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Manganese in PDB 4zbc: A Dehydrated Form of Glucose Isomerase Collected at 100K.

Enzymatic activity of A Dehydrated Form of Glucose Isomerase Collected at 100K.

All present enzymatic activity of A Dehydrated Form of Glucose Isomerase Collected at 100K.:
5.3.1.5;

Protein crystallography data

The structure of A Dehydrated Form of Glucose Isomerase Collected at 100K., PDB code: 4zbc was solved by J.Sandy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.58 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.629, 93.641, 97.640, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 18.2

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Manganese atom in the A Dehydrated Form of Glucose Isomerase Collected at 100K. (pdb code 4zbc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the A Dehydrated Form of Glucose Isomerase Collected at 100K., PDB code: 4zbc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in 4zbc

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Manganese binding site 1 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:12.7
occ:1.00
 O4 A:GLC407 2.0 14.4 1.0
OD2 A:ASP287 2.1 11.5 1.0
OE2 A:GLU181 2.1 10.6 1.0
O3 A:GLC407 2.1 15.1 1.0
OE1 A:GLU217 2.2 7.6 1.0
OD2 A:ASP245 2.2 10.9 1.0
CD A:GLU181 3.0 11.5 1.0
C3 A:GLC407 3.0 15.9 1.0
C4 A:GLC407 3.1 14.8 1.0
CG A:ASP287 3.1 10.8 1.0
OE1 A:GLU181 3.3 12.1 1.0
CD A:GLU217 3.4 8.8 1.0
CG A:ASP245 3.4 10.6 1.0
CB A:ASP287 3.6 10.1 1.0
O A:HOH514 3.7 10.6 1.0
CE1 A:HIS220 3.9 8.6 1.0
CB A:ASP245 4.0 9.6 1.0
O A:HOH633 4.0 12.1 1.0
CG A:GLU217 4.1 8.5 1.0
CB A:GLU217 4.1 8.5 1.0
OD1 A:ASP287 4.2 10.1 1.0
CG A:GLU181 4.4 11.2 1.0
OE2 A:GLU217 4.4 9.9 1.0
OD1 A:ASP245 4.4 10.6 1.0
C5 A:GLC407 4.4 16.3 1.0
C2 A:GLC407 4.5 16.5 1.0
NE2 A:HIS220 4.5 8.8 1.0
MN A:MN402 4.5 12.1 1.0
ND1 A:HIS220 4.7 8.4 1.0

Manganese binding site 2 out of 11 in 4zbc

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Manganese binding site 2 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:12.1
occ:1.00
 OE2 A:GLU217 2.0 9.9 1.0
OD1 A:ASP257 2.2 10.5 1.0
OD2 A:ASP255 2.2 9.6 1.0
O A:HOH514 2.3 10.6 1.0
OD1 A:ASP255 2.4 8.4 1.0
NE2 A:HIS220 2.5 8.8 1.0
CG A:ASP255 2.6 8.4 1.0
CD A:GLU217 2.8 8.8 1.0
OE1 A:GLU217 2.9 7.6 1.0
CG A:ASP257 3.1 10.2 1.0
CD2 A:HIS220 3.1 8.1 1.0
OD2 A:ASP257 3.3 10.5 1.0
CE1 A:HIS220 3.5 8.6 1.0
O A:HOH525 3.7 13.5 1.0
ND2 A:ASN247 3.9 8.8 1.0
O3 A:GLC407 4.0 15.1 1.0
O A:HOH593 4.0 9.4 1.0
CB A:ASP255 4.1 8.3 1.0
CG A:GLU217 4.2 8.5 1.0
CG A:HIS220 4.3 7.8 1.0
OD2 A:ASP287 4.3 11.5 1.0
ND1 A:HIS220 4.4 8.4 1.0
CB A:ASP257 4.5 9.5 1.0
MN A:MN401 4.5 12.7 1.0
O A:HOH622 4.7 22.5 1.0
CE A:LYS183 4.8 8.1 1.0
CA A:ASP257 4.9 9.5 1.0
N A:ASP257 5.0 8.6 1.0

Manganese binding site 3 out of 11 in 4zbc

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Manganese binding site 3 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:47.2
occ:1.00
 OG1 A:THR91 2.6 8.2 1.0
O A:HOH717 2.8 11.4 1.0
O A:VAL135 2.9 9.8 1.0
CB A:THR91 3.1 8.7 1.0
N A:THR91 3.1 9.8 1.0
CE2 A:TYR134 3.4 10.5 1.0
OG1 A:THR90 3.6 11.4 1.0
CA A:THR91 3.6 9.1 1.0
CA A:ALA136 3.7 9.4 1.0
C A:VAL135 3.9 10.0 1.0
O A:THR91 4.0 10.1 1.0
C A:THR90 4.1 9.7 1.0
CD2 A:TYR134 4.2 11.6 1.0
CB A:ALA136 4.2 9.0 1.0
CA A:THR90 4.2 10.7 1.0
N A:ALA136 4.3 9.7 1.0
CZ A:TYR134 4.3 10.5 1.0
C A:THR91 4.3 9.6 1.0
OH A:TYR134 4.3 10.3 1.0
CG2 A:THR91 4.5 8.4 1.0
CG2 A:THR119 4.5 10.5 1.0
CB A:THR90 4.5 11.1 1.0
CD1 A:LEU93 4.7 9.0 1.0
O A:HOH616 4.7 23.3 1.0
OG1 A:THR119 4.8 9.1 1.0
O A:HOH571 4.8 14.5 1.0
N A:TRP137 4.8 8.7 1.0
C A:ALA136 4.8 9.4 1.0
O A:HOH763 4.9 15.4 1.0

Manganese binding site 4 out of 11 in 4zbc

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Manganese binding site 4 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:15.2
occ:1.00
 O A:HOH518 2.2 11.0 1.0
OD2 A:ASP150 2.2 10.3 1.0
CG A:ASP150 3.3 9.9 1.0
O6 A:GLC408 3.9 18.8 1.0
CB A:ASP150 3.9 9.5 1.0
OD2 A:ASP153 4.0 8.5 1.0
O B:HOH538 4.2 12.2 1.0
OD1 A:ASP150 4.3 9.7 1.0
C6 A:GLC408 4.9 32.9 1.0

Manganese binding site 5 out of 11 in 4zbc

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Manganese binding site 5 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:46.1
occ:1.00
 O A:HOH734 2.2 28.1 1.0
OD1 A:ASN250 2.3 15.3 1.0
O A:HOH651 2.7 44.9 1.0
CG A:ASN250 3.2 15.3 1.0
CB A:ASN250 3.7 13.6 1.0
CA A:ASN250 3.9 13.3 1.0
O A:GLY263 4.1 11.0 1.0
C A:GLY263 4.4 10.4 1.0
ND2 A:ASN250 4.4 17.0 1.0
C A:ASN250 4.6 13.7 1.0
CA A:GLY263 4.7 10.8 1.0
N A:ASP264 4.9 10.3 1.0
N A:GLY251 5.0 14.6 1.0
O A:GLN249 5.0 8.6 1.0

Manganese binding site 6 out of 11 in 4zbc

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Manganese binding site 6 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:32.1
occ:1.00
 O A:HOH539 2.1 17.6 1.0
O A:HOH504 2.2 21.8 1.0
OD1 A:ASP9 4.0 11.2 1.0
OD2 A:ASP9 4.1 11.2 1.0
O A:GLN4 4.3 14.4 1.0
O A:HOH690 4.4 27.1 1.0
CG A:ASP9 4.5 11.2 1.0
OG1 A:THR6 4.5 12.3 1.0
CG2 A:THR6 4.9 11.8 1.0

Manganese binding site 7 out of 11 in 4zbc

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Manganese binding site 7 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:11.3
occ:1.00
 OE1 B:GLU217 2.1 8.8 1.0
O2 B:GLC406 2.1 14.9 1.0
OE2 B:GLU181 2.1 10.6 1.0
OD2 B:ASP245 2.1 10.1 1.0
OD2 B:ASP287 2.2 9.7 1.0
O3 B:GLC406 2.2 15.2 1.0
CD B:GLU181 3.0 8.8 1.0
C2 B:GLC406 3.0 17.1 1.0
C3 B:GLC406 3.1 17.3 1.0
CG B:ASP287 3.2 10.0 1.0
OE1 B:GLU181 3.2 9.6 1.0
CD B:GLU217 3.3 9.0 1.0
CG B:ASP245 3.3 10.2 1.0
CB B:ASP287 3.6 9.8 1.0
O B:HOH530 3.7 7.6 1.0
CB B:ASP245 3.9 9.7 1.0
CE1 B:HIS220 4.0 7.8 1.0
CG B:GLU217 4.0 8.5 1.0
O B:HOH621 4.0 14.9 1.0
CB B:GLU217 4.1 8.7 1.0
C4 B:GLC406 4.2 18.1 1.0
OE2 B:GLU217 4.3 10.3 1.0
OD1 B:ASP245 4.3 9.1 1.0
OD1 B:ASP287 4.3 10.6 1.0
CG B:GLU181 4.4 8.8 1.0
NE2 B:HIS220 4.5 7.7 1.0
C1 B:GLC406 4.5 17.0 1.0
MN B:MN402 4.6 12.9 1.0
ND1 B:HIS220 4.7 7.5 1.0

Manganese binding site 8 out of 11 in 4zbc

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Manganese binding site 8 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:12.9
occ:1.00
 OE2 B:GLU217 2.1 10.3 1.0
OD2 B:ASP255 2.2 9.0 1.0
OD1 B:ASP257 2.3 11.8 1.0
O B:HOH530 2.3 7.6 1.0
OD1 B:ASP255 2.3 9.7 1.0
NE2 B:HIS220 2.5 7.7 1.0
CG B:ASP255 2.6 9.4 1.0
CD B:GLU217 2.9 9.0 1.0
OE1 B:GLU217 3.0 8.8 1.0
CD2 B:HIS220 3.1 8.0 1.0
CG B:ASP257 3.2 10.8 1.0
OD2 B:ASP257 3.3 12.0 1.0
CE1 B:HIS220 3.5 7.8 1.0
O B:HOH574 3.7 15.2 1.0
ND2 B:ASN247 4.0 8.8 1.0
O3 B:GLC406 4.0 15.2 1.0
O B:HOH628 4.0 7.4 1.0
CB B:ASP255 4.1 9.6 1.0
CG B:HIS220 4.3 7.3 1.0
CG B:GLU217 4.3 8.5 1.0
OD2 B:ASP287 4.4 9.7 1.0
ND1 B:HIS220 4.5 7.5 1.0
MN B:MN401 4.6 11.3 1.0
CB B:ASP257 4.6 9.3 1.0
CE B:LYS183 4.8 8.4 1.0
O B:HOH599 4.9 19.2 1.0
CA B:ASP257 5.0 9.5 1.0
N B:ASP257 5.0 8.5 1.0

Manganese binding site 9 out of 11 in 4zbc

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Manganese binding site 9 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:25.4
occ:1.00
 O B:ALA339 2.2 11.8 1.0
O A:HOH563 2.3 10.6 1.0
O A:HOH725 2.5 10.8 1.0
C B:ALA339 3.3 11.8 1.0
CA B:ALA339 3.9 11.5 1.0
OD1 A:ASP153 3.9 9.1 1.0
NH1 A:ARG157 4.1 10.8 1.0
CB B:ALA339 4.2 11.4 1.0
OD2 A:ASP156 4.3 10.2 1.0
N B:ARG340 4.4 11.7 1.0
O2 A:GLC408 4.4 33.6 1.0
CA B:ARG340 4.7 12.0 0.5
NH2 A:ARG157 4.7 10.5 1.0
CA B:ARG340 4.8 12.5 0.5
CZ A:ARG157 4.9 10.2 1.0
CG A:ASP153 4.9 8.7 1.0
O5 A:GLC408 4.9 38.1 1.0

Manganese binding site 10 out of 11 in 4zbc

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Manganese binding site 10 out of 11 in the A Dehydrated Form of Glucose Isomerase Collected at 100K.


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 100K. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:44.3
occ:1.00
 OD1 B:ASN250 2.4 15.3 1.0
CG B:ASN250 3.4 16.1 1.0
CB B:ASN250 3.7 14.4 1.0
CA B:ASN250 4.0 13.3 1.0
O B:GLY263 4.2 11.7 1.0
C B:GLY263 4.4 11.7 1.0
ND2 B:ASN250 4.6 18.3 1.0
C B:ASN250 4.6 14.0 1.0
CA B:GLY263 4.8 11.8 1.0
N B:ASP264 4.8 10.2 1.0
O B:HOH588 4.9 18.0 1.0
N B:GLY251 5.0 15.3 1.0
O B:GLN249 5.0 8.5 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 23:13:04 2024

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