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Manganese in PDB 7cx7: Crystal Structure of Arabinose Isomerase From Hybrid AI8

Enzymatic activity of Crystal Structure of Arabinose Isomerase From Hybrid AI8

All present enzymatic activity of Crystal Structure of Arabinose Isomerase From Hybrid AI8:
5.3.1.4;

Protein crystallography data

The structure of Crystal Structure of Arabinose Isomerase From Hybrid AI8, PDB code: 7cx7 was solved by N.K.Q.Hoang, I.Dhanasingh, T.P.Cao, J.Y.Sung, S.M.Shin, D.W.Lee, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 204.591, 81.907, 192.001, 90, 117.9, 90
R / Rfree (%) 19.2 / 26.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Arabinose Isomerase From Hybrid AI8 (pdb code 7cx7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Crystal Structure of Arabinose Isomerase From Hybrid AI8, PDB code: 7cx7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 7cx7

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Manganese binding site 1 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:41.0
occ:1.00
 NE2 A:HIS448 2.1 43.7 1.0
NE2 A:HIS349 2.3 42.6 1.0
OE2 A:GLU307 2.4 60.0 1.0
O A:HOH642 2.4 40.6 1.0
OE1 A:GLU307 2.8 59.9 1.0
CD A:GLU307 2.9 50.4 1.0
OE2 A:GLU332 2.9 49.6 1.0
OE1 A:GLU332 3.0 53.6 1.0
CE1 A:HIS448 3.0 42.9 1.0
CD A:GLU332 3.1 46.5 1.0
CD2 A:HIS349 3.1 41.0 1.0
CD2 A:HIS448 3.2 37.9 1.0
CE1 A:HIS349 3.3 38.0 1.0
ND1 A:HIS448 4.2 36.1 1.0
CG A:GLU332 4.3 44.5 1.0
CG A:HIS448 4.3 34.8 1.0
CG A:HIS349 4.3 40.6 1.0
ND1 A:HIS349 4.3 35.4 1.0
CD2 A:HIS447 4.3 41.2 1.0
NE2 A:HIS447 4.4 40.7 1.0
CG A:GLU307 4.4 45.7 1.0
CB A:GLU332 4.7 39.8 1.0
CZ A:PHE330 4.8 29.6 1.0

Manganese binding site 2 out of 9 in 7cx7

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Manganese binding site 2 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:61.1
occ:1.00
 O B:GLY398 2.1 30.9 1.0
O A:GLY398 2.2 27.3 1.0
O A:HOH649 2.3 29.6 1.0
C B:GLY398 3.1 27.4 1.0
OD2 B:ASP195 3.2 41.2 1.0
C A:GLY398 3.3 25.2 1.0
OD2 A:ASP195 3.5 39.2 1.0
CA B:GLY398 3.6 29.7 1.0
CB B:ASP195 3.8 43.0 1.0
CA A:GLY398 3.9 22.2 1.0
CB A:ASP195 3.9 38.9 1.0
O B:HOH606 3.9 30.8 1.0
CG B:ASP195 4.0 40.0 1.0
OD2 B:ASP396 4.0 44.2 1.0
O B:HOH660 4.1 39.1 1.0
OD1 B:ASP396 4.1 34.0 1.0
CG A:ASP195 4.2 41.2 1.0
O A:HOH662 4.2 27.7 1.0
O B:HOH652 4.3 33.0 1.0
N B:HIS399 4.3 27.1 1.0
CG B:ASP396 4.5 39.2 1.0
N A:HIS399 4.5 27.1 1.0
OD2 A:ASP396 4.6 41.9 1.0
OD1 A:ASP396 4.7 38.1 1.0
N B:GLY398 4.7 29.3 1.0
CA B:HIS399 4.8 29.9 1.0
CA A:HIS399 4.9 29.1 1.0
CG A:ASP396 5.0 35.6 1.0
N A:GLY398 5.0 21.1 1.0

Manganese binding site 3 out of 9 in 7cx7

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Manganese binding site 3 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:45.5
occ:1.00
 NE2 B:HIS349 2.1 47.9 1.0
NE2 B:HIS448 2.2 63.4 1.0
OE1 B:GLU332 2.4 57.8 1.0
OE1 B:GLU307 2.4 43.4 1.0
OE2 B:GLU307 2.7 52.6 1.0
CD B:GLU307 2.8 42.5 1.0
O B:HOH647 2.9 26.2 1.0
CE1 B:HIS349 3.0 54.5 1.0
CD B:GLU332 3.0 50.5 1.0
CE1 B:HIS448 3.1 59.2 1.0
OE2 B:GLU332 3.2 60.4 1.0
CD2 B:HIS448 3.2 56.9 1.0
CD2 B:HIS349 3.2 53.1 1.0
ND1 B:HIS349 4.1 51.1 1.0
NE2 B:HIS447 4.2 44.1 1.0
CD2 B:HIS447 4.2 45.0 1.0
CG B:GLU332 4.2 48.6 1.0
CG B:GLU307 4.3 39.8 1.0
ND1 B:HIS448 4.3 50.2 1.0
CG B:HIS349 4.3 51.9 1.0
CG B:HIS448 4.3 48.3 1.0
CZ B:PHE330 4.8 32.7 1.0
CB B:GLU332 4.9 44.2 1.0
CB B:GLU307 4.9 34.5 1.0

Manganese binding site 4 out of 9 in 7cx7

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Manganese binding site 4 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:58.0
occ:1.00
 O D:GLY398 2.1 34.6 1.0
O C:GLY398 2.1 36.5 1.0
O C:HOH611 2.2 27.4 1.0
O D:HOH620 2.3 32.3 1.0
O D:HOH602 2.3 29.9 1.0
C D:GLY398 3.1 32.5 1.0
C C:GLY398 3.3 32.6 1.0
CA D:GLY398 3.5 31.6 1.0
OD2 C:ASP195 3.6 38.2 1.0
CB C:ASP195 3.8 38.2 1.0
O C:HOH623 4.0 40.1 1.0
CA C:GLY398 4.0 29.9 1.0
O C:HOH618 4.0 25.4 1.0
O D:HOH603 4.1 33.3 1.0
CG C:ASP195 4.2 39.4 1.0
OD2 D:ASP195 4.2 44.5 1.0
CB D:ASP195 4.2 35.5 1.0
OD2 C:ASP396 4.3 46.6 1.0
OD1 D:ASP396 4.3 38.1 1.0
N D:HIS399 4.3 32.7 1.0
OD1 C:ASP396 4.3 45.7 1.0
N C:HIS399 4.3 34.2 1.0
O D:HOH646 4.4 32.3 1.0
OD2 D:ASP396 4.6 42.7 1.0
CA C:HIS399 4.7 31.6 1.0
N D:GLY398 4.7 31.4 1.0
CG C:ASP396 4.7 46.5 1.0
CG D:ASP195 4.8 40.0 1.0
CA D:HIS399 4.8 30.1 1.0
CG D:ASP396 4.8 40.5 1.0

Manganese binding site 5 out of 9 in 7cx7

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Manganese binding site 5 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:45.4
occ:1.00
 NE2 C:HIS448 2.1 53.3 1.0
OE1 C:GLU307 2.2 50.0 1.0
NE2 C:HIS349 2.3 67.3 1.0
O C:HOH649 2.3 42.7 1.0
OE2 C:GLU332 2.6 51.7 1.0
OE1 C:GLU332 2.6 60.8 1.0
CD C:GLU332 2.9 45.5 1.0
CE1 C:HIS448 3.0 49.8 1.0
CD2 C:HIS349 3.1 66.6 1.0
CD2 C:HIS448 3.1 50.6 1.0
CD C:GLU307 3.3 58.0 1.0
CE1 C:HIS349 3.3 62.5 1.0
OE2 C:GLU307 3.7 63.9 1.0
ND1 C:HIS448 4.1 44.3 1.0
CG C:HIS448 4.2 41.9 1.0
CG C:GLU332 4.2 44.5 1.0
NE2 C:HIS447 4.2 50.8 1.0
CG C:HIS349 4.3 64.2 1.0
ND1 C:HIS349 4.3 59.8 1.0
O F:HOH645 4.4 36.5 1.0
CD2 C:HIS447 4.4 49.1 1.0
CG C:GLU307 4.5 62.5 1.0
CB C:GLU332 4.8 39.9 1.0
CZ C:PHE330 4.9 30.2 1.0

Manganese binding site 6 out of 9 in 7cx7

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Manganese binding site 6 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:43.1
occ:1.00
 NE2 D:HIS349 2.2 47.3 1.0
NE2 D:HIS448 2.3 50.6 1.0
OE2 D:GLU307 2.6 49.3 1.0
OE1 D:GLU332 2.6 52.3 1.0
OE2 D:GLU332 2.8 52.6 1.0
CD D:GLU332 2.9 48.9 1.0
CD D:GLU307 3.1 51.7 1.0
OE1 D:GLU307 3.1 52.3 1.0
CD2 D:HIS349 3.1 51.4 1.0
CD2 D:HIS448 3.2 46.2 1.0
CE1 D:HIS349 3.3 45.4 1.0
CE1 D:HIS448 3.3 49.4 1.0
CE1 D:HIS447 3.8 49.4 1.0
ND1 D:HIS447 4.0 46.1 1.0
CG D:GLU332 4.1 48.7 1.0
CG D:HIS349 4.3 47.0 1.0
ND1 D:HIS349 4.3 43.3 1.0
CG D:GLU307 4.4 48.4 1.0
ND1 D:HIS448 4.4 49.0 1.0
CG D:HIS448 4.4 41.9 1.0
CB D:GLU332 4.7 40.5 1.0
CZ D:PHE330 4.9 34.6 1.0

