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Manganese in PDB 4zb0: A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.

Enzymatic activity of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.

All present enzymatic activity of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.:
5.3.1.5;

Protein crystallography data

The structure of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature., PDB code: 4zb0 was solved by J.Sandy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.38 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.485, 95.020, 98.484, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 18

Manganese Binding Sites:

The binding sites of Manganese atom in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. (pdb code 4zb0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature., PDB code: 4zb0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4zb0

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Manganese binding site 1 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.5
occ:1.00
 OE1 A:GLU217 2.0 12.7 1.0
OD2 A:ASP245 2.1 14.8 1.0
OD2 A:ASP287 2.1 13.4 1.0
O4 A:GLC406 2.1 19.2 1.0
OE2 A:GLU181 2.2 15.1 1.0
O3 A:GLC406 2.2 17.1 1.0
C4 A:GLC406 3.1 18.7 1.0
CD A:GLU181 3.1 11.9 1.0
C3 A:GLC406 3.1 18.3 1.0
CD A:GLU217 3.2 13.5 1.0
CG A:ASP287 3.2 13.1 1.0
CG A:ASP245 3.3 14.3 1.0
OE1 A:GLU181 3.3 14.3 1.0
CB A:ASP287 3.7 12.4 1.0
O A:HOH540 3.8 14.1 1.0
CB A:ASP245 3.9 14.4 1.0
O A:HOH548 4.0 25.9 1.0
CG A:GLU217 4.0 12.7 1.0
CE1 A:HIS220 4.0 11.2 1.0
CB A:GLU217 4.1 12.9 1.0
OE2 A:GLU217 4.2 13.2 1.0
OD1 A:ASP245 4.2 14.1 1.0
OD1 A:ASP287 4.3 12.2 1.0
CG A:GLU181 4.4 11.9 1.0
C5 A:GLC406 4.5 23.1 1.0
C2 A:GLC406 4.6 19.7 1.0
NE2 A:HIS220 4.6 12.7 1.0
ND1 A:HIS220 4.7 10.8 1.0
MN A:MN403 4.7 15.2 1.0

Manganese binding site 2 out of 10 in 4zb0

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Manganese binding site 2 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:17.6
occ:1.00
 O A:HOH608 2.1 15.2 1.0
O A:HOH676 2.1 16.2 1.0
OD1 A:ASP80 2.2 18.2 1.0
CG A:ASP80 3.2 21.2 1.0
OD2 A:ASP80 3.5 31.3 1.0
O A:ASP80 4.0 13.6 1.0
C A:ASP80 4.3 16.8 1.0
OD1 A:ASP81 4.5 21.4 1.0
CB A:ASP80 4.5 18.8 1.0
N A:ASP81 4.7 16.0 1.0
CA A:ASP81 4.7 18.4 1.0
CA A:ASP80 4.9 16.8 1.0

Manganese binding site 3 out of 10 in 4zb0

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Manganese binding site 3 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:15.2
occ:1.00
 OE2 A:GLU217 2.1 13.2 1.0
O A:HOH540 2.1 14.1 1.0
OD1 A:ASP257 2.2 13.7 1.0
OD2 A:ASP255 2.3 15.0 1.0
NE2 A:HIS220 2.3 12.7 1.0
OD1 A:ASP255 2.4 14.0 1.0
CG A:ASP255 2.7 14.3 1.0
CD A:GLU217 2.9 13.5 1.0
CD2 A:HIS220 3.0 11.2 1.0
CG A:ASP257 3.2 14.6 1.0
OE1 A:GLU217 3.2 12.7 1.0
OD2 A:ASP257 3.4 15.1 1.0
CE1 A:HIS220 3.4 11.2 1.0
O A:HOH516 3.8 21.5 1.0
ND2 A:ASN247 3.9 13.2 1.0
O3 A:GLC406 4.0 17.1 1.0
O A:HOH523 4.1 11.1 1.0
CB A:ASP255 4.2 13.6 1.0
CG A:HIS220 4.2 11.1 1.0
CG A:GLU217 4.3 12.7 1.0
ND1 A:HIS220 4.3 10.8 1.0
OD2 A:ASP287 4.4 13.4 1.0
CB A:ASP257 4.6 13.5 1.0
MN A:MN401 4.7 14.5 1.0
CE A:LYS183 4.9 12.0 1.0
O A:HOH565 4.9 26.5 1.0
CA A:ASP257 5.0 13.8 1.0
N A:ASP257 5.0 12.9 1.0

Manganese binding site 4 out of 10 in 4zb0

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Manganese binding site 4 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:33.5
occ:1.00
 NE2 A:HIS71 2.3 24.6 1.0
CE1 A:HIS71 3.0 28.1 1.0
CD2 A:HIS71 3.4 27.2 1.0
OE2 A:GLU67 4.1 41.3 1.0
ND1 A:HIS71 4.2 29.3 1.0
CG A:HIS71 4.4 23.9 1.0

Manganese binding site 5 out of 10 in 4zb0

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Manganese binding site 5 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:73.2
occ:1.00
 O B:HOH667 2.7 17.6 1.0
O B:HOH555 2.9 21.8 1.0
O A:ALA201 3.2 15.9 1.0
NH1 A:ARG205 3.6 57.6 1.0
CB B:ALA238 3.7 19.3 1.0
CZ A:ARG205 3.8 50.9 1.0
C A:ALA201 3.8 15.3 1.0
CB A:ALA201 3.8 15.5 1.0
OE2 B:GLU204 3.8 35.5 1.0
CG A:ARG205 4.0 30.4 1.0
NH2 A:ARG205 4.0 51.5 1.0
CA A:ALA201 4.1 14.5 1.0
NE A:ARG205 4.3 48.6 1.0
CB B:LEU200 4.3 14.9 1.0
O B:LEU200 4.4 13.0 1.0
CG B:GLU204 4.4 23.4 1.0
CD B:GLU204 4.5 27.7 1.0
CD A:ARG205 4.8 40.9 1.0
N A:PHE202 4.8 16.0 1.0
CD1 B:LEU200 4.8 16.4 1.0
CD2 B:LEU200 4.9 17.0 1.0
C B:LEU200 4.9 13.8 1.0
CG B:LEU200 4.9 15.4 1.0
CA B:ALA238 5.0 18.7 1.0

Manganese binding site 6 out of 10 in 4zb0

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Manganese binding site 6 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:17.6
occ:1.00
 HO4 B:GLC406 1.0 20.0 1.0
O4 B:GLC406 2.0 20.0 1.0
OE2 B:GLU181 2.1 17.1 1.0
OE1 B:GLU217 2.2 18.2 1.0
OD2 B:ASP287 2.3 16.4 1.0
OD2 B:ASP245 2.3 14.4 1.0
O3 B:GLC406 2.4 20.0 1.0
HO3 B:GLC406 2.7 20.0 1.0
C3 B:GLC406 2.9 20.0 1.0
C4 B:GLC406 2.9 20.0 1.0
H3 B:GLC406 2.9 20.0 1.0
CD B:GLU181 3.0 16.5 1.0
H4 B:GLC406 3.2 20.0 1.0
OE1 B:GLU181 3.2 15.9 1.0
CG B:ASP287 3.3 15.7 1.0
CG B:ASP245 3.4 15.4 1.0
CD B:GLU217 3.5 14.9 1.0
CB B:ASP287 3.7 14.2 1.0
O B:HOH520 3.8 14.7 1.0
CB B:ASP245 4.0 14.7 1.0
CE1 B:HIS220 4.1 12.7 1.0
CG B:GLU217 4.2 13.5 1.0
CB B:GLU217 4.2 12.2 1.0
C5 B:GLC406 4.3 20.0 1.0
OD1 B:ASP287 4.3 15.4 1.0
C2 B:GLC406 4.4 20.0 1.0
OD1 B:ASP245 4.4 14.9 1.0
CG B:GLU181 4.4 15.3 1.0
OE2 B:GLU217 4.5 16.3 1.0
H5 B:GLC406 4.5 20.0 1.0
NE2 B:HIS220 4.6 14.0 1.0
H2 B:GLC406 4.7 20.0 1.0
MN B:MN402 4.7 16.1 1.0
ND1 B:HIS220 4.8 13.6 1.0
HO2 B:GLC406 4.9 20.0 1.0
ND2 B:ASN215 5.0 14.7 1.0
O2 B:GLC406 5.0 20.0 1.0

Manganese binding site 7 out of 10 in 4zb0

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Manganese binding site 7 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:16.1
occ:1.00
 OE2 B:GLU217 2.1 16.3 1.0
O B:HOH520 2.2 14.7 1.0
OD1 B:ASP257 2.2 15.9 1.0
OD2 B:ASP255 2.2 13.9 1.0
OD1 B:ASP255 2.4 13.2 1.0
NE2 B:HIS220 2.5 14.0 1.0
CG B:ASP255 2.6 14.2 1.0
CD B:GLU217 2.9 14.9 1.0
CD2 B:HIS220 3.0 11.7 1.0
OE1 B:GLU217 3.1 18.2 1.0
HO3 B:GLC406 3.2 20.0 1.0
CG B:ASP257 3.2 15.7 1.0
OD2 B:ASP257 3.3 19.5 1.0
CE1 B:HIS220 3.5 12.7 1.0
O B:HOH551 3.9 20.1 1.0
ND2 B:ASN247 4.0 13.5 1.0
O B:HOH572 4.0 15.0 1.0
O3 B:GLC406 4.0 20.0 1.0
CB B:ASP255 4.1 13.1 1.0
CG B:HIS220 4.2 12.7 1.0
CG B:GLU217 4.3 13.5 1.0
OD2 B:ASP287 4.4 16.4 1.0
ND1 B:HIS220 4.4 13.6 1.0
CB B:ASP257 4.6 15.0 1.0
MN B:MN401 4.7 17.6 1.0
O B:HOH553 4.8 27.8 1.0
HO2 B:GLC406 4.8 20.0 1.0
CA B:ASP257 5.0 15.0 1.0

Manganese binding site 8 out of 10 in 4zb0

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Manganese binding site 8 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:52.5
occ:1.00
 O B:THR6 2.7 16.0 1.0
O B:GLY47 2.9 16.1 1.0
N B:PHE11 3.1 15.2 1.0
N B:HIS49 3.2 15.5 1.0
C B:THR6 3.4 16.2 1.0
CA B:PRO7 3.4 15.8 1.0
N B:ARG10 3.5 18.1 1.0
CB B:PHE11 3.5 14.8 1.0
C B:ALA48 3.6 17.0 1.0
N B:PRO7 3.7 15.7 1.0
CD2 B:PHE11 3.7 16.4 1.0
CB B:HIS49 3.7 19.1 1.0
CA B:PHE11 3.8 15.4 1.0
CA B:ALA48 3.8 15.5 1.0
O B:PHE11 3.8 15.1 1.0
C B:PRO7 3.8 17.0 1.0
O B:PRO7 3.9 17.5 1.0
C B:GLY47 3.9 17.9 1.0
CG B:PHE11 4.0 16.0 1.0
CA B:HIS49 4.0 18.5 1.0
C B:ARG10 4.0 18.0 1.0
CB B:ASP9 4.0 16.2 1.0
CA B:ARG10 4.1 20.9 1.0
C B:ASP9 4.1 18.1 1.0
N B:ASP9 4.2 15.3 1.0
C B:PHE11 4.3 14.8 1.0
N B:ALA48 4.3 14.7 1.0
CA B:ASP9 4.3 16.5 1.0
O B:ALA48 4.4 17.4 1.0
CA B:THR6 4.5 18.2 1.0
N B:THR6 4.6 16.6 1.0
CB B:PRO7 4.7 17.4 1.0
CE2 B:PHE11 4.7 16.6 1.0
CD B:PRO7 4.7 16.8 1.0
N B:GLU8 4.7 15.2 1.0
O B:ASP9 4.9 17.9 1.0
CG B:PRO7 4.9 17.3 1.0
CG B:HIS49 5.0 20.9 1.0
OD2 B:ASP9 5.0 19.4 1.0

Manganese binding site 9 out of 10 in 4zb0

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Manganese binding site 9 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:49.0
occ:1.00
 O B:ASP101 2.8 17.3 1.0
OG1 B:THR105 2.8 11.8 1.0
NZ B:LYS149 3.0 19.8 1.0
CE B:LYS149 3.1 19.6 1.0
N B:GLY142 3.2 13.4 1.0
O B:THR105 3.3 12.8 1.0
CA B:GLU141 3.5 14.9 1.0
O B:GLY142 3.5 14.9 1.0
O B:ARG140 3.6 15.8 1.0
C B:THR105 3.8 13.9 1.0
C B:ASP101 3.8 15.4 1.0
C B:GLU141 3.8 14.5 1.0
CD B:LYS149 3.8 21.4 1.0
CB B:THR105 3.9 15.1 1.0
OE1 B:GLU141 3.9 13.6 1.0
OD1 B:ASP101 4.1 20.6 1.0
CA B:GLY102 4.1 15.8 1.0
NH1 B:ARG188 4.2 19.5 1.0
CA B:GLY142 4.2 13.4 1.0
C B:GLY142 4.3 15.3 1.0
N B:ALA106 4.3 12.7 1.0
N B:GLY102 4.3 15.4 1.0
CB B:GLU141 4.4 13.8 1.0
CA B:THR105 4.4 13.6 1.0
C B:ARG140 4.4 16.1 1.0
N B:GLU141 4.5 16.8 1.0
CG B:ASP101 4.5 18.5 1.0
CA B:ALA106 4.6 13.8 1.0
CG B:LYS149 4.6 20.4 1.0
CD B:GLU141 4.8 15.9 1.0
OD2 B:ASP101 4.8 18.3 1.0
CA B:ASP101 4.9 16.2 1.0
O B:HOH614 4.9 16.3 1.0
O B:GLU141 5.0 14.4 1.0

Manganese binding site 10 out of 10 in 4zb0

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Manganese binding site 10 out of 10 in the A Dehydrated Form of Glucose Isomerase Collected at Room Temperature.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of A Dehydrated Form of Glucose Isomerase Collected at Room Temperature. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn405

b:55.3
occ:1.00
 O B:GLN4 4.1 19.8 1.0
OD1 B:ASP9 4.2 17.7 1.0
OD2 B:ASP9 4.2 19.4 1.0
OG1 B:THR6 4.6 15.6 1.0
CG B:ASP9 4.6 18.2 1.0
CG2 B:THR6 4.8 18.6 1.0

Reference:

C.M.Lobley, J.Sandy, J.Sanchez-Weatherby, M.Mazzorana, T.Krojer, R.P.Nowak, T.L.Sorensen. A Generic Protocol For Protein Crystal Dehydration Using the HC1B Humidity Controller. Acta Crystallogr D Struct V. 72 629 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27139626
DOI: 10.1107/S2059798316003065
Page generated: Sat Oct 5 23:12:59 2024

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