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Zinc in PDB 2v9m: L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A)

Enzymatic activity of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A)

All present enzymatic activity of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A):
4.1.2.19;

Protein crystallography data

The structure of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A), PDB code: 2v9m was solved by D.Grueninger, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.30
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 83.407, 83.407, 97.299, 90.00, 90.00, 90.00
R / Rfree (%) 10.4 / 14.1

Other elements in 2v9m:

The structure of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) (pdb code 2v9m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A), PDB code: 2v9m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2v9m

Go back to Zinc Binding Sites List in 2v9m
Zinc binding site 1 out of 4 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1275

b:11.0
occ:1.00
 NE2 A:HIS212 2.0 10.7 1.0
NE2 A:HIS143 2.0 9.1 1.0
NE2 A:HIS141 2.1 9.7 1.0
O A:HOH2408 2.1 18.0 1.0
O A:HOH2246 2.4 33.6 0.8
CD2 A:HIS212 2.9 10.3 1.0
CE1 A:HIS141 3.0 10.6 1.0
CE1 A:HIS143 3.0 8.6 1.0
CD2 A:HIS143 3.1 8.8 1.0
CE1 A:HIS212 3.1 11.5 1.0
CD2 A:HIS141 3.1 10.5 1.0
CG A:HIS212 4.2 10.2 1.0
ND1 A:HIS212 4.2 10.8 1.0
ND1 A:HIS141 4.2 10.3 1.0
ND1 A:HIS143 4.2 8.2 1.0
CG A:HIS143 4.2 7.8 1.0
CG A:HIS141 4.2 9.5 1.0
O A:HOH2080 4.4 64.3 1.0
N A:GLY31 4.5 12.8 1.0
OE1 A:GLU117 4.7 30.2 0.3
CZ3 A:TRP209 4.8 27.4 1.0
CA A:GLY30 5.0 9.6 1.0

Zinc binding site 2 out of 4 in 2v9m

Go back to Zinc Binding Sites List in 2v9m
Zinc binding site 2 out of 4 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1277

b:14.0
occ:1.00
 OD2 A:ASP157 2.0 13.4 1.0
O2 A:CIT1278 2.1 12.0 1.0
CG A:ASP157 2.8 12.3 1.0
O1 A:CIT1278 2.8 27.3 1.0
C1 A:CIT1278 2.8 23.0 1.0
OD1 A:ASP157 3.0 12.5 1.0
C2 A:CIT1278 4.2 27.4 1.0
O A:HOH2282 4.2 25.3 1.0
CB A:ASP157 4.2 13.6 1.0
CB A:ALA159 4.4 11.8 1.0
N A:ALA159 4.4 11.3 1.0
N A:THR158 4.6 11.5 1.0
O A:HOH2283 4.7 30.4 1.0
CA A:ASP157 4.9 12.4 1.0
C A:ASP157 5.0 11.8 1.0

Zinc binding site 3 out of 4 in 2v9m

Go back to Zinc Binding Sites List in 2v9m
Zinc binding site 3 out of 4 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1275

b:9.8
occ:1.00
 NE2 B:HIS212 2.0 8.5 1.0
NE2 B:HIS143 2.0 7.9 1.0
NE2 B:HIS141 2.0 9.2 1.0
O B:HOH2387 2.2 10.6 1.0
O B:HOH2388 2.6 27.8 1.0
CD2 B:HIS212 2.9 9.8 1.0
CE1 B:HIS143 3.0 8.3 1.0
CE1 B:HIS141 3.1 8.9 1.0
CE1 B:HIS212 3.1 9.8 1.0
CD2 B:HIS143 3.1 7.7 1.0
CD2 B:HIS141 3.1 9.5 1.0
CG B:HIS212 4.1 8.1 1.0
ND1 B:HIS143 4.2 7.5 1.0
ND1 B:HIS212 4.2 9.5 1.0
N B:GLY31 4.2 9.9 1.0
ND1 B:HIS141 4.2 8.8 1.0
CG B:HIS143 4.2 6.8 1.0
CG B:HIS141 4.2 8.8 1.0
O B:HOH2065 4.3 56.0 1.0
CZ3 B:TRP209 4.8 19.1 1.0
CA B:GLY31 4.8 10.5 1.0
CA B:GLY30 4.9 9.3 1.0
CE3 B:TRP209 5.0 15.4 1.0

Zinc binding site 4 out of 4 in 2v9m

Go back to Zinc Binding Sites List in 2v9m
Zinc binding site 4 out of 4 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1276

b:10.4
occ:1.00
 OE2 B:GLU200 1.9 10.6 1.0
NE2 B:HIS204 2.0 9.3 1.0
CD B:GLU200 2.9 9.8 1.0
CD2 B:HIS204 2.9 9.5 1.0
CE1 B:HIS204 3.0 9.6 1.0
OE1 B:GLU200 3.1 12.7 1.0
CA B:GLY181 4.0 9.6 1.0
CG B:HIS204 4.1 8.8 1.0
ND1 B:HIS204 4.1 9.6 1.0
CG B:GLU200 4.2 10.4 1.0
CB B:LYS203 4.4 12.8 0.6
CB B:LYS203 4.5 12.6 0.4
CB B:GLU200 4.6 10.2 1.0
CA B:GLU200 4.7 10.0 1.0
CG2 B:THR158 4.8 9.7 1.0
O B:GLU200 4.8 10.3 1.0
OG1 B:THR158 4.9 10.5 1.0
N B:GLY181 4.9 8.9 1.0
C B:GLY181 5.0 10.3 1.0

Reference:

D.Grueninger, N.Treiber, M.O.P.Ziegler, J.W.A.Koetter, M.-S.Schulze, G.E.Schulz. Designed Protein-Protein Association. Science V. 319 206 2008.
ISSN: ISSN 0036-8075
PubMed: 18187656
DOI: 10.1126/SCIENCE.1150421
Page generated: Wed Dec 16 03:54:52 2020

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