Manganese binding site 7 out of 9 in 7cx7

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Manganese binding site 7 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn503

b:70.1
occ:1.00
 O E:GLY398 1.9 39.0 1.0
O E:HOH610 2.2 28.2 1.0
C E:GLY398 3.0 31.8 1.0
O E:HOH626 3.4 38.3 1.0
OD2 E:ASP195 3.7 47.2 1.0
CA E:GLY398 3.7 32.4 1.0
CB E:ASP195 3.9 43.0 1.0
OD2 E:ASP396 4.0 43.9 1.0
N E:HIS399 4.1 32.9 1.0
OD1 E:ASP396 4.3 42.0 1.0
CG E:ASP195 4.3 43.9 1.0
CA E:HIS399 4.5 34.0 1.0
CG E:ASP396 4.6 43.5 1.0
N E:GLY398 4.8 38.5 1.0

Manganese binding site 8 out of 9 in 7cx7

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Manganese binding site 8 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


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 Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn504

b:58.0
occ:1.00
 OE1 E:GLU332 2.3 51.0 1.0
NE2 E:HIS448 2.4 49.9 1.0
NE2 E:HIS349 2.4 53.1 1.0
OE1 E:GLU307 2.4 57.1 1.0
O E:HOH644 2.8 27.5 1.0
CD E:GLU307 3.0 57.9 1.0
OE2 E:GLU307 3.1 61.7 1.0
CD E:GLU332 3.1 55.3 1.0
CD2 E:HIS448 3.3 42.0 1.0
CE1 E:HIS349 3.3 59.6 1.0
OE2 E:GLU332 3.3 66.9 1.0
CE1 E:HIS448 3.4 50.3 1.0
CD2 E:HIS349 3.4 56.7 1.0
NE2 E:HIS447 4.0 46.1 1.0
CD2 E:HIS447 4.0 47.5 1.0
CG E:GLU307 4.4 54.5 1.0
ND1 E:HIS349 4.4 59.7 1.0
CG E:HIS448 4.4 45.4 1.0
ND1 E:HIS448 4.5 50.2 1.0
CG E:HIS349 4.5 60.1 1.0
CG E:GLU332 4.5 54.3 1.0
CB E:GLU332 5.0 51.9 1.0

Manganese binding site 9 out of 9 in 7cx7

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Manganese binding site 9 out of 9 in the Crystal Structure of Arabinose Isomerase From Hybrid AI8


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Arabinose Isomerase From Hybrid AI8 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn503

b:53.2
occ:1.00
 OE1 F:GLU332 1.9 51.6 1.0
OE1 F:GLU307 2.2 52.9 1.0
NE2 F:HIS448 2.3 45.7 1.0
NE2 F:HIS349 2.3 47.1 1.0
CD F:GLU332 2.8 53.7 1.0
OE2 F:GLU332 3.1 64.4 1.0
CD F:GLU307 3.1 56.7 1.0
CD2 F:HIS448 3.2 38.6 1.0
CE1 F:HIS349 3.2 49.0 1.0
CD2 F:HIS349 3.3 46.7 1.0
CE1 F:HIS448 3.3 44.7 1.0
OE2 F:GLU307 3.4 71.0 1.0
CD2 F:HIS447 4.0 49.9 1.0
NE2 F:HIS447 4.2 49.0 1.0
CG F:GLU332 4.2 52.0 1.0
CG F:HIS448 4.3 43.0 1.0
ND1 F:HIS349 4.3 49.9 1.0
ND1 F:HIS448 4.4 44.3 1.0
CG F:HIS349 4.4 50.0 1.0
CG F:GLU307 4.5 56.7 1.0
CZ F:PHE330 4.7 55.7 1.0
CB F:GLU332 4.8 51.0 1.0

Reference:

N.K.Q.Hoang, I.Dhanasingh, T.P.Cao, J.Y.Sung, S.M.Shin, D.W.Lee, S.H.Lee. Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Wt To Be Published.
Page generated: Sun Oct 6 08:19:15 2024

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