Zinc in PDB 4qqr: Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana

Protein crystallography data

The structure of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana, PDB code: 4qqr was solved by X.Han, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.78 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.589, 61.943, 176.774, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 26.5

Other elements in 4qqr:

The structure of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana (pdb code 4qqr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana, PDB code: 4qqr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4qqr

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Zinc binding site 1 out of 7 in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:79.8
occ:1.00
 NE2 A:HIS123 2.4 54.2 1.0
OD2 A:ASP135 2.5 52.8 1.0
CD2 A:HIS123 3.1 53.5 1.0
CG A:ASP135 3.3 52.5 1.0
OD1 A:ASP135 3.4 55.4 1.0
CL A:CL405 3.5 82.8 1.0
CE1 A:HIS123 3.6 52.7 1.0
O A:GLY130 4.0 52.1 1.0
N A:LYS132 4.3 51.3 1.0
CG A:HIS123 4.3 53.7 1.0
CA A:PHE131 4.5 47.1 1.0
ND1 A:HIS123 4.6 51.7 1.0
CD1 A:PHE131 4.7 43.4 1.0
CB A:ASP135 4.7 51.4 1.0
CG A:LYS132 4.7 52.4 1.0
CB A:LYS132 4.8 53.1 1.0
C A:GLY130 4.8 49.4 1.0
C A:PHE131 4.9 50.0 1.0
CD A:LYS132 5.0 59.7 1.0

Zinc binding site 2 out of 7 in 4qqr

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Zinc binding site 2 out of 7 in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:64.0
occ:1.00
 OE2 B:GLU80 2.4 52.7 1.0
OE2 A:GLU159 2.5 45.6 1.0
OE1 B:GLU80 2.8 52.5 1.0
OE1 A:GLU159 2.8 44.4 1.0
CD B:GLU80 3.0 53.4 1.0
CD A:GLU159 3.0 47.7 1.0
NH2 A:ARG102 3.9 50.5 1.0
CG B:GLU80 4.5 50.8 1.0
CG A:GLU159 4.5 46.9 1.0
CZ A:ARG102 4.6 46.6 1.0
NE A:ARG102 4.7 49.7 1.0
O A:HOH513 4.7 45.0 1.0

Zinc binding site 3 out of 7 in 4qqr

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Zinc binding site 3 out of 7 in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:60.7
occ:1.00
 OD2 A:ASP77 1.7 50.1 1.0
ND1 A:HIS82 2.5 54.0 1.0
SG A:CYS79 2.6 46.8 1.0
CG A:ASP77 2.7 56.7 1.0
OD1 A:ASP77 3.2 53.9 1.0
CG A:HIS82 3.3 51.4 1.0
CB A:CYS79 3.3 45.3 1.0
CE1 A:HIS82 3.4 57.0 1.0
CB A:HIS82 3.5 51.5 1.0
N A:CYS79 3.8 47.7 1.0
O A:ASP77 3.9 53.7 1.0
CB A:ASP77 4.0 56.8 1.0
CA A:CYS79 4.1 49.0 1.0
N A:HIS82 4.3 44.4 1.0
C A:ASP77 4.3 59.5 1.0
CD2 A:HIS82 4.4 59.7 1.0
NE2 A:HIS82 4.5 61.8 1.0
CA A:HIS82 4.5 47.0 1.0
C A:CYS79 4.7 47.6 1.0
CA A:ASP77 4.7 60.9 1.0
O A:CYS79 4.9 43.1 1.0

Zinc binding site 4 out of 7 in 4qqr

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Zinc binding site 4 out of 7 in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:89.1
occ:1.00
 SG A:CYS115 2.9 48.7 1.0
N A:ARG73 3.8 79.0 1.0
C A:GLY72 3.9 73.3 1.0
N A:MET168 3.9 43.2 1.0
NH2 A:ARG262 3.9 70.4 1.0
CB A:CYS115 4.1 41.2 1.0
CA A:ARG73 4.2 77.0 1.0
O A:GLY72 4.2 66.6 1.0
CB A:ARG73 4.2 66.8 1.0
CA A:GLY72 4.3 65.5 1.0
CA A:MET168 4.5 43.9 1.0
CG A:MET168 4.6 48.8 1.0
CZ A:ARG262 4.8 75.4 1.0
OG1 A:THR113 4.9 47.4 1.0
CA A:ARG167 4.9 40.3 1.0
NE A:ARG262 4.9 75.1 1.0
C A:ARG167 4.9 39.6 1.0

Zinc binding site 5 out of 7 in 4qqr

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Zinc binding site 5 out of 7 in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:72.5
occ:1.00
 OD2 B:ASP135 2.3 54.1 1.0
NE2 B:HIS123 2.5 53.9 1.0
CG B:ASP135 3.1 56.6 1.0
CD2 B:HIS123 3.3 51.8 1.0
OD1 B:ASP135 3.3 55.9 1.0
CL B:CL404 3.4 73.8 1.0
CE1 B:HIS123 3.5 53.2 1.0
O B:GLY130 4.1 53.9 1.0
N B:LYS132 4.2 57.0 1.0
CA B:PHE131 4.4 50.9 1.0
CG B:HIS123 4.5 56.3 1.0
CB B:ASP135 4.5 53.0 1.0
CD1 B:PHE131 4.6 49.1 1.0
ND1 B:HIS123 4.6 55.0 1.0
C B:PHE131 4.8 55.0 1.0
CB B:LYS132 4.8 55.9 1.0
CD1 B:ILE129 4.9 65.1 1.0
C B:GLY130 4.9 55.1 1.0

Zinc binding site 6 out of 7 in 4qqr

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Zinc binding site 6 out of 7 in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:68.6
occ:1.00
 ND1 B:HIS82 2.5 56.0 1.0
SG B:CYS79 2.5 49.5 1.0
CG B:HIS82 3.4 58.0 1.0
CE1 B:HIS82 3.4 52.4 1.0
N B:CYS79 3.5 46.2 1.0
CB B:CYS79 3.5 49.1 1.0
CB B:HIS82 3.6 49.9 1.0
CA B:CYS79 4.1 54.0 1.0
NE2 B:HIS82 4.5 46.9 1.0
CD2 B:HIS82 4.5 54.0 1.0
C B:TRP78 4.5 52.9 1.0
CA B:TRP78 4.7 52.1 1.0
N B:TRP78 4.8 50.5 1.0
N B:HIS82 4.8 50.3 1.0
C B:CYS79 4.8 50.0 1.0
CA B:HIS82 4.9 47.9 1.0
O B:CYS79 4.9 46.1 1.0

Zinc binding site 7 out of 7 in 4qqr

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Zinc binding site 7 out of 7 in the Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase- Reductase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:95.2
occ:1.00
 O B:HOH526 2.5 36.6 1.0
SG B:CYS115 2.6 41.6 1.0
CB B:CYS115 3.4 41.4 1.0
N B:MET168 4.8 42.3 1.0
CG B:MET168 4.8 42.6 1.0
CA B:CYS115 4.9 43.7 1.0
OG1 B:THR113 5.0 41.0 1.0

Reference:

X.Han, X.Liu. Structural Insight Into Nucleotide Rhamnose Synthase/Epimerase-Reductase From Arabidopsis Thaliana To Be Published.
Page generated: Sun Oct 27 06:44:28 2024

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