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Manganese in PDB 6ph9: Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex

Enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex

All present enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex:
3.6.1.54;

Protein crystallography data

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex, PDB code: 6ph9 was solved by J.Cho, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 1.92
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.990, 105.990, 52.570, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 19.9

Other elements in 6ph9:

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex (pdb code 6ph9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex, PDB code: 6ph9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 1 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:33.5
occ:1.00
 OD1 A:ASP8 1.9 32.7 1.0
O A:HOH415 2.2 35.3 1.0
NE2 A:HIS10 2.3 35.4 1.0
NE2 A:HIS197 2.3 37.1 1.0
OD2 A:ASP41 2.5 30.9 1.0
CG A:ASP8 2.8 28.4 1.0
CE1 A:HIS197 3.1 40.0 1.0
CE1 A:HIS10 3.2 40.6 1.0
CD2 A:HIS10 3.3 37.4 1.0
CD2 A:HIS197 3.3 35.2 1.0
CB A:ASP8 3.3 28.0 1.0
MN A:MN302 3.4 30.1 1.0
CG A:ASP41 3.5 30.7 1.0
CB A:ASP41 3.6 26.5 1.0
O A:HOH436 3.7 43.2 1.0
OD2 A:ASP8 3.9 34.7 1.0
CA A:ASP8 3.9 23.3 1.0
O A:HIS195 4.0 33.1 1.0
CA A:HIS195 4.2 35.6 1.0
ND1 A:HIS197 4.3 42.4 1.0
ND1 A:HIS10 4.3 38.8 1.0
CG A:HIS10 4.4 33.5 1.0
CG A:HIS197 4.4 38.5 1.0
CE1 A:HIS114 4.5 31.2 1.0
C A:HIS195 4.5 34.4 1.0
OD1 A:ASP41 4.6 31.2 1.0
NE2 A:HIS114 4.7 29.6 1.0
N A:HIS195 4.7 27.8 1.0
C A:ASP8 4.9 26.1 1.0
N A:ASP8 4.9 24.4 1.0
ND1 A:HIS195 4.9 33.4 1.0
OD1 A:ASN79 4.9 35.5 1.0

Manganese binding site 2 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 2 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:30.1
occ:1.00
 O A:HOH415 1.9 35.3 1.0
OD1 A:ASN79 2.0 35.5 1.0
OD2 A:ASP41 2.1 30.9 1.0
NE2 A:HIS114 2.2 29.6 1.0
ND1 A:HIS195 2.3 33.4 1.0
CE1 A:HIS114 3.0 31.2 1.0
CG A:ASP41 3.1 30.7 1.0
CG A:ASN79 3.2 34.5 1.0
CE1 A:HIS195 3.2 40.6 1.0
CG A:HIS195 3.3 35.1 1.0
CD2 A:HIS114 3.3 31.6 1.0
O A:HOH436 3.4 43.2 1.0
MN A:MN301 3.4 33.5 1.0
CA A:HIS195 3.5 35.6 1.0
OD1 A:ASP41 3.6 31.2 1.0
CB A:HIS195 3.6 30.6 1.0
OD1 A:ASP8 3.7 32.7 1.0
ND2 A:ASN79 3.9 34.4 1.0
ND1 A:HIS114 4.1 28.9 1.0
O A:HIS195 4.2 33.1 1.0
N A:ASN79 4.3 30.7 1.0
CB A:ASP41 4.3 26.5 1.0
CB A:ASN79 4.3 29.8 1.0
NE2 A:HIS195 4.3 37.6 1.0
CG A:HIS114 4.3 28.4 1.0
C A:HIS195 4.4 34.4 1.0
CD2 A:HIS195 4.4 35.0 1.0
N A:HIS195 4.5 27.8 1.0
CG A:ASP8 4.8 28.4 1.0
CA A:ASN79 4.9 33.8 1.0

Manganese binding site 3 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 3 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:43.7
occ:0.81
 O A:HOH584 2.3 51.8 1.0
O A:HOH520 2.4 40.5 1.0
O A:HOH596 2.5 42.3 1.0
O A:HOH459 2.6 39.0 1.0
O A:HOH578 2.6 36.1 1.0
O A:HOH547 2.8 41.4 0.5
OD1 A:ASP34 4.4 30.7 1.0
O A:HOH547 4.5 46.2 0.5
O A:ALA33 4.5 31.5 1.0
O A:HOH507 4.5 43.0 1.0
O A:GLN32 4.7 40.3 1.0
O A:GLY70 4.7 28.8 1.0

Manganese binding site 4 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 4 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:42.2
occ:0.27
 O A:HOH544 2.1 57.3 1.0
O A:HOH497 2.4 40.2 1.0
O A:HOH511 2.5 43.2 1.0
NZ A:LYS227 3.9 41.5 1.0
O A:HOH552 4.3 53.2 1.0
OE1 A:GLU234 4.4 32.7 1.0
OE2 A:GLU234 4.6 35.8 1.0
CE A:LYS227 4.8 39.9 1.0
O A:HOH527 4.8 47.9 1.0
CD A:GLU234 4.9 33.3 1.0

Reference:

J.Cho, M.Lee, C.Cochrane, C.Webster, B.Fenton, J.Zhao, J.Hong, P.Zhao. Structural Basis of the Udp-Diacylglucosamine Pyrophosphohydrolase Lpxh Inhibition By Sulfonyl Piperazine Antibiotics Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1912876117
Page generated: Sun Oct 6 05:51:04 2024

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