Atomistry » Manganese » PDB 2jck-2nym » 2jla
Atomistry »
  Manganese »
    PDB 2jck-2nym »
      2jla »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy