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Manganese in PDB 8qzi: Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis:
2.3.1.292;

Protein crystallography data

The structure of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis, PDB code: 8qzi was solved by S.Gavalda, L.Mourey, J.D.Pedelacq, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.28 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.335, 280.843, 47.34, 90, 92.83, 90
R / Rfree (%) 19.6 / 24.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis (pdb code 8qzi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis, PDB code: 8qzi:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8qzi

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Manganese binding site 1 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:59.8
occ:1.00
 O A:HOH404 2.0 61.7 1.0
OE2 A:GLU116 2.1 61.5 1.0
OD1 A:ASP114 2.1 73.9 1.0
OD2 A:ASP114 2.4 51.5 1.0
CG A:ASP114 2.5 50.9 1.0
O A:HOH402 2.6 67.4 1.0
OE2 A:GLU157 2.9 86.6 1.0
O3A A:COA301 3.3 49.4 1.0
CD A:GLU116 3.3 57.2 1.0
CD A:GLU157 3.4 85.3 1.0
OE1 A:GLU157 3.5 96.5 1.0
O A:ALA115 3.6 43.6 1.0
CG A:GLU116 3.9 55.7 1.0
CB A:ASP114 4.0 53.4 1.0
O1A A:COA301 4.1 54.7 1.0
OE1 A:GLU116 4.3 52.9 1.0
N A:ALA115 4.4 49.6 1.0
P1A A:COA301 4.4 39.4 1.0
C A:ALA115 4.4 41.5 1.0
CE2 A:PHE153 4.5 57.2 1.0
CB A:GLU157 4.6 68.3 1.0
CG A:GLU157 4.6 71.9 1.0
CA A:ASP114 4.8 40.4 1.0
O A:HOH407 4.8 48.8 1.0
C A:ASP114 5.0 54.2 1.0

Manganese binding site 2 out of 8 in 8qzi

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Manganese binding site 2 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:61.9
occ:1.00
 O A:HOH405 1.9 54.7 1.0
O2A A:COA301 2.0 62.0 1.0
O A:HOH403 2.0 64.7 1.0
O A:HOH407 2.3 48.8 1.0
O A:HIS93 2.3 58.8 1.0
ND1 A:HIS93 2.3 54.8 1.0
CE1 A:HIS93 3.0 55.7 1.0
C A:HIS93 3.3 44.8 1.0
P1A A:COA301 3.3 39.4 1.0
CG A:HIS93 3.5 48.0 1.0
O1A A:COA301 3.6 54.7 1.0
CA A:HIS93 3.9 44.9 1.0
N A:HIS93 4.0 43.7 1.0
CB A:HIS93 4.0 47.3 1.0
OE2 A:GLU51 4.1 88.3 1.0
O A:HOH402 4.1 67.4 1.0
O F:HOH2202 4.1 54.2 1.0
O3A A:COA301 4.1 49.4 1.0
NE2 A:HIS93 4.3 59.9 1.0
N A:CYS94 4.3 50.2 1.0
CD A:GLU51 4.4 83.4 1.0
C5B A:COA301 4.4 28.3 1.0
OE1 A:GLU51 4.5 81.9 1.0
O5B A:COA301 4.5 34.7 1.0
CD2 A:HIS93 4.5 58.2 1.0
CA A:CYS94 4.6 46.2 1.0
O F:ALA2068 5.0 116.0 1.0

Manganese binding site 3 out of 8 in 8qzi

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Manganese binding site 3 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


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 Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:66.1
occ:1.00
 OE2 B:GLU116 1.9 90.8 1.0
O B:HOH402 2.1 56.9 1.0
O B:HOH401 2.2 41.4 1.0
OD1 B:ASP114 2.3 65.3 1.0
OE2 B:GLU157 2.5 110.5 1.0
OD2 B:ASP114 2.5 62.4 1.0
CG B:ASP114 2.8 58.4 1.0
O2A B:COA301 3.0 45.8 1.0
CD B:GLU116 3.1 80.6 1.0
CD B:GLU157 3.4 103.9 1.0
O B:ALA115 3.6 41.2 1.0
CG B:GLU116 3.6 69.1 1.0
OE1 B:GLU157 3.9 112.5 1.0
O3A B:COA301 4.1 53.9 1.0
OE1 B:GLU116 4.1 84.5 1.0
P1A B:COA301 4.2 37.2 1.0
CB B:ASP114 4.3 50.6 1.0
C B:ALA115 4.4 46.5 1.0
CG B:GLU157 4.5 84.9 1.0
N B:ALA115 4.6 51.7 1.0
CE2 B:PHE153 4.6 48.0 1.0
CB B:GLU157 4.7 70.5 1.0
O B:HOH404 4.8 45.3 1.0
OG1 B:THR92 4.8 50.3 1.0
CB B:GLU116 4.9 65.7 1.0
CA B:ASP114 5.0 47.2 1.0

