Zinc in PDB 7ye3: Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes

Enzymatic activity of Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes

All present enzymatic activity of Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes:
5.3.1.17;

Protein crystallography data

The structure of Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes, PDB code: 7ye3 was solved by Y.Yamamoto, S.Oiki, R.Takase, B.Mikami, W.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.57 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.035, 189.102, 114.852, 90, 107.12, 90
R / Rfree (%) 19.3 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes (pdb code 7ye3). 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 Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes, PDB code: 7ye3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7ye3

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Zinc binding site 1 out of 6 in the Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes


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 Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:88.5
occ:1.00
 OE1 A:GLU205 1.9 113.9 1.0
NE2 A:HIS248 2.3 82.2 1.0
NE2 A:HIS200 2.4 90.3 1.0
NE2 A:HIS198 2.4 91.3 1.0
CD2 A:HIS248 2.7 78.0 1.0
CD2 A:HIS200 2.9 88.4 1.0
CD A:GLU205 2.9 99.3 1.0
CE1 A:HIS198 3.3 89.4 1.0
CD2 A:HIS198 3.3 94.8 1.0
CG A:GLU205 3.4 77.2 1.0
CE1 A:HIS248 3.5 87.4 1.0
CE1 A:HIS200 3.6 90.7 1.0
CE A:MET262 3.8 92.0 1.0
C2 A:MES302 3.9 134.6 1.0
OE2 A:GLU205 4.0 106.9 1.0
CG A:HIS248 4.0 74.7 1.0
CG A:HIS200 4.2 91.9 1.0
CB A:GLU205 4.3 63.3 1.0
ND1 A:HIS248 4.4 83.7 1.0
C3 A:MES302 4.4 133.0 1.0
ND1 A:HIS198 4.4 89.4 1.0
CG A:HIS198 4.4 95.5 1.0
O1 A:MES302 4.5 133.2 1.0
ND1 A:HIS200 4.5 95.4 1.0
OH A:TYR207 4.6 85.1 1.0

Zinc binding site 2 out of 6 in 7ye3

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Zinc binding site 2 out of 6 in the Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes


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 Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:105.8
occ:1.00
 OE2 B:GLU205 1.9 133.2 1.0
NE2 B:HIS198 2.1 86.0 1.0
NE2 B:HIS200 2.4 90.9 1.0
NE2 B:HIS248 2.4 104.0 1.0
CD2 B:HIS248 2.4 104.5 1.0
CD B:GLU205 2.9 108.5 1.0
CD2 B:HIS198 3.0 83.8 1.0
CD2 B:HIS200 3.1 88.2 1.0
CE1 B:HIS198 3.2 87.9 1.0
CG B:GLU205 3.4 97.4 1.0
CE1 B:HIS200 3.5 87.9 1.0
CE1 B:HIS248 3.7 107.6 1.0
CG B:HIS248 3.8 105.8 1.0
CE B:MET262 3.8 79.4 1.0
OE1 B:GLU205 4.1 103.7 1.0
CG B:HIS198 4.2 88.9 1.0
ND1 B:HIS198 4.3 89.5 1.0
CG B:HIS200 4.3 87.6 1.0
CB B:GLU205 4.4 89.0 1.0
ND1 B:HIS248 4.4 108.9 1.0
OH B:TYR207 4.4 96.1 1.0
ND1 B:HIS200 4.5 85.6 1.0
O1 B:MES302 4.6 101.2 1.0
C2 B:MES302 4.6 105.5 1.0
CE B:MET272 4.8 124.5 1.0
CB B:HIS248 4.9 100.7 1.0

Zinc binding site 3 out of 6 in 7ye3

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Zinc binding site 3 out of 6 in the Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes


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 Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:97.2
occ:1.00
 OE1 C:GLU205 1.9 110.3 1.0
NE2 C:HIS198 2.0 103.0 1.0
NE2 C:HIS200 2.4 89.5 1.0
CD2 C:HIS198 2.9 88.4 1.0
CD C:GLU205 3.0 80.6 1.0
CE1 C:HIS198 3.0 87.5 1.0
NE2 C:HIS248 3.1 94.8 1.0
CD2 C:HIS200 3.2 90.5 1.0
CD2 C:HIS248 3.4 88.5 1.0
CE1 C:HIS200 3.5 92.9 1.0
CG C:GLU205 3.5 72.6 1.0
CE1 C:HIS248 3.5 101.4 1.0
CG C:HIS248 3.9 92.3 1.0
OE2 C:GLU205 4.0 74.1 1.0
ND1 C:HIS248 4.0 97.0 1.0
ND1 C:HIS198 4.1 84.3 1.0
CG C:HIS198 4.1 78.9 1.0
CG C:HIS200 4.4 90.6 1.0
CB C:GLU205 4.4 67.9 1.0
ND1 C:HIS200 4.5 92.1 1.0
C6 C:MES302 4.6 113.5 1.0
OH C:TYR207 4.7 67.8 1.0
O1 C:MES302 4.8 111.0 1.0
CB C:HIS248 4.9 91.1 1.0

Zinc binding site 4 out of 6 in 7ye3

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Zinc binding site 4 out of 6 in the Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes


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 Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:129.9
occ:1.00
 OE2 D:GLU205 1.8 150.8 1.0
CD D:GLU205 2.7 122.8 1.0
CD2 D:HIS248 2.8 92.6 1.0
NE2 D:HIS248 2.9 96.0 1.0
NE2 D:HIS200 3.1 151.2 1.0
CG D:GLU205 3.1 95.8 1.0
CD2 D:HIS200 3.4 150.2 1.0
CG D:HIS248 3.8 93.8 1.0
CE D:MET262 3.9 107.9 1.0
OE1 D:GLU205 3.9 127.7 1.0
CE1 D:HIS200 4.0 153.1 1.0
CE1 D:HIS248 4.0 99.5 1.0
CB D:GLU205 4.1 80.4 1.0
OH D:TYR207 4.4 81.8 1.0
ND1 D:HIS248 4.4 102.0 1.0
CG D:HIS200 4.4 147.4 1.0
ND1 D:HIS200 4.7 153.6 1.0
CB D:HIS248 4.8 82.7 1.0

Zinc binding site 5 out of 6 in 7ye3

Go back to Zinc Binding Sites List in 7ye3
Zinc binding site 5 out of 6 in the Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes


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 Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:126.0
occ:1.00
 OE2 E:GLU205 2.1 100.4 1.0
NE2 E:HIS248 3.1 73.4 1.0
CE1 E:HIS198 3.1 129.4 1.0
CE1 E:HIS248 3.2 70.3 1.0
CD E:GLU205 3.2 86.2 1.0
CD2 E:HIS200 3.3 117.6 1.0
NE2 E:HIS200 3.4 123.0 1.0
CD2 E:HIS248 3.5 75.8 1.0
ND1 E:HIS248 3.6 79.2 1.0
ND1 E:HIS198 3.7 128.7 1.0
CG E:GLU205 3.8 86.8 1.0
CG E:HIS248 3.8 82.8 1.0
CG E:HIS200 3.9 114.0 1.0
CE1 E:HIS200 4.0 123.6 1.0
OE1 E:GLU205 4.2 75.9 1.0
ND1 E:HIS200 4.2 122.5 1.0
NE2 E:HIS198 4.3 134.4 1.0
OH E:TYR207 4.5 84.4 1.0
CB E:HIS200 4.7 106.5 1.0
CB E:GLU205 4.7 77.6 1.0
CB E:HIS248 4.8 92.6 1.0

Zinc binding site 6 out of 6 in 7ye3

Go back to Zinc Binding Sites List in 7ye3
Zinc binding site 6 out of 6 in the Crystal Structure of Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes


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 Lactobacillus Rhamnosus 4-Deoxy-L-Threo-5- Hexosulose-Uronate Ketol-Isomerase Kdui Complexed with Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:100.6
occ:1.00
 OE2 F:GLU205 1.9 134.6 1.0
NE2 F:HIS198 2.3 97.6 1.0
NE2 F:HIS200 2.4 75.7 1.0
NE2 F:HIS248 2.4 84.6 1.0
CD2 F:HIS200 2.8 75.0 1.0
CD F:GLU205 2.9 100.1 1.0
CD2 F:HIS248 3.0 83.1 1.0
CD2 F:HIS198 3.2 100.4 1.0
CE1 F:HIS198 3.3 101.5 1.0
CG F:GLU205 3.4 85.0 1.0
CE1 F:HIS248 3.6 86.4 1.0
CE1 F:HIS200 3.6 82.0 1.0
CE F:MET262 3.8 99.0 1.0
OE1 F:GLU205 4.0 87.3 1.0
CG F:HIS200 4.1 77.8 1.0
CG F:HIS248 4.2 90.0 1.0
CG F:HIS198 4.3 103.3 1.0
ND1 F:HIS198 4.3 104.7 1.0
O1 F:MES302 4.4 108.5 1.0
O F:HIS198 4.4 138.1 1.0
CB F:GLU205 4.5 74.8 1.0
ND1 F:HIS200 4.5 83.5 1.0
ND1 F:HIS248 4.5 88.0 1.0
C2 F:MES302 4.7 109.9 1.0
OH F:TYR207 4.7 91.1 1.0
C3 F:MES302 4.9 111.2 1.0

Reference:

H.Iwase, Y.Yamamoto, A.Yamada, K.Kawai, S.Oiki, B.Mikami, R.Takase, W.Hashimoto. Lactobacillus Enzymes For Degradation and Metabolism of Glycosaminoglycan Heparin To Be Published.
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