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Manganese in PDB 5d02: Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant

Enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant

All present enzymatic activity of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant:
2.5.1.54;

Protein crystallography data

The structure of Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant, PDB code: 5d02 was solved by L.C.Heyes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.55 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.540, 135.546, 76.009, 90.00, 96.27, 90.00
R / Rfree (%) 17.6 / 22.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant (pdb code 5d02). 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 GLU176GLN Variant, PDB code: 5d02:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5d02

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Manganese binding site 1 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant


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 GLU176GLN Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:26.4
occ:1.00
 OE2 A:GLU304 2.1 23.2 1.0
O A:HOH532 2.1 28.2 1.0
OD2 A:ASP324 2.1 25.5 1.0
NE2 A:HIS270 2.4 26.4 1.0
SG A:CYS63 2.6 23.3 1.0
CD A:GLU304 3.0 24.8 1.0
CG A:ASP324 3.1 25.2 1.0
O2' A:PEP402 3.2 34.2 1.0
OE1 A:GLU304 3.2 24.6 1.0
CD2 A:HIS270 3.3 26.6 1.0
CE1 A:HIS270 3.4 26.2 1.0
CB A:ASP324 3.6 25.1 1.0
CB A:CYS63 3.7 23.2 1.0
C1 A:PEP402 4.0 33.5 1.0
NZ A:LYS99 4.1 22.7 1.0
NH2 A:ARG94 4.1 26.6 1.0
OD1 A:ASP324 4.2 23.9 1.0
CA A:CYS63 4.2 22.8 1.0
O A:HOH608 4.3 28.4 1.0
CG A:GLU304 4.3 24.5 1.0
CG A:HIS270 4.4 25.4 1.0
ND1 A:HIS270 4.5 26.1 1.0
C2 A:PEP402 4.5 36.3 1.0
O A:HOH629 4.5 44.6 1.0
O1 A:PEP402 4.8 35.1 1.0
O A:CYS63 4.8 22.7 1.0
CA A:ASP324 4.8 25.4 1.0
N A:ASP324 4.8 23.7 1.0
C3 A:PEP402 4.8 37.5 1.0
CE A:LYS99 4.8 24.1 1.0
C A:CYS63 4.9 21.9 1.0
CZ A:ARG94 5.0 26.9 1.0

Manganese binding site 2 out of 4 in 5d02

Go back to Manganese Binding Sites List in 5d02
Manganese binding site 2 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant


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 GLU176GLN Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:37.0
occ:1.00
 OE2 B:GLU304 1.8 25.3 1.0
OD2 B:ASP324 2.1 40.0 1.0
O B:HOH614 2.3 41.5 1.0
NE2 B:HIS270 2.3 33.4 1.0
SG B:CYS63 2.6 33.6 1.0
CD B:GLU304 2.9 33.7 1.0
CG B:ASP324 3.1 40.6 1.0
O1 B:PEP402 3.1 37.1 1.0
CD2 B:HIS270 3.3 33.2 1.0
OE1 B:GLU304 3.3 34.7 1.0
CE1 B:HIS270 3.3 33.9 1.0
CB B:ASP324 3.4 38.0 1.0
CB B:CYS63 3.5 31.2 1.0
C1 B:PEP402 4.0 33.9 1.0
NZ B:LYS99 4.1 33.5 1.0
OD1 B:ASP324 4.2 38.9 1.0
NH1 B:ARG94 4.2 28.6 1.0
CG B:GLU304 4.2 31.7 1.0
CA B:CYS63 4.2 33.3 1.0
C2 B:PEP402 4.3 37.5 1.0
ND1 B:HIS270 4.4 30.7 1.0
CG B:HIS270 4.4 32.5 1.0
O B:HOH648 4.5 32.3 1.0
C3 B:PEP402 4.6 35.8 1.0
CA B:ASP324 4.7 40.2 1.0
O2 B:PEP402 4.8 37.7 1.0
N B:ASP324 4.8 38.9 1.0
O2' B:PEP402 4.9 32.6 1.0
O B:CYS63 4.9 30.6 1.0
CE B:LYS99 4.9 37.0 1.0
C B:CYS63 4.9 32.9 1.0

