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Manganese in PDB 7cyy: Crystal Structure of Arabinose Isomerase From Hybrid AI8 with Adonitol

Enzymatic activity of Crystal Structure of Arabinose Isomerase From Hybrid AI8 with Adonitol

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

Protein crystallography data

The structure of Crystal Structure of Arabinose Isomerase From Hybrid AI8 with Adonitol, PDB code: 7cyy 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) 48.18 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 205.582, 82.12, 192.726, 90, 117.93, 90
R / Rfree (%) 18.7 / 26.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Arabinose Isomerase From Hybrid AI8 with Adonitol (pdb code 7cyy). 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 with Adonitol, PDB code: 7cyy:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 7cyy

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


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

b:56.2
occ:1.00
 O E:HOH609 2.3 37.8 1.0
O A:GLY398 2.3 34.8 1.0
O A:HOH606 2.3 33.0 1.0
O E:GLY398 2.3 38.4 1.0
O E:HOH611 2.3 33.8 1.0
C E:GLY398 3.2 36.8 1.0
OD2 A:ASP195 3.4 41.6 1.0
O A:HOH655 3.4 36.9 1.0
C A:GLY398 3.5 31.7 1.0
O A:HOH635 3.5 38.9 1.0
CB A:ASP195 3.6 38.4 1.0
CA E:GLY398 3.6 39.9 1.0
CG A:ASP195 4.0 47.5 1.0
CA A:GLY398 4.2 29.3 1.0
O E:HOH606 4.2 41.1 1.0
OD2 A:ASP396 4.3 39.0 1.0
CB E:ASP195 4.3 34.5 1.0
OD2 E:ASP195 4.3 42.1 1.0
OD1 A:ASP396 4.4 38.0 1.0
N E:HIS399 4.4 39.2 1.0
O E:HOH622 4.5 28.3 1.0
N A:HIS399 4.5 34.1 1.0
OD1 E:ASP396 4.6 41.3 1.0
CA A:HIS399 4.6 34.5 1.0
OD2 E:ASP396 4.7 43.2 1.0
CG A:ASP396 4.8 40.4 1.0
N E:GLY398 4.8 41.4 1.0
CG E:ASP195 4.8 42.0 1.0
CA E:HIS399 4.9 36.9 1.0
CA A:ASP195 5.0 39.3 1.0
CB A:GLU198 5.0 38.8 1.0

Manganese binding site 2 out of 9 in 7cyy

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


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

b:45.5
occ:1.00
 OE2 A:GLU332 2.0 52.8 1.0
O5 D:RB0501 2.0 53.7 1.0
NE2 A:HIS448 2.1 46.4 1.0
NE2 A:HIS349 2.4 43.8 1.0
OE1 A:GLU307 2.7 49.6 1.0
O4 D:RB0501 2.8 50.1 1.0
C5 D:RB0501 2.8 58.9 1.0
OE2 A:GLU307 3.0 55.9 1.0
C4 D:RB0501 3.1 57.7 1.0
CD A:GLU307 3.1 49.3 1.0
CE1 A:HIS448 3.1 45.4 1.0
CD2 A:HIS448 3.1 40.9 1.0
CD A:GLU332 3.2 51.0 1.0
CD2 A:HIS349 3.3 41.4 1.0
CE1 A:HIS349 3.4 44.4 1.0
OE1 A:GLU332 3.9 57.3 1.0
NE2 A:HIS447 4.2 46.6 1.0
ND1 A:HIS448 4.2 42.9 1.0
CG A:HIS448 4.3 40.0 1.0
CD2 A:HIS447 4.3 46.4 1.0
CG A:GLU307 4.3 48.8 1.0
CG A:GLU332 4.3 45.9 1.0
CG A:HIS349 4.4 43.3 1.0
ND1 A:HIS349 4.5 42.4 1.0
C3 D:RB0501 4.6 67.9 1.0
CZ A:PHE330 4.8 30.0 1.0
CB A:GLU307 4.9 45.1 1.0

