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Manganese in PDB 2jla: Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein

Enzymatic activity of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein

All present enzymatic activity of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein:
2.2.1.9;

Protein crystallography data

The structure of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein, PDB code: 2jla was solved by A.Dawson, P.K.Fyfe, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.05 / 2.81
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 95.830, 95.830, 463.170, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 23.3

Other elements in 2jla:

The structure of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein (pdb code 2jla). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein, PDB code: 2jla:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 2jla

Go back to Manganese Binding Sites List in 2jla
Manganese binding site 1 out of 5 in the Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1558

b:19.9
occ:1.00
 OD1 A:ASP442 2.0 19.9 1.0
O1A A:TPP1557 2.1 13.2 1.0
OD1 A:ASN469 2.2 17.2 1.0
O A:HOH2098 2.2 8.8 1.0
O3B A:TPP1557 2.2 11.1 1.0
O A:GLY471 2.2 20.2 1.0
CG A:ASP442 3.0 18.0 1.0
PB A:TPP1557 3.2 12.2 1.0
CG A:ASN469 3.2 17.5 1.0
PA A:TPP1557 3.3 15.3 1.0
C A:GLY471 3.4 20.2 1.0
O3A A:TPP1557 3.4 14.0 1.0
OD2 A:ASP442 3.5 17.8 1.0
ND2 A:ASN469 3.7 18.3 1.0
N A:ASP442 3.8 17.2 1.0
N A:GLY471 4.1 19.4 1.0
N A:GLN473 4.2 21.6 1.0
N A:GLY472 4.2 20.4 1.0
O2B A:TPP1557 4.2 11.7 1.0
O7 A:TPP1557 4.3 15.9 1.0
CA A:GLY472 4.3 20.9 1.0
N A:ASN469 4.3 16.6 1.0
CA A:GLY471 4.3 19.8 1.0
CB A:ASP442 4.3 16.8 1.0
O2A A:TPP1557 4.4 14.6 1.0
O A:VAL467 4.4 15.8 1.0
O1B A:TPP1557 4.4 12.0 1.0
CB A:ASN469 4.5 17.0 1.0
N A:LEU443 4.6 16.3 1.0
CA A:ASP442 4.6 16.9 1.0
CA A:GLY441 4.6 17.3 1.0
CG A:GLN473 4.6 21.4 1.0
C A:GLY441 4.7 17.7 1.0
C A:ASN469 4.7 17.3 1.0
CA A:ASN469 4.7 17.0 1.0
N A:ASN470 4.8 17.3 1.0
C A:GLY472 4.8 21.2 1.0
CB A:GLN473 4.9 21.4 1.0

Manganese binding site 2 out of 5 in 2jla

Go back to Manganese Binding Sites List in 2jla
Manganese binding site 2 out of 5 in the Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1558

b:20.6
occ:1.00
 O1A B:TPP1557 1.9 19.9 1.0
OD1 B:ASN469 2.0 17.6 1.0
O B:GLY471 2.1 20.1 1.0
OD1 B:ASP442 2.1 18.0 1.0
O B:HOH2099 2.2 2.0 1.0
O3B B:TPP1557 2.3 18.6 1.0
CG B:ASN469 3.0 16.8 1.0
CG B:ASP442 3.1 17.1 1.0
C B:GLY471 3.2 20.0 1.0
PA B:TPP1557 3.2 19.7 1.0
PB B:TPP1557 3.3 19.2 1.0
OD2 B:ASP442 3.4 16.9 1.0
O3A B:TPP1557 3.4 18.9 1.0
ND2 B:ASN469 3.5 17.5 1.0
N B:GLY471 3.9 19.3 1.0
N B:ASP442 4.0 16.4 1.0
N B:GLY472 4.0 20.2 1.0
N B:GLN473 4.1 21.4 1.0
CA B:GLY471 4.1 19.6 1.0
CA B:GLY472 4.2 20.8 1.0
O2B B:TPP1557 4.2 19.1 1.0
O7 B:TPP1557 4.2 19.3 1.0
O2A B:TPP1557 4.2 18.4 1.0
N B:ASN469 4.3 16.4 1.0
CB B:ASP442 4.4 16.3 1.0
CB B:ASN469 4.4 16.6 1.0
O1B B:TPP1557 4.6 18.1 1.0
C B:ASN469 4.6 17.1 1.0
O B:VAL467 4.6 16.4 1.0
CG B:GLN473 4.6 21.2 1.0
CA B:ASN469 4.6 16.7 1.0
N B:LEU443 4.7 16.1 1.0
C B:GLY472 4.7 21.2 1.0
CA B:ASP442 4.7 16.4 1.0
N B:ASN470 4.8 17.7 1.0
CA B:GLY441 4.8 16.7 1.0
CB B:GLN473 4.8 21.4 1.0
C B:GLY441 4.8 16.8 1.0
C B:ASN470 4.9 19.0 1.0
O B:ASN469 4.9 16.7 1.0

