Atomistry » Zinc » PDB 2gzf-2h6t » 2v29
Atomistry »
  Zinc »
    PDB 2gzf-2h6t »
      2v29 »

Zinc in PDB 2v29: L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W)

Enzymatic activity of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W)

All present enzymatic activity of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W):
4.1.2.19;

Protein crystallography data

The structure of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W), PDB code: 2v29 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) 42.22 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 82.873, 82.873, 98.109, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.7

Zinc Binding Sites:

The binding sites of Zinc atom in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W) (pdb code 2v29). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W), PDB code: 2v29:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2v29

Go back to Zinc Binding Sites List in 2v29
Zinc binding site 1 out of 5 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W)


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 K15W) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1273

b:27.3
occ:1.00
OD1 B:ASP47 1.8 29.7 1.0
NE2 B:HIS50 2.0 20.6 1.0
O A:HOH2171 2.1 26.4 1.0
O A:HOH2170 2.9 31.8 1.0
CE1 B:HIS50 2.9 22.0 1.0
CG B:ASP47 3.0 30.4 1.0
CD2 B:HIS50 3.0 22.5 1.0
CB B:ASP47 3.7 29.7 1.0
CA B:ASP47 3.8 28.8 1.0
OD2 B:ASP47 3.9 32.1 1.0
ND1 B:HIS46 3.9 32.2 1.0
CE1 B:HIS46 3.9 31.8 1.0
ND1 B:HIS50 4.1 17.6 1.0
CG B:HIS50 4.1 23.1 1.0
N B:ASP47 4.4 29.1 1.0
O B:HIS46 4.6 29.2 1.0
C B:HIS46 4.7 29.1 1.0
NE2 B:HIS46 4.8 32.7 1.0
CG B:HIS46 4.8 31.2 1.0
C B:ASP47 5.0 29.1 1.0

Zinc binding site 2 out of 5 in 2v29

Go back to Zinc Binding Sites List in 2v29
Zinc binding site 2 out of 5 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W)


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 K15W) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1274

b:18.2
occ:1.00
NE2 B:HIS141 2.1 16.4 1.0
NE2 B:HIS212 2.1 18.5 1.0
NE2 B:HIS143 2.2 14.5 1.0
O B:HOH2184 2.3 27.6 1.0
O1 B:EDO1276 2.3 46.3 1.0
O A:HOH2172 2.8 35.2 1.0
CD2 B:HIS212 3.0 14.5 1.0
CD2 B:HIS141 3.1 17.8 1.0
CE1 B:HIS141 3.1 17.0 1.0
CD2 B:HIS143 3.2 14.9 1.0
CE1 B:HIS143 3.2 16.8 1.0
CE1 B:HIS212 3.2 19.2 1.0
C1 B:EDO1276 3.4 47.2 1.0
CG B:HIS212 4.2 16.7 1.0
ND1 B:HIS141 4.2 14.5 1.0
CG B:HIS141 4.2 17.9 1.0
ND1 B:HIS212 4.2 17.9 1.0
N B:GLY31 4.3 26.2 1.0
ND1 B:HIS143 4.3 18.1 1.0
CG B:HIS143 4.3 16.2 1.0
C2 B:EDO1276 4.3 45.9 1.0
O B:HOH2131 4.4 0.5 0.5
CZ3 B:TRP209 4.6 21.9 1.0
CE3 B:TRP209 4.9 20.8 1.0
CA B:GLY31 5.0 25.5 1.0

Zinc binding site 3 out of 5 in 2v29

Go back to Zinc Binding Sites List in 2v29
Zinc binding site 3 out of 5 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W)


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 K15W) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1275

b:18.6
occ:1.00
OXT A:ACT1282 2.0 38.1 1.0
NE2 A:HIS212 2.1 16.9 1.0
NE2 A:HIS141 2.1 21.2 1.0
NE2 A:HIS143 2.1 15.3 1.0
O A:ACT1282 2.4 35.8 1.0
C A:ACT1282 2.6 34.9 1.0
CD2 A:HIS212 2.9 14.8 1.0
O A:HOH2179 2.9 53.0 1.0
CE1 A:HIS141 3.0 18.7 1.0
CE1 A:HIS143 3.1 15.3 1.0
CE1 A:HIS212 3.1 18.3 1.0
CD2 A:HIS143 3.1 14.7 1.0
CD2 A:HIS141 3.1 19.3 1.0
CH3 A:ACT1282 4.0 35.7 1.0
CG A:HIS212 4.1 17.1 1.0
ND1 A:HIS141 4.2 18.9 1.0
ND1 A:HIS212 4.2 17.7 1.0
ND1 A:HIS143 4.2 16.9 1.0
CG A:HIS141 4.3 19.6 1.0
CG A:HIS143 4.3 14.6 1.0
N A:GLY31 4.4 27.4 1.0
CZ3 A:TRP209 4.8 23.9 1.0

Zinc binding site 4 out of 5 in 2v29

Go back to Zinc Binding Sites List in 2v29
Zinc binding site 4 out of 5 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W)


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 K15W) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1276

b:20.8
occ:1.00
OE2 B:GLU200 1.8 18.4 1.0
OD2 A:ASP47 2.1 18.2 1.0
NE2 A:HIS46 2.1 19.6 1.0
NE2 B:HIS204 2.2 13.8 1.0
CG A:ASP47 2.7 19.3 1.0
OD1 A:ASP47 2.8 19.9 1.0
CD B:GLU200 2.9 19.5 1.0
CD2 B:HIS204 2.9 13.7 1.0
CD2 A:HIS46 2.9 17.4 1.0
CE1 A:HIS46 3.1 18.9 1.0
OE1 B:GLU200 3.2 17.2 1.0
CE1 B:HIS204 3.4 16.1 1.0
CA B:GLY181 4.0 18.0 1.0
CG A:HIS46 4.1 17.9 1.0
ND1 A:HIS46 4.1 16.5 1.0
CB A:ASP47 4.2 19.4 1.0
CG B:HIS204 4.2 16.1 1.0
CG B:GLU200 4.2 18.4 1.0
O A:HOH2032 4.2 17.8 1.0
ND1 B:HIS204 4.4 17.2 1.0
O A:HOH2034 4.4 32.6 1.0
CB B:LYS203 4.5 19.2 1.0
CB B:GLU200 4.6 18.6 1.0
CG2 B:THR158 4.7 17.4 1.0
CA B:GLU200 4.8 19.0 1.0
OG1 B:THR158 4.8 17.9 1.0
N A:ASP47 4.8 19.1 1.0
CA A:ASP47 4.9 20.0 1.0
O B:GLU200 5.0 18.0 1.0
N B:GLY181 5.0 18.1 1.0

Zinc binding site 5 out of 5 in 2v29

Go back to Zinc Binding Sites List in 2v29
Zinc binding site 5 out of 5 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli (Mutant K15W)


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 K15W) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1277

b:78.0
occ:1.00
NE2 A:HIS204 2.2 19.7 1.0
O A:HOH2174 2.4 29.2 1.0
OE2 A:GLU200 2.7 28.0 1.0
O A:HOH2173 2.8 41.0 1.0
CD2 A:HIS204 3.1 17.8 1.0
CE1 A:HIS204 3.3 20.3 1.0
CD A:GLU200 3.7 28.0 1.0
OE1 A:GLU200 3.8 35.2 1.0
CG2 A:THR158 4.1 18.8 1.0
OG1 A:THR158 4.2 19.9 1.0
CG A:HIS204 4.3 19.2 1.0
ND1 A:HIS204 4.4 18.9 1.0
CA A:GLY181 4.5 19.8 1.0
CB A:THR158 4.5 18.1 1.0
CB A:LYS203 4.6 20.4 1.0

Reference:

D.Grueninger, G.E.Schulz. Antenna Domain Mobility and Enzymatic Reaction of L-Rhamnulose-1-Phosphate Aldolase. Biochemistry V. 47 607 2008.
ISSN: ISSN 0006-2960
PubMed: 18085797
DOI: 10.1021/BI7012799
Page generated: Sat Sep 26 04:00:10 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy