B:HOH456 2.4 38.2 1.0
CG B:ASP175 3.0 37.1 1.0
CD2 B:HIS35 3.0 34.0 1.0
CE1 B:HIS70 3.1 35.2 1.0
CG B:ASP37 3.1 38.1 1.0
CE1 B:HIS35 3.2 34.7 1.0
CG B:HIS70 3.2 33.1 1.0
OD1 B:ASP175 3.4 42.2 1.0
C3 B:GOL232 3.4 60.8 1.0
CB B:HIS70 3.5 33.0 1.0
OD2 B:ASP37 3.5 42.6 1.0
CE B:MSE72 4.1 35.0 1.0
CG B:HIS35 4.2 34.3 1.0
ND1 B:HIS35 4.2 33.3 1.0
NE2 B:HIS70 4.2 34.9 1.0
CB B:ASP175 4.3 36.3 1.0
CD2 B:HIS70 4.3 33.1 1.0
CB B:ASP37 4.4 38.2 1.0
O2 B:GOL232 4.6 62.7 1.0
C2 B:GOL232 4.6 61.4 1.0
CA B:ASP37 4.9 36.7 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Oct 26 12:03:28 2024

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