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Manganese in PDB 5dcb: Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep

Enzymatic activity of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep

All present enzymatic activity of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep, PDB code: 5dcb was solved by L.C.Heyes, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.96 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.458, 140.310, 75.500, 90.00, 96.89, 90.00
R / Rfree (%) 16.9 / 21.2

Other elements in 5dcb:

The structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep (pdb code 5dcb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep, PDB code: 5dcb:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5dcb

Go back to Manganese Binding Sites List in 5dcb
Manganese binding site 1 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.2
occ:1.00
 OD2 A:ASP324 2.0 18.5 1.0
OE2 A:GLU304 2.0 20.7 1.0
O A:HOH503 2.1 22.5 1.0
NE2 A:HIS270 2.4 22.4 1.0
SG A:CYS63 2.6 22.7 1.0
CD A:GLU304 2.9 21.2 1.0
CG A:ASP324 2.9 19.6 1.0
OE1 A:GLU304 3.2 20.7 1.0
CD2 A:HIS270 3.2 22.3 1.0
CB A:ASP324 3.3 20.9 1.0
CE1 A:HIS270 3.4 22.5 1.0
CB A:CYS63 3.5 23.0 1.0
NH2 A:ARG94 3.7 22.6 1.0
O3P A:PEP407 4.0 30.4 1.0
OD1 A:ASP324 4.0 19.6 1.0
CA A:CYS63 4.1 22.2 1.0
CE A:LYS99 4.2 31.3 1.0
O A:HOH593 4.2 23.5 1.0
CG A:GLU304 4.3 20.4 1.0
O A:HOH626 4.4 20.4 1.0
CG A:HIS270 4.4 22.1 1.0
ND1 A:HIS270 4.4 22.2 1.0
NZ A:LYS99 4.4 30.6 1.0
O A:CYS63 4.6 21.6 1.0
CZ A:ARG94 4.6 21.6 1.0
CA A:ASP324 4.6 21.7 1.0
C A:CYS63 4.7 22.3 1.0
CG A:LYS99 4.7 28.4 1.0
N A:ASP324 4.7 22.2 1.0
O2 A:PEP407 4.8 33.5 1.0
C3 A:PEP407 4.8 30.8 1.0
CD A:LYS99 4.9 29.5 1.0

Manganese binding site 2 out of 4 in 5dcb

Go back to Manganese Binding Sites List in 5dcb
Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:21.1
occ:1.00
 OD2 B:ASP324 2.0 21.0 1.0
OE2 B:GLU304 2.1 21.4 1.0
O B:HOH528 2.1 40.6 1.0
NE2 B:HIS270 2.2 23.6 1.0
SG B:CYS63 2.5 21.9 1.0
CD B:GLU304 2.9 20.8 1.0
CG B:ASP324 3.0 21.3 1.0
OE1 B:GLU304 3.1 21.9 1.0
CE1 B:HIS270 3.2 24.4 1.0
CD2 B:HIS270 3.2 24.4 1.0
CB B:ASP324 3.3 21.9 1.0
CB B:CYS63 3.6 20.8 1.0
NH1 B:ARG94 3.8 22.3 1.0
O1P B:PEP403 4.1 23.8 1.0
OD1 B:ASP324 4.1 21.5 1.0
CE B:LYS99 4.1 30.0 1.0
CA B:CYS63 4.1 20.9 1.0
O B:HOH606 4.2 27.4 1.0
O B:HOH538 4.2 19.4 1.0
CG B:GLU304 4.3 20.4 1.0
NZ B:LYS99 4.3 29.1 1.0
ND1 B:HIS270 4.3 24.0 1.0
CG B:HIS270 4.4 24.4 1.0
CZ B:ARG94 4.6 22.1 1.0
CA B:ASP324 4.6 22.3 1.0
O B:CYS63 4.7 21.0 1.0
N B:ASP324 4.8 22.2 1.0
O2 B:PEP403 4.8 26.4 1.0
C B:CYS63 4.8 20.8 1.0
C3 B:PEP403 4.8 27.2 1.0
CG B:LYS99 5.0 27.1 1.0

Manganese binding site 3 out of 4 in 5dcb

Go back to Manganese Binding Sites List in 5dcb
Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:40.6
occ:1.00
 OE2 C:GLU304 2.0 41.7 1.0
OD2 C:ASP324 2.2 40.7 1.0
O C:HOH503 2.3 26.4 1.0
NE2 C:HIS270 2.3 40.4 1.0
SG C:CYS63 2.5 42.3 1.0
CD C:GLU304 2.8 40.2 1.0
OE1 C:GLU304 3.0 40.6 1.0
CG C:ASP324 3.1 42.2 1.0
CD2 C:HIS270 3.1 39.5 1.0
CE1 C:HIS270 3.3 40.9 1.0
CB C:ASP324 3.4 41.9 1.0
CB C:CYS63 3.6 42.6 1.0
NH2 C:ARG94 3.7 33.9 1.0
CD C:LYS99 3.9 44.9 1.0
O1P C:PEP402 4.0 35.6 1.0
CA C:CYS63 4.1 41.4 1.0
CE C:LYS99 4.2 44.3 1.0
OD1 C:ASP324 4.2 41.6 1.0
CG C:GLU304 4.3 39.2 1.0
CG C:HIS270 4.3 39.8 1.0
O C:HOH514 4.3 35.6 1.0
O C:HOH557 4.3 33.4 1.0
ND1 C:HIS270 4.4 40.1 1.0
CZ C:ARG94 4.6 34.3 1.0
CA C:ASP324 4.7 42.7 1.0
NZ C:LYS99 4.7 45.8 1.0
N C:ASP324 4.7 42.1 1.0
O2 C:PEP402 4.9 41.9 1.0
O C:CYS63 4.9 38.8 1.0
C C:CYS63 4.9 40.1 1.0
C3 C:PEP402 4.9 39.6 1.0

Manganese binding site 4 out of 4 in 5dcb

Go back to Manganese Binding Sites List in 5dcb
Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:19.4
occ:1.00
 OE2 D:GLU304 2.0 18.9 1.0
O D:HOH569 2.1 23.7 1.0
OD2 D:ASP324 2.1 18.1 1.0
NE2 D:HIS270 2.3 17.8 1.0
SG D:CYS63 2.5 19.6 1.0
CD D:GLU304 2.9 19.0 1.0
CG D:ASP324 3.0 19.3 1.0
OE1 D:GLU304 3.1 18.6 1.0
CE1 D:HIS270 3.2 17.2 1.0
CD2 D:HIS270 3.3 17.8 1.0
CB D:ASP324 3.5 19.2 1.0
CB D:CYS63 3.6 18.2 1.0
NH2 D:ARG94 3.7 20.7 1.0
CA D:CYS63 4.1 17.3 1.0
O2P D:PEP404 4.1 28.3 1.0
OD1 D:ASP324 4.1 20.5 1.0
CD D:LYS99 4.2 28.4 1.0
NZ D:LYS99 4.2 30.1 1.0
O D:HOH631 4.2 20.5 1.0
CG D:GLU304 4.3 18.3 1.0
O D:HOH658 4.3 20.1 1.0
ND1 D:HIS270 4.3 17.4 1.0
CG D:HIS270 4.4 17.7 1.0
CE D:LYS99 4.6 30.8 1.0
CZ D:ARG94 4.6 20.0 1.0
O D:CYS63 4.7 15.5 1.0
O2 D:PEP404 4.7 27.7 1.0
CA D:ASP324 4.7 20.2 1.0
C D:CYS63 4.8 16.9 1.0
N D:ASP324 4.8 20.4 1.0
C3 D:PEP404 4.8 26.0 1.0

Reference:

L.C.Heyes, E.J.Parker. Structure of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase Regulated and Complexed with Pep at 2.05 Angstroms To Be Published.
Page generated: Sat Oct 5 23:53:03 2024

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