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Zinc in PDB 5lu7: Heptose Isomerase Gmha Mutant - D61A

Enzymatic activity of Heptose Isomerase Gmha Mutant - D61A

All present enzymatic activity of Heptose Isomerase Gmha Mutant - D61A:
5.3.1.28;

Protein crystallography data

The structure of Heptose Isomerase Gmha Mutant - D61A, PDB code: 5lu7 was solved by M.Vivoli, N.J.Harmer, J.Pang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.54 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.200, 83.680, 126.100, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Heptose Isomerase Gmha Mutant - D61A (pdb code 5lu7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Heptose Isomerase Gmha Mutant - D61A, PDB code: 5lu7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5lu7

Go back to Zinc Binding Sites List in 5lu7
Zinc binding site 1 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:20.8
occ:0.23
 OE2 A:GLU68 1.9 29.3 1.0
NE2 A:HIS64 1.9 21.2 1.0
NE2 A:HIS183 1.9 19.6 1.0
OE1 D:GLN175 2.1 19.6 1.0
CE1 A:HIS64 2.8 24.4 1.0
CD A:GLU68 2.8 28.9 1.0
CD2 A:HIS183 2.8 20.1 1.0
CE1 A:HIS183 3.0 17.2 1.0
CD2 A:HIS64 3.0 20.2 1.0
OE1 A:GLU68 3.2 34.9 1.0
CD D:GLN175 3.3 23.1 1.0
O3 D:M7P201 3.6 27.8 1.0
NE2 D:GLN175 3.8 15.7 1.0
ND1 A:HIS64 4.0 22.6 1.0
CG A:HIS183 4.0 21.5 1.0
ND1 A:HIS183 4.1 18.5 1.0
CG A:GLU68 4.1 21.6 1.0
CG A:HIS64 4.1 20.9 1.0
CD1 A:LEU179 4.4 18.5 1.0
CG D:GLN175 4.5 18.7 1.0
O D:HOH352 4.6 34.6 1.0
CB D:GLN175 4.6 17.2 1.0
CA D:GLY57 4.8 17.5 1.0
CE1 A:PHE73 5.0 25.2 1.0
CA D:PRO172 5.0 17.2 1.0
C3 D:M7P201 5.0 21.1 1.0

Zinc binding site 2 out of 4 in 5lu7

Go back to Zinc Binding Sites List in 5lu7
Zinc binding site 2 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:26.3
occ:0.28
 OE2 D:GLU68 1.9 32.3 1.0
OE1 A:GLN175 1.9 20.9 1.0
NE2 D:HIS183 2.0 16.6 1.0
NE2 D:HIS64 2.1 26.0 1.0
CE1 D:HIS183 2.9 19.3 1.0
CD D:GLU68 3.0 29.6 1.0
CD2 D:HIS64 3.0 24.8 1.0
CE1 D:HIS64 3.1 22.3 1.0
CD A:GLN175 3.1 20.5 1.0
CD2 D:HIS183 3.1 20.9 1.0
OE1 D:GLU68 3.6 33.0 1.0
NE2 A:GLN175 3.7 18.8 1.0
O3 A:M7P202 3.8 30.1 1.0
ND1 D:HIS183 4.1 15.6 1.0
ND1 D:HIS64 4.1 24.8 1.0
CG D:HIS64 4.2 25.0 1.0
CG D:HIS183 4.2 20.2 1.0
CG D:GLU68 4.2 24.4 1.0
CG A:GLN175 4.3 17.0 1.0
CB A:GLN175 4.4 18.6 1.0
CA A:PRO172 4.6 18.3 1.0
CD1 D:LEU179 4.6 20.6 1.0
CE1 D:PHE73 4.8 21.5 1.0
CA A:GLY57 4.8 18.5 1.0
CB A:PRO172 4.8 25.4 1.0

Zinc binding site 3 out of 4 in 5lu7

Go back to Zinc Binding Sites List in 5lu7
Zinc binding site 3 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:25.8
occ:0.21
 OE1 B:GLU68 1.9 33.7 1.0
OE1 C:GLN175 1.9 19.8 1.0
NE2 B:HIS183 2.0 27.7 1.0
NE2 B:HIS64 2.1 24.5 1.0
O B:HOH302 2.6 33.4 1.0
O C:HOH301 3.0 30.9 1.0
CD2 B:HIS183 3.0 27.3 1.0
CD B:GLU68 3.0 37.1 1.0
CE1 B:HIS183 3.0 19.4 1.0
CE1 B:HIS64 3.0 27.6 1.0
CD C:GLN175 3.0 24.2 1.0
CD2 B:HIS64 3.1 22.8 1.0
OE2 B:GLU68 3.5 40.1 1.0
NE2 C:GLN175 3.6 20.6 1.0
O3 C:M7P201 3.9 26.0 1.0
ND1 B:HIS183 4.1 25.9 1.0
CG B:HIS183 4.1 27.9 1.0
ND1 B:HIS64 4.1 24.8 1.0
CG B:HIS64 4.2 27.0 1.0
CG B:GLU68 4.2 26.6 1.0
CG C:GLN175 4.3 20.0 1.0
CB C:GLN175 4.4 18.4 1.0
CA C:PRO172 4.5 22.4 1.0
CD1 B:LEU179 4.6 22.1 1.0
CB C:PRO172 4.6 29.4 1.0
CA C:GLY57 4.8 19.7 1.0
CE1 B:PHE73 4.8 28.5 1.0

Zinc binding site 4 out of 4 in 5lu7

Go back to Zinc Binding Sites List in 5lu7
Zinc binding site 4 out of 4 in the Heptose Isomerase Gmha Mutant - D61A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Heptose Isomerase Gmha Mutant - D61A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:31.3
occ:0.31
 OE2 C:GLU68 1.9 33.9 1.0
NE2 C:HIS183 2.0 26.9 1.0
OE1 B:GLN175 2.1 22.7 1.0
NE2 C:HIS64 2.1 23.6 1.0
O C:HOH304 2.7 31.1 1.0
CD C:GLU68 2.8 30.1 1.0
CD2 C:HIS183 2.9 17.7 1.0
CD2 C:HIS64 3.0 22.3 1.0
CE1 C:HIS64 3.1 28.4 1.0
CD B:GLN175 3.1 23.2 1.0
CE1 C:HIS183 3.1 25.1 1.0
OE1 C:GLU68 3.2 38.2 1.0
NE2 B:GLN175 3.6 23.7 1.0
O3 B:M7P202 3.7 27.1 1.0
CG C:GLU68 4.0 24.3 1.0
CG C:HIS183 4.1 22.4 1.0
CG C:HIS64 4.1 25.2 1.0
ND1 C:HIS64 4.1 27.8 1.0
ND1 C:HIS183 4.2 18.7 1.0
CG B:GLN175 4.4 19.8 1.0
CB B:GLN175 4.6 20.7 1.0
CD1 C:LEU179 4.7 23.8 1.0
CA B:GLY57 4.7 19.8 1.0
CE1 C:PHE73 4.7 26.1 1.0
CA B:PRO172 4.9 22.1 1.0

Reference:

M.Vivoli, J.Pang, N.J.Harmer. A Half-Site Multimeric Enzyme Achieves Its Cooperativity Without Conformational Changes. Sci Rep V. 7 16529 2017.
ISSN: ESSN 2045-2322
PubMed: 29184087
DOI: 10.1038/S41598-017-16421-2
Page generated: Sun Oct 27 21:27:19 2024

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