Manganese binding site 3 out of 5 in 2jla

Go back to Manganese Binding Sites List in 2jla
Manganese binding site 3 out of 5 in the Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1558

b:17.4
occ:1.00
 O1A C:TPP1557 2.0 13.6 1.0
OD1 C:ASP442 2.0 17.3 1.0
O3B C:TPP1557 2.0 12.2 1.0
OD1 C:ASN469 2.2 14.2 1.0
O C:HOH2086 2.2 34.5 1.0
O C:GLY471 2.2 20.6 1.0
CG C:ASP442 3.0 17.1 1.0
PB C:TPP1557 3.2 11.4 1.0
C C:GLY471 3.2 20.3 1.0
CG C:ASN469 3.3 15.3 1.0
PA C:TPP1557 3.4 15.7 1.0
OD2 C:ASP442 3.5 17.3 1.0
O3A C:TPP1557 3.5 13.1 1.0
ND2 C:ASN469 3.8 15.6 1.0
N C:ASP442 3.9 16.4 1.0
N C:GLY471 3.9 18.8 1.0
N C:GLY472 4.1 20.1 1.0
N C:GLN473 4.1 20.5 1.0
CA C:GLY471 4.1 19.5 1.0
O C:HOH2085 4.2 5.6 1.0
CA C:GLY472 4.2 20.0 1.0
O2B C:TPP1557 4.2 12.3 1.0
O7 C:TPP1557 4.3 16.9 1.0
CB C:ASP442 4.3 16.5 1.0
N C:ASN469 4.3 16.4 1.0
O1B C:TPP1557 4.3 12.2 1.0
O2A C:TPP1557 4.4 13.2 1.0
O C:VAL467 4.4 16.2 1.0
N C:LEU443 4.5 15.8 1.0
CG C:GLN473 4.5 20.8 1.0
CB C:ASN469 4.6 16.0 1.0
CA C:ASP442 4.6 16.5 1.0
CA C:GLY441 4.6 16.3 1.0
N C:ASN470 4.7 17.2 1.0
C C:GLY472 4.7 20.1 1.0
C C:GLY441 4.7 16.5 1.0
C C:ASN469 4.7 16.7 1.0
CA C:ASN469 4.8 16.3 1.0
CB C:GLN473 4.8 20.8 1.0
C C:ASN470 4.9 18.4 1.0

Manganese binding site 4 out of 5 in 2jla

Go back to Manganese Binding Sites List in 2jla
Manganese binding site 4 out of 5 in the Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1562

b:22.5
occ:1.00
 O C:HOH2087 2.1 19.3 1.0
NE2 C:HIS509 2.3 19.0 1.0
OD2 C:ASP523 2.3 22.7 1.0
CE1 C:HIS509 3.2 18.7 1.0
CG C:ASP523 3.2 21.4 1.0
CD2 C:HIS509 3.3 18.4 1.0
CB C:ASP523 3.4 21.4 1.0
ND1 C:HIS509 4.3 18.0 1.0
OD1 C:ASP523 4.4 21.6 1.0
CG C:HIS509 4.4 17.8 1.0
O C:ALA520 4.6 20.1 1.0
CA C:ALA520 4.7 19.9 1.0
NZ C:LYS507 4.7 25.5 1.0
CA C:ASP523 4.8 21.1 1.0

Manganese binding site 5 out of 5 in 2jla

Go back to Manganese Binding Sites List in 2jla
Manganese binding site 5 out of 5 in the Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of E.Coli Mend, 2-Succinyl-5-Enolpyruvyl- 6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase - Semet Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1558

b:13.2
occ:1.00
 O1A D:TPP1557 2.1 11.2 1.0
O3B D:TPP1557 2.1 12.0 1.0
OD1 D:ASP442 2.1 17.9 1.0
OD1 D:ASN469 2.2 18.1 1.0
O D:HOH2111 2.3 22.2 1.0
O D:GLY471 2.4 20.7 1.0
CG D:ASP442 3.0 16.1 1.0
PB D:TPP1557 3.2 10.9 1.0
CG D:ASN469 3.2 16.9 1.0
C D:GLY471 3.3 20.6 1.0
PA D:TPP1557 3.3 12.6 1.0
OD2 D:ASP442 3.3 16.0 1.0
O3A D:TPP1557 3.4 11.7 1.0
ND2 D:ASN469 3.7 16.8 1.0
N D:ASP442 3.9 16.3 1.0
N D:GLY471 4.0 19.7 1.0
N D:GLY472 4.0 20.8 1.0
CA D:GLY472 4.1 21.4 1.0
N D:GLN473 4.1 22.2 1.0
CA D:GLY471 4.2 20.1 1.0
O7 D:TPP1557 4.2 12.8 1.0
O2B D:TPP1557 4.3 10.0 1.0
O1B D:TPP1557 4.3 11.2 1.0
CB D:ASP442 4.3 15.7 1.0
O2A D:TPP1557 4.4 11.2 1.0
N D:ASN469 4.4 16.7 1.0
O D:VAL467 4.5 16.8 1.0
N D:LEU443 4.5 15.7 1.0
CB D:ASN469 4.6 17.1 1.0
CG D:GLN473 4.6 22.0 1.0
CA D:ASP442 4.6 16.0 1.0
C D:GLY472 4.7 21.9 1.0
C D:ASN469 4.7 17.6 1.0
CA D:GLY441 4.7 16.3 1.0
CA D:ASN469 4.8 17.1 1.0
N D:ASN470 4.8 18.2 1.0
C D:GLY441 4.8 16.5 1.0
CB D:GLN473 4.9 22.2 1.0
C D:ASN470 5.0 19.2 1.0

Reference:

A.Dawson, P.K.Fyfe, W.N.Hunter. Specificity and Reactivity in Menaquinone Biosynthesis: the Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3- Cyclohexadiene-1-Carboxylate Synthase). J.Mol.Biol. V. 384 1353 2008.
ISSN: ISSN 0022-2836
PubMed: 18983854
DOI: 10.1016/J.JMB.2008.10.048
Page generated: Sat Oct 5 14:35:22 2024

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