Manganese binding site 3 out of 9 in 7cyy

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


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 with Adonitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:52.5
occ:1.00
 O1 B:RB0501 1.9 56.5 1.0
OE2 B:GLU332 2.1 52.2 1.0
NE2 B:HIS349 2.1 50.5 1.0
NE2 B:HIS448 2.4 48.5 1.0
O2 B:RB0501 2.5 60.2 1.0
OE1 B:GLU307 2.6 52.7 1.0
CD2 B:HIS349 3.0 53.0 1.0
C1 B:RB0501 3.0 54.1 1.0
OE2 B:GLU307 3.0 61.5 1.0
CE1 B:HIS349 3.1 50.4 1.0
CD B:GLU307 3.1 53.4 1.0
C2 B:RB0501 3.2 58.3 1.0
CD B:GLU332 3.2 54.5 1.0
CD2 B:HIS448 3.3 43.8 1.0
CE1 B:HIS448 3.3 47.6 1.0
OE1 B:GLU332 3.9 58.7 1.0
CG B:HIS349 4.1 51.2 1.0
ND1 B:HIS349 4.1 54.8 1.0
CG B:GLU332 4.2 46.7 1.0
NE2 B:HIS447 4.3 45.1 1.0
CD2 B:HIS447 4.3 45.1 1.0
ND1 B:HIS448 4.4 45.4 1.0
CG B:HIS448 4.4 41.8 1.0
CG B:GLU307 4.5 42.4 1.0
C3 B:RB0501 4.6 66.8 1.0
CB B:GLU332 4.7 42.4 1.0
OH B:TYR334 4.8 72.5 1.0
CZ B:PHE330 4.8 45.2 1.0

Manganese binding site 4 out of 9 in 7cyy

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


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 with Adonitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:55.7
occ:1.00
 O B:GLY398 2.2 38.9 1.0
O B:HOH637 2.5 44.7 1.0
O B:HOH603 2.6 36.6 1.0
C B:GLY398 3.2 40.4 1.0
CA B:GLY398 3.7 36.2 1.0
OD2 B:ASP195 3.8 41.7 1.0
CB B:ASP195 4.0 39.1 1.0
OD1 B:ASP396 4.2 37.5 1.0
O B:HOH634 4.4 38.6 1.0
N B:HIS399 4.4 42.5 1.0
CG B:ASP195 4.4 41.2 1.0
OD2 B:ASP396 4.7 43.4 1.0
CA B:HIS399 4.7 43.2 1.0
N B:GLY398 4.8 37.5 1.0
CG B:ASP396 4.8 42.3 1.0

Manganese binding site 5 out of 9 in 7cyy

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


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 with Adonitol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:54.0
occ:1.00
 NE2 C:HIS448 2.1 55.1 1.0
OE1 C:GLU332 2.2 49.8 1.0
OE1 C:GLU307 2.2 62.3 1.0
O5 F:RB0501 2.3 62.0 1.0
C5 F:RB0501 2.4 57.8 1.0
NE2 C:HIS349 2.5 57.5 1.0
OE2 C:GLU307 2.8 53.8 1.0
CD C:GLU307 2.8 55.4 1.0
CE1 C:HIS448 3.1 49.8 1.0
CD2 C:HIS448 3.1 51.9 1.0
CD C:GLU332 3.3 52.3 1.0
CD2 C:HIS349 3.3 54.6 1.0
CE1 C:HIS349 3.4 56.7 1.0
C4 F:RB0501 3.6 63.5 1.0
OE2 C:GLU332 3.8 58.7 1.0
NE2 C:HIS447 4.0 57.6 1.0
ND1 C:HIS448 4.2 47.2 1.0
CG C:HIS448 4.2 47.7 1.0
CD2 C:HIS447 4.3 53.9 1.0
CG C:GLU307 4.3 50.8 1.0
O4 F:RB0501 4.3 70.4 1.0
CG C:HIS349 4.5 59.4 1.0
ND1 C:HIS349 4.5 60.7 1.0
CG C:GLU332 4.5 47.9 1.0
O3 F:RB0501 4.7 57.2 1.0
CZ C:PHE330 4.7 40.0 1.0
C3 F:RB0501 4.8 61.8 1.0

Manganese binding site 6 out of 9 in 7cyy

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


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 with Adonitol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn503

b:60.3
occ:1.00
 O2 D:RB0502 1.9 61.4 1.0
NE2 D:HIS349 2.1 51.4 1.0
NE2 D:HIS448 2.1 55.6 1.0
OE1 D:GLU332 2.2 51.0 1.0
OE1 D:GLU307 2.3 63.0 1.0
OE2 D:GLU307 2.7 57.7 1.0
CD D:GLU307 2.8 59.2 1.0
CD2 D:HIS448 3.0 46.0 1.0
CE1 D:HIS349 3.0 56.9 1.0
CD2 D:HIS349 3.1 57.0 1.0
CE1 D:HIS448 3.1 50.7 1.0
O1 D:RB0502 3.2 62.2 1.0
C2 D:RB0502 3.2 63.1 1.0
CD D:GLU332 3.3 56.3 1.0
C1 D:RB0502 3.7 61.2 1.0
O D:HOH602 3.7 55.9 1.0
OE2 D:GLU332 3.8 65.7 1.0
C3 D:RB0502 4.1 68.7 1.0
CG D:HIS448 4.1 47.3 1.0
ND1 D:HIS349 4.1 58.8 1.0
CD2 D:HIS447 4.2 52.1 1.0
ND1 D:HIS448 4.2 47.3 1.0
CG D:HIS349 4.2 60.1 1.0
CG D:GLU307 4.3 57.4 1.0
NE2 D:HIS447 4.4 50.0 1.0
CG D:GLU332 4.6 50.9 1.0
O3 D:RB0502 4.6 68.8 1.0
CZ D:PHE330 4.8 50.8 1.0
CB D:GLU307 4.9 52.5 1.0
CE2 D:PHE330 4.9 46.4 1.0
CB D:GLU332 4.9 50.2 1.0

Manganese binding site 7 out of 9 in 7cyy

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


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 with Adonitol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn504

b:59.9
occ:1.00
 O D:GLY398 2.2 43.6 1.0
C D:GLY398 3.1 38.7 1.0
O D:HOH608 3.2 39.8 1.0
CA D:GLY398 3.6 36.7 1.0
OD2 D:ASP396 3.7 47.9 1.0
CB D:ASP195 3.9 41.1 1.0
OD2 D:ASP195 4.1 49.2 1.0
N D:HIS399 4.3 37.3 1.0
CG D:ASP195 4.5 49.1 1.0
CG D:ASP396 4.5 47.1 1.0
OD1 D:ASP396 4.5 43.6 1.0
N D:GLY398 4.6 42.5 1.0
CA D:HIS399 4.7 32.5 1.0

Manganese binding site 8 out of 9 in 7cyy

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


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 with Adonitol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn502

b:50.6
occ:1.00
 NE2 E:HIS448 2.1 54.5 1.0
OE1 E:GLU332 2.2 59.0 1.0
NE2 E:HIS349 2.4 50.7 1.0
OE2 E:GLU307 2.4 49.1 1.0
C1 E:RB0501 2.6 55.1 1.0
O2 E:RB0501 2.6 55.7 1.0
OE1 E:GLU307 2.9 53.3 1.0
O1 E:RB0501 3.0 55.1 1.0
CD E:GLU307 3.0 46.4 1.0
CE1 E:HIS448 3.0 45.3 1.0
C2 E:RB0501 3.1 56.7 1.0
CD2 E:HIS448 3.2 46.5 1.0
CD2 E:HIS349 3.2 51.1 1.0
CD E:GLU332 3.3 55.5 1.0
CE1 E:HIS349 3.4 52.5 1.0
OE2 E:GLU332 3.7 60.1 1.0
NE2 E:HIS447 4.1 52.7 1.0
ND1 E:HIS448 4.2 39.2 1.0
CG E:HIS448 4.3 40.4 1.0
CD2 E:HIS447 4.3 51.8 1.0
CG E:HIS349 4.4 53.6 1.0
C3 E:RB0501 4.4 66.2 1.0
O3 E:RB0501 4.4 60.9 1.0
CG E:GLU307 4.5 41.6 1.0
ND1 E:HIS349 4.5 53.2 1.0
CG E:GLU332 4.5 52.6 1.0
OH E:TYR334 4.5 75.0 1.0
CZ E:PHE330 4.7 43.4 1.0
CB E:GLU332 4.7 43.5 1.0

Manganese binding site 9 out of 9 in 7cyy

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


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 with Adonitol within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn503

b:56.2
occ:1.00
 OE1 F:GLU332 2.0 58.1 1.0
NE2 F:HIS448 2.2 55.1 1.0
OE1 F:GLU307 2.4 56.8 1.0
NE2 F:HIS349 2.5 56.0 1.0
O5 F:RB0502 2.7 66.4 1.0
O4 F:RB0502 2.7 64.6 1.0
CD2 F:HIS448 2.9 46.5 1.0
CD F:GLU332 3.0 64.0 1.0
OE2 F:GLU307 3.0 66.5 1.0
CD F:GLU307 3.1 59.5 1.0
CE1 F:HIS448 3.3 51.7 1.0
C5 F:RB0502 3.3 64.3 1.0
CD2 F:HIS349 3.3 55.6 1.0
OE2 F:GLU332 3.3 65.0 1.0
CE1 F:HIS349 3.5 57.6 1.0
C4 F:RB0502 3.5 66.1 1.0
O F:HOH612 3.8 58.1 1.0
CD2 F:HIS447 4.0 49.5 1.0
CG F:HIS448 4.2 47.7 1.0
NE2 F:HIS447 4.2 54.1 1.0
ND1 F:HIS448 4.3 51.4 1.0
CG F:GLU332 4.3 53.4 1.0
CG F:HIS349 4.5 60.4 1.0
ND1 F:HIS349 4.5 61.6 1.0
CG F:GLU307 4.5 55.1 1.0
CZ F:PHE330 4.7 53.5 1.0
CB F:GLU332 4.8 51.8 1.0
C3 F:RB0502 4.8 72.1 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 Hybrid AI8 with Adonitol To Be Published.
Page generated: Sun Oct 6 08:19:21 2024

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