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Zinc in PDB 2v9o: 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: 2v9o 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) 44.95 / 1.95
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 86.193, 86.193, 89.873, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.9

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 2v9o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A), PDB code: 2v9o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2v9o

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Zinc binding site 1 out of 6 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:29.5
occ:1.00
 NE2 A:HIS141 2.1 22.9 1.0
NE2 A:HIS212 2.2 26.7 1.0
NE2 A:HIS143 2.2 25.4 1.0
CD2 A:HIS141 3.0 26.9 1.0
CE1 A:HIS141 3.0 30.3 1.0
CD2 A:HIS212 3.1 22.1 1.0
CE1 A:HIS143 3.2 25.9 1.0
CD2 A:HIS143 3.2 22.6 1.0
CE1 A:HIS212 3.3 24.2 1.0
O A:HOH2062 3.4 41.3 1.0
ND1 A:HIS141 4.1 29.2 1.0
N A:GLY31 4.2 29.4 1.0
CG A:HIS141 4.2 27.3 1.0
CG A:HIS212 4.2 27.2 1.0
ND1 A:HIS143 4.3 23.2 1.0
ND1 A:HIS212 4.3 24.3 1.0
CG A:HIS143 4.4 23.9 1.0
OE1 A:GLU117 4.4 31.5 1.0
ND2 A:ASN32 4.7 28.1 1.0
CA A:GLY31 4.7 26.1 1.0
CZ3 A:TRP209 4.9 28.3 1.0
CE3 A:TRP209 5.0 29.5 1.0

Zinc binding site 2 out of 6 in 2v9o

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Zinc binding site 2 out of 6 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:Zn1276

b:55.2
occ:1.00
 OG1 A:THR115 3.5 31.4 1.0
O A:HOH2039 3.6 24.3 1.0
ND2 A:ASN29 3.6 30.9 1.0
O A:ASN29 3.8 29.7 1.0
N A:GLY76 3.8 27.5 1.0
OG A:SER116 3.9 37.7 1.0
ND2 A:ASN32 3.9 28.1 1.0
CA A:SER75 4.1 27.8 1.0
N A:SER116 4.1 30.4 1.0
O A:HOH2044 4.2 29.7 1.0
O A:GLY74 4.4 27.3 1.0
CB A:THR115 4.4 30.7 1.0
O A:GLY31 4.4 28.1 1.0
C A:SER75 4.5 27.5 1.0
CA A:THR115 4.5 29.6 1.0
CB A:ASN29 4.6 27.9 1.0
CG A:ASN29 4.6 31.6 1.0
OG A:SER75 4.6 31.8 1.0
CB A:SER116 4.8 30.2 1.0
CG A:ASN32 4.8 28.8 1.0
C A:THR115 4.9 30.5 1.0
CB A:SER75 4.9 27.2 1.0
CB A:ASN32 4.9 26.4 1.0
CA A:GLY76 4.9 26.1 1.0
C A:ASN29 4.9 29.1 1.0
N A:SER75 5.0 25.4 1.0

Zinc binding site 3 out of 6 in 2v9o

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Zinc binding site 3 out of 6 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
E:Zn1275

b:35.5
occ:1.00
 O E:HOH2115 1.7 49.3 1.0
NE2 E:HIS141 2.0 25.1 1.0
NE2 E:HIS143 2.2 26.9 1.0
NE2 E:HIS212 2.3 28.3 1.0
CD2 E:HIS141 2.9 26.6 1.0
CD2 E:HIS212 3.0 23.3 1.0
CE1 E:HIS141 3.1 29.7 1.0
CE1 E:HIS143 3.1 27.2 1.0
CD2 E:HIS143 3.2 24.0 1.0
CE1 E:HIS212 3.4 23.9 1.0
O E:HOH2070 3.9 40.4 1.0
CG E:HIS141 4.1 27.8 1.0
ND1 E:HIS141 4.1 29.6 1.0
N E:GLY31 4.1 29.4 1.0
CG E:HIS212 4.2 27.5 1.0
ND1 E:HIS143 4.3 23.9 1.0
CG E:HIS143 4.3 23.9 1.0
ND1 E:HIS212 4.4 25.4 1.0
OE1 E:GLU117 4.6 32.1 1.0
CA E:GLY31 4.7 26.3 1.0
ND2 E:ASN32 4.8 28.5 1.0
CZ3 E:TRP209 4.8 28.3 1.0
CE3 E:TRP209 4.9 28.6 1.0

Zinc binding site 4 out of 6 in 2v9o

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Zinc binding site 4 out of 6 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
E:Zn1276

b:61.4
occ:1.00
 ND2 E:ASN29 3.5 29.6 1.0
N E:GLY76 3.6 27.1 1.0
O E:ASN29 3.7 30.5 1.0
O E:HOH2046 3.7 28.8 1.0
OG E:SER116 3.8 36.6 1.0
OG1 E:THR115 3.9 29.8 1.0
CA E:SER75 4.1 28.6 1.0
ND2 E:ASN32 4.1 28.5 1.0
O E:HOH2050 4.2 32.5 1.0
C E:SER75 4.3 28.5 1.0
N E:SER116 4.4 29.9 1.0
O E:GLY74 4.4 28.9 1.0
O E:GLY31 4.4 26.7 1.0
CG E:ASN29 4.5 31.8 1.0
CB E:ASN29 4.5 28.2 1.0
CA E:GLY76 4.6 26.6 1.0
OG E:SER75 4.7 31.1 1.0
CB E:THR115 4.7 30.2 1.0
CA E:THR115 4.7 29.9 1.0
C E:ASN29 4.8 28.9 1.0
CB E:SER75 4.8 27.8 1.0
CB E:SER116 4.9 29.6 1.0
CB E:ASN32 4.9 27.1 1.0
N E:SER75 5.0 27.1 1.0
CG E:ASN32 5.0 29.2 1.0

Zinc binding site 5 out of 6 in 2v9o

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Zinc binding site 5 out of 6 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 5 of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1277

b:39.5
occ:1.00
 OE1 A:GLU200 1.5 25.6 1.0
NE2 E:HIS46 2.0 24.8 1.0
OD2 E:ASP47 2.1 41.1 1.0
NE2 A:HIS204 2.2 28.8 1.0
CG E:ASP47 2.6 34.5 1.0
CD A:GLU200 2.7 34.2 1.0
OD1 E:ASP47 2.7 36.8 1.0
CD2 A:HIS204 2.8 21.2 1.0
CE1 E:HIS46 2.9 22.2 1.0
CD2 E:HIS46 3.0 26.9 1.0
OE2 A:GLU200 3.3 34.6 1.0
CE1 A:HIS204 3.4 27.4 1.0
CG A:GLU200 3.9 29.1 1.0
ND1 E:HIS46 3.9 25.2 1.0
CG E:HIS46 4.0 26.7 1.0
CB E:ASP47 4.0 32.2 1.0
CG A:HIS204 4.1 27.1 1.0
CB A:LYS203 4.2 27.0 1.0
CA A:GLY181 4.2 28.4 1.0
ND1 A:HIS204 4.3 18.7 1.0
OG1 A:THR158 4.4 32.0 1.0
CB A:GLU200 4.5 30.7 1.0
CG2 A:THR158 4.6 27.1 1.0
N E:ASP47 4.7 29.5 1.0
O A:HOH2088 4.7 49.5 1.0
CA E:ASP47 4.7 32.3 1.0
O E:HOH2038 4.8 40.2 1.0
CG A:LYS203 4.8 29.5 1.0
CA A:GLU200 4.8 29.6 1.0
O A:GLU200 4.9 30.7 1.0
CB A:THR158 5.0 30.8 1.0
N A:GLY181 5.0 30.8 1.0

Zinc binding site 6 out of 6 in 2v9o

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Zinc binding site 6 out of 6 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 6 of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant A87M- T109F-E192A) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1278

b:50.4
occ:1.00
 OE1 E:GLU200 1.6 25.7 1.0
NE2 E:HIS204 2.2 29.2 1.0
CD2 E:HIS204 2.7 20.1 1.0
CD E:GLU200 2.8 33.1 1.0
OE2 E:GLU200 3.3 35.5 1.0
CE1 E:HIS204 3.4 26.9 1.0
CG E:HIS204 4.0 27.3 1.0
CG E:GLU200 4.0 29.5 1.0
CB E:LYS203 4.2 27.6 1.0
CA E:GLY181 4.2 29.6 1.0
ND1 E:HIS204 4.3 21.2 1.0
OG1 E:THR158 4.5 29.6 1.0
CG2 E:THR158 4.6 28.3 1.0
CB E:GLU200 4.6 30.5 1.0
CG E:LYS203 4.8 29.6 1.0
O E:GLU200 4.8 30.0 1.0
CA E:GLU200 4.8 30.1 1.0
N E:GLY181 5.0 31.1 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: Thu Oct 17 04:15:05 2024

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