Manganese binding site 4 out of 8 in 8qzi

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Manganese binding site 4 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


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 Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:54.9
occ:1.00
 O B:HOH405 1.9 59.1 1.0
O B:HOH404 2.0 45.3 1.0
ND1 B:HIS93 2.0 67.0 1.0
O B:HIS93 2.1 71.3 1.0
O B:HOH407 2.1 59.5 1.0
O1A B:COA301 2.1 50.5 1.0
CE1 B:HIS93 2.7 61.9 1.0
CG B:HIS93 3.2 61.3 1.0
C B:HIS93 3.2 58.1 1.0
P1A B:COA301 3.5 37.2 1.0
O3A B:COA301 3.7 53.9 1.0
CA B:HIS93 3.8 54.6 1.0
CB B:HIS93 3.8 45.3 1.0
N B:HIS93 3.8 42.2 1.0
NE2 B:HIS93 3.9 63.1 1.0
OE2 B:GLU51 4.0 80.9 1.0
C5B B:COA301 4.1 35.8 1.0
OE1 B:GLU51 4.1 108.9 1.0
CD2 B:HIS93 4.2 63.3 1.0
N B:CYS94 4.3 43.0 1.0
CD B:GLU51 4.3 95.4 1.0
O2A B:COA301 4.4 45.8 1.0
CB F:ASP2104 4.5 108.1 1.0
O5B B:COA301 4.5 32.6 1.0
O B:HOH401 4.5 41.4 1.0
CA B:CYS94 4.7 43.5 1.0

Manganese binding site 5 out of 8 in 8qzi

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Manganese binding site 5 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


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 Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:67.5
occ:1.00
 OE1 C:GLU116 1.8 73.1 1.0
O C:HOH406 2.0 58.6 1.0
O C:HOH408 2.3 50.8 1.0
OD1 C:ASP114 2.4 55.5 1.0
OE2 C:GLU157 2.4 94.0 1.0
OD2 C:ASP114 2.5 54.6 1.0
CG C:ASP114 2.8 53.1 1.0
CD C:GLU116 3.0 63.1 1.0
CD C:GLU157 3.3 90.1 1.0
O C:ALA115 3.5 41.5 1.0
CG C:GLU116 3.6 54.5 1.0
O1A C:COA301 3.6 59.5 1.0
OE1 C:GLU157 3.9 99.2 1.0
OE2 C:GLU116 4.0 70.2 1.0
O3A C:COA301 4.2 88.9 1.0
O5A C:COA301 4.2 123.6 1.0
CB C:ASP114 4.3 50.6 1.0
CG C:GLU157 4.4 67.9 1.0
CE2 C:PHE153 4.4 47.4 1.0
C C:ALA115 4.4 41.7 1.0
CB C:GLU157 4.6 53.0 1.0
N C:ALA115 4.6 49.8 1.0
P1A C:COA301 4.7 46.8 1.0
P2A C:COA301 4.9 117.0 1.0
CB C:GLU116 4.9 57.8 1.0
O C:HOH407 4.9 40.4 1.0
OG1 C:THR92 4.9 49.1 1.0
CD2 C:PHE153 5.0 49.4 1.0
CA C:ASP114 5.0 46.7 1.0

Manganese binding site 6 out of 8 in 8qzi

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Manganese binding site 6 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:47.3
occ:1.00
 O C:HIS93 2.0 62.7 1.0
O2A C:COA301 2.0 50.4 1.0
O C:HOH409 2.1 65.1 1.0
ND1 C:HIS93 2.2 62.7 1.0
O C:HOH407 2.2 40.4 1.0
O C:HOH402 2.3 110.9 1.0
C C:HIS93 3.0 47.6 1.0
CE1 C:HIS93 3.0 59.7 1.0
O4A C:COA301 3.2 123.2 1.0
CG C:HIS93 3.3 52.0 1.0
P1A C:COA301 3.5 46.8 1.0
CA C:HIS93 3.6 50.1 1.0
N C:HIS93 3.6 45.9 1.0
CB C:HIS93 3.7 44.7 1.0
P2A C:COA301 3.8 117.0 1.0
OE1 C:GLU51 3.8 82.3 1.0
O5A C:COA301 3.9 123.6 1.0
OE2 C:GLU51 4.1 66.1 1.0
N C:CYS94 4.1 42.7 1.0
NE2 C:HIS93 4.2 58.9 1.0
CD C:GLU51 4.2 74.8 1.0
O1A C:COA301 4.2 59.5 1.0
O3A C:COA301 4.2 88.9 1.0
CD2 C:HIS93 4.3 59.9 1.0
CA C:CYS94 4.5 46.3 1.0
C5B C:COA301 4.6 36.8 1.0
O5B C:COA301 4.6 38.8 1.0
O C:HOH408 4.7 50.8 1.0
C C:THR92 4.9 50.8 1.0

