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Zinc in PDB 2v9e: L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)

Enzymatic activity of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)

All present enzymatic activity of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S):
4.1.2.19;

Protein crystallography data

The structure of L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S), PDB code: 2v9e 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) 45.88 / 1.58
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.520, 107.520, 115.017, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.6

Zinc Binding Sites:

The binding sites of Zinc atom in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S) (pdb code 2v9e). 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 E192A-K248W-A273S), PDB code: 2v9e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2v9e

Go back to Zinc Binding Sites List in 2v9e
Zinc binding site 1 out of 6 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)


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 E192A-K248W-A273S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1275

b:9.3
occ:1.00
 O A:ACT1281 2.0 20.2 1.0
NE2 A:HIS212 2.0 9.6 1.0
NE2 A:HIS143 2.1 7.8 1.0
NE2 A:HIS141 2.1 9.2 1.0
OXT A:ACT1281 2.6 20.7 1.0
C A:ACT1281 2.6 20.1 1.0
CD2 A:HIS212 3.0 8.3 1.0
CD2 A:HIS141 3.1 9.7 1.0
CE1 A:HIS143 3.1 8.8 1.0
CD2 A:HIS143 3.1 7.4 1.0
CE1 A:HIS141 3.1 9.2 1.0
CE1 A:HIS212 3.1 10.0 1.0
CH3 A:ACT1281 4.1 19.7 1.0
CG A:HIS212 4.1 8.7 1.0
ND1 A:HIS212 4.2 8.8 1.0
ND1 A:HIS143 4.2 8.7 1.0
ND1 A:HIS141 4.2 9.2 1.0
CG A:HIS143 4.2 8.3 1.0
CG A:HIS141 4.2 8.9 1.0
N A:GLY31 4.5 11.5 1.0
C A:GLY30 4.6 12.4 1.0
CA A:GLY30 4.7 11.7 1.0
CZ3 A:TRP209 4.9 10.7 1.0

Zinc binding site 2 out of 6 in 2v9e

Go back to Zinc Binding Sites List in 2v9e
Zinc binding site 2 out of 6 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)


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 E192A-K248W-A273S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1276

b:17.4
occ:1.00
 NE2 A:HIS50 1.9 19.4 1.0
OXT A:ACT1278 2.0 17.6 1.0
NE2 B:HIS103 2.1 16.0 1.0
ND1 A:HIS46 2.1 21.6 1.0
C A:ACT1278 2.7 18.6 1.0
O A:ACT1278 2.8 19.0 1.0
CE1 A:HIS50 2.9 20.4 1.0
CD2 A:HIS50 2.9 20.1 1.0
CE1 A:HIS46 3.0 21.5 1.0
CE1 B:HIS103 3.0 15.1 1.0
CD2 B:HIS103 3.1 14.3 1.0
CG A:HIS46 3.2 21.1 1.0
O A:HIS46 3.5 20.8 1.0
CB A:HIS46 3.6 20.8 1.0
O A:HOH2280 3.8 66.1 1.0
ND1 A:HIS50 4.0 20.2 1.0
CG A:HIS50 4.0 21.4 1.0
C A:HIS46 4.1 21.4 1.0
ND1 B:HIS103 4.2 14.6 1.0
NE2 A:HIS46 4.2 21.1 1.0
CH3 A:ACT1278 4.2 18.9 1.0
CG B:HIS103 4.2 13.6 1.0
CD1 B:TYR55 4.2 15.6 1.0
CD2 A:HIS46 4.3 22.4 1.0
CA A:HIS46 4.4 21.1 1.0
CG B:TYR55 4.8 15.7 1.0
CE1 B:TYR55 4.8 16.1 1.0
N A:ASP47 4.9 21.3 1.0
CB B:TYR55 4.9 16.1 1.0
O A:HOH2178 5.0 50.7 1.0

Zinc binding site 3 out of 6 in 2v9e

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Zinc binding site 3 out of 6 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)


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 E192A-K248W-A273S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1277

b:26.4
occ:1.00
 NE2 A:HIS204 2.1 15.1 1.0
OE2 A:GLU200 2.3 19.8 1.0
CD2 A:HIS204 2.9 14.2 1.0
CE1 A:HIS204 3.2 14.5 1.0
CD A:GLU200 3.3 20.0 1.0
OE1 A:GLU200 3.6 24.2 1.0
OG1 A:THR158 4.0 17.3 1.0
O A:HOH2185 4.1 41.6 1.0
CG A:HIS204 4.1 13.8 1.0
ND1 A:HIS204 4.2 14.3 1.0
CB A:LYS203 4.3 16.0 0.3
CA A:GLY181 4.4 14.1 1.0
CG2 A:THR158 4.4 15.1 1.0
CG A:LYS203 4.5 17.2 0.3
CB A:THR158 4.7 15.4 1.0
CG A:GLU200 4.7 16.6 1.0
CB A:LYS203 4.8 16.5 0.4
O A:GLU200 5.0 14.0 1.0
CB A:GLU200 5.0 14.8 1.0
CA A:GLU200 5.0 14.4 1.0