Manganese binding site 3 out of 4 in 5d02

Go back to Manganese Binding Sites List in 5d02
Manganese binding site 3 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant


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 GLU176GLN Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:36.6
occ:1.00
 OE2 C:GLU304 1.9 31.8 1.0
OD2 C:ASP324 2.3 35.0 1.0
NE2 C:HIS270 2.3 33.9 1.0
O C:HOH502 2.3 34.8 1.0
SG C:CYS63 2.5 37.7 1.0
CD C:GLU304 2.8 33.4 1.0
OE1 C:GLU304 3.1 33.7 1.0
CG C:ASP324 3.2 40.0 1.0
CE1 C:HIS270 3.2 32.9 1.0
CD2 C:HIS270 3.3 33.2 1.0
CB C:CYS63 3.5 34.7 1.0
CB C:ASP324 3.5 40.7 1.0
O1 C:PEP402 3.7 32.0 1.0
NH2 C:ARG94 3.9 29.6 1.0
CA C:CYS63 4.1 32.3 1.0
NZ C:LYS99 4.1 67.1 1.0
OD1 C:ASP324 4.2 42.4 1.0
CE C:LYS99 4.3 65.3 1.0
O C:HOH601 4.3 37.1 1.0
CG C:GLU304 4.3 29.7 1.0
O C:HOH532 4.3 34.3 1.0
ND1 C:HIS270 4.3 31.4 1.0
CG C:HIS270 4.4 31.9 1.0
C1 C:PEP402 4.5 27.1 1.0
O C:CYS63 4.7 29.6 1.0
C C:CYS63 4.7 30.8 1.0
CZ C:ARG94 4.8 30.0 1.0
CD C:LYS99 4.8 63.0 1.0
CA C:ASP324 4.8 41.9 1.0
N C:ASP324 4.9 42.0 1.0

Manganese binding site 4 out of 4 in 5d02

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Manganese binding site 4 out of 4 in the Neisseria Meningitidis 3 Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase GLU176GLN Variant


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 GLU176GLN Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:39.0
occ:1.00
 OD2 D:ASP324 1.9 37.2 1.0
OE2 D:GLU304 2.2 37.3 1.0
O D:HOH522 2.2 35.6 1.0
NE2 D:HIS270 2.4 38.1 1.0
SG D:CYS63 2.6 36.6 1.0
O2' D:PEP402 2.9 42.4 1.0
CG D:ASP324 3.0 37.4 1.0
CD D:GLU304 3.0 36.1 1.0
OE1 D:GLU304 3.1 36.9 1.0
CD2 D:HIS270 3.3 37.9 1.0
CE1 D:HIS270 3.4 37.3 1.0
CB D:ASP324 3.5 36.8 1.0
CB D:CYS63 3.7 33.6 1.0
C1 D:PEP402 3.9 41.6 1.0
OD1 D:ASP324 4.0 35.2 1.0
NH2 D:ARG94 4.1 35.3 1.0
NZ D:LYS99 4.1 31.4 1.0
CA D:CYS63 4.2 32.9 1.0
O D:HOH617 4.4 32.9 1.0
CG D:GLU304 4.4 35.8 1.0
ND1 D:HIS270 4.5 38.0 1.0
CG D:HIS270 4.5 37.8 1.0
C2 D:PEP402 4.5 44.0 1.0
O1 D:PEP402 4.7 38.9 1.0
O D:CYS63 4.8 34.1 1.0
CA D:ASP324 4.8 36.5 1.0
C D:CYS63 4.9 32.4 1.0
CE D:LYS99 4.9 32.6 1.0
N D:ASP324 4.9 35.4 1.0
O D:HOH502 4.9 57.9 1.0
CZ D:ARG94 4.9 35.1 1.0
C3 D:PEP402 4.9 45.4 1.0

Reference:

L.C.Heyes, L.C.Heyes. N/A N/A.
Page generated: Sat Oct 5 23:49:28 2024

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