Manganese binding site 7 out of 8 in 8qzi

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Manganese binding site 7 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:62.6
occ:1.00
 OE2 D:GLU116 2.0 66.6 1.0
O D:HOH405 2.2 56.7 1.0
O D:HOH403 2.5 51.0 1.0
OD1 D:ASP114 2.5 58.4 1.0
OD2 D:ASP114 2.6 63.8 1.0
OE2 D:GLU157 2.6 72.0 1.0
CG D:ASP114 2.9 57.2 1.0
CD D:GLU116 3.1 63.2 1.0
CD D:GLU157 3.5 70.5 1.0
O3A D:COA301 3.5 71.1 1.0
O D:ALA115 3.5 40.4 1.0
CG D:GLU116 3.6 58.4 1.0
O2A D:COA301 3.9 47.4 1.0
OE1 D:GLU157 4.0 75.0 1.0
OE1 D:GLU116 4.2 66.6 1.0
CB D:ASP114 4.4 55.3 1.0
C D:ALA115 4.5 46.3 1.0
P1A D:COA301 4.5 38.7 1.0
CG D:GLU157 4.5 62.4 1.0
CE2 D:PHE153 4.5 52.5 1.0
N D:ALA115 4.5 40.6 1.0
P2A D:COA301 4.6 95.2 1.0
O6A D:COA301 4.6 105.1 1.0
O D:HOH411 4.7 53.1 1.0
O5A D:COA301 4.7 96.8 1.0
CB D:GLU157 4.7 51.9 1.0
OG1 D:THR92 4.9 54.2 1.0
CB D:GLU116 5.0 52.9 1.0

Manganese binding site 8 out of 8 in 8qzi

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Manganese binding site 8 out of 8 in the Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Pptt-Acp From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn303

b:43.1
occ:1.00
 O D:HOH407 1.7 56.2 1.0
O D:HOH406 1.9 57.7 1.0
O D:HIS93 2.1 64.9 1.0
O1A D:COA301 2.1 62.4 1.0
ND1 D:HIS93 2.4 45.5 1.0
O D:HOH411 2.4 53.1 1.0
C D:HIS93 3.1 54.1 1.0
CE1 D:HIS93 3.2 48.2 1.0
P1A D:COA301 3.4 38.7 1.0
CG D:HIS93 3.4 45.3 1.0
O3A D:COA301 3.5 71.1 1.0
CA D:HIS93 3.7 43.1 1.0
O4A D:COA301 3.7 92.5 1.0
N D:HIS93 3.7 43.1 1.0
CB D:HIS93 3.8 44.3 1.0
OE2 D:GLU51 4.1 68.3 1.0
P2A D:COA301 4.2 95.2 1.0
N D:CYS94 4.2 42.4 1.0
C5B D:COA301 4.2 45.4 1.0
O D:HOH403 4.3 51.0 1.0
OE1 D:GLU51 4.3 80.0 1.0
CD D:GLU51 4.4 70.0 1.0
O2A D:COA301 4.4 47.4 1.0
NE2 D:HIS93 4.4 47.7 1.0
O5B D:COA301 4.4 31.3 1.0
O6A D:COA301 4.4 105.1 1.0
CD2 D:HIS93 4.5 46.7 1.0
CA D:CYS94 4.6 42.7 1.0
O E:ALA2067 4.7 124.8 1.0
C D:THR92 4.9 53.5 1.0
CD1 E:LEU2065 5.0 122.8 1.0

Reference:

S.Gavalda, A.Faille, S.Fioccola, M.C.Nguyen, C.Carivenc, K.Rottier, Y.Rufin, S.Saitta, G.Czaplicki, C.Guilhot, C.Chalut, M.Brut, L.Mourey, J.D.Pedelacq. Catalytic Cycle of Type II 4'-Phosphopantetheinyl Transferases Acs Catalysis V. 14 8561 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C06249
Page generated: Sun Oct 6 13:45:04 2024

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