Zinc binding site 4 out of 6 in 2v9e

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Zinc binding site 4 out of 6 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)


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 E192A-K248W-A273S) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1275

b:11.6
occ:1.00
 NE2 B:HIS212 2.0 10.2 1.0
NE2 B:HIS143 2.0 9.2 1.0
O B:ACT1278 2.1 25.3 1.0
NE2 B:HIS141 2.1 10.2 1.0
OXT B:ACT1278 2.5 25.2 1.0
C B:ACT1278 2.7 25.0 1.0
CD2 B:HIS212 2.9 9.4 1.0
CE1 B:HIS143 3.0 9.9 1.0
CD2 B:HIS143 3.1 8.1 1.0
CD2 B:HIS141 3.1 9.4 1.0
CE1 B:HIS212 3.1 11.1 1.0
CE1 B:HIS141 3.1 10.2 1.0
CG B:HIS212 4.1 10.0 1.0
ND1 B:HIS143 4.1 8.7 1.0
CH3 B:ACT1278 4.1 24.2 1.0
ND1 B:HIS212 4.2 10.1 1.0
CG B:HIS143 4.2 8.9 1.0
ND1 B:HIS141 4.2 10.0 1.0
CG B:HIS141 4.3 8.8 1.0
O B:HOH2159 4.3 65.8 1.0
N B:GLY31 4.5 11.7 1.0
C B:GLY30 4.6 12.4 1.0
CA B:GLY30 4.7 11.8 1.0
CZ3 B:TRP209 4.9 11.6 1.0

Zinc binding site 5 out of 6 in 2v9e

Go back to Zinc Binding Sites List in 2v9e
Zinc binding site 5 out of 6 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)


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 E192A-K248W-A273S) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1276

b:21.5
occ:1.00
 OXT A:ACT1280 2.0 28.6 1.0
NE2 A:HIS103 2.0 15.5 1.0
NE2 B:HIS50 2.0 20.8 1.0
OXT A:ACT1279 2.1 23.5 1.0
C A:ACT1280 2.8 29.2 1.0
C A:ACT1279 2.9 23.4 1.0
CD2 B:HIS50 2.9 21.9 1.0
O A:ACT1280 2.9 29.0 1.0
CD2 A:HIS103 2.9 14.6 1.0
O A:ACT1279 3.0 23.6 1.0
CE1 A:HIS103 3.0 14.5 1.0
CE1 B:HIS50 3.1 21.0 1.0
N B:GLN52 3.4 24.7 0.4
N B:GLN52 3.6 24.4 0.6
C B:GLN51 3.9 24.7 0.4
CB A:TYR55 4.1 16.4 1.0
CG B:HIS50 4.1 22.5 1.0
CG A:HIS103 4.1 14.0 1.0
ND1 A:HIS103 4.1 14.7 1.0
CH3 A:ACT1280 4.2 28.8 1.0
ND1 B:HIS50 4.2 21.1 1.0
N B:GLN51 4.2 24.5 0.4
CA B:GLN51 4.3 24.7 0.4
CH3 A:ACT1279 4.3 23.7 1.0
CB A:PRO53 4.3 22.9 1.0
O A:HOH2282 4.3 34.1 1.0
CD1 A:TYR55 4.4 15.7 1.0
CB B:GLN52 4.5 24.1 1.0
CA B:GLN52 4.5 24.4 1.0
CG A:TYR55 4.5 16.1 1.0
C B:GLN51 4.6 24.1 0.6
CB B:GLN51 4.6 24.8 0.4
O B:GLN51 4.6 24.9 0.4
CG A:PRO53 4.7 24.1 1.0
N B:GLN51 4.7 24.1 0.6
CA B:GLN51 4.9 24.1 0.6

Zinc binding site 6 out of 6 in 2v9e

Go back to Zinc Binding Sites List in 2v9e
Zinc binding site 6 out of 6 in the L-Rhamnulose-1-Phosphate Aldolase From Escherichia Coli ( Mutant E192A-K248W-A273S)


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 E192A-K248W-A273S) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1277

b:34.6
occ:1.00
 NE2 B:HIS204 2.2 15.1 1.0
OE2 B:GLU200 2.5 21.0 1.0
CD2 B:HIS204 2.9 14.7 1.0
CE1 B:HIS204 3.3 15.1 1.0
CD B:GLU200 3.3 20.1 1.0
OE1 B:GLU200 3.6 23.2 1.0
CG B:HIS204 4.2 14.6 1.0
OG1 B:THR158 4.2 17.2 1.0
ND1 B:HIS204 4.3 15.3 1.0
CA B:GLY181 4.4 14.2 1.0
CB B:LYS203 4.5 16.0 0.4
CG2 B:THR158 4.7 15.3 1.0
CG B:GLU200 4.7 17.2 1.0
CG B:LYS203 4.8 17.1 0.4
CB B:THR158 4.8 15.3 1.0
CB B:LYS203 4.8 16.5 0.6
CD B:LYS203 4.9 19.3 0.4
CA B:GLU200 4.9 14.5 1.0
O B:GLU200 4.9 14.1 1.0
CB B:GLU200 4.9 14.9 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 04:11:38 2024

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