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Manganese in PDB 6qrx: X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy

Enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy:
5.3.1.5;

Protein crystallography data

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy, PDB code: 6qrx was solved by H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.74 / 1.17
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.612, 97.636, 102.598, 90.00, 90.00, 90.00
R / Rfree (%) 10.9 / 12.8

Other elements in 6qrx:

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy (pdb code 6qrx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy, PDB code: 6qrx:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6qrx

Go back to Manganese Binding Sites List in 6qrx
Manganese binding site 1 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:14.6
occ:0.46
MN A:MN414 0.0 14.6 0.5
MN A:MN414 0.7 12.1 0.5
MN A:MN414 1.6 7.7 0.0
OD1 A:ASP257 1.8 15.0 0.6
OD2 A:ASP255 1.9 14.6 0.4
OD1 A:ASP257 1.9 11.7 0.4
O A:HOH566 1.9 18.8 1.0
OE2 A:GLU217 2.0 11.4 0.9
OE2 A:GLU217 2.1 9.0 0.1
OD1 A:ASP255 2.6 11.9 0.6
OD2 A:ASP255 2.6 13.3 0.6
CG A:ASP257 2.7 14.9 0.6
CG A:ASP255 2.8 14.3 0.4
CG A:ASP257 2.8 11.8 0.4
OD2 A:ASP257 2.9 16.6 0.6
NE2 A:HIS220 2.9 11.4 0.7
CG A:ASP255 2.9 12.1 0.6
OD1 A:ASP255 3.0 15.4 0.4
CD A:GLU217 3.0 10.9 0.9
OD2 A:ASP257 3.1 12.5 0.4
HD21 A:ASN247 3.2 12.7 1.0
OE1 A:GLU217 3.3 13.2 0.9
CD A:GLU217 3.3 8.8 0.1
NE2 A:HIS220 3.5 9.5 0.3
O A:HOH572 3.6 64.1 0.6
HD22 A:ASN247 3.6 12.7 1.0
HD2 A:HIS220 3.6 10.6 0.3
CD2 A:HIS220 3.7 10.8 0.7
O A:HOH548 3.7 39.4 1.0
HD2 A:HIS220 3.7 12.9 0.7
ND2 A:ASN247 3.7 10.6 1.0
CE1 A:HIS220 3.8 11.2 0.7
CD2 A:HIS220 3.8 8.8 0.3
OE1 A:GLU217 4.0 8.5 0.1
HE1 A:HIS220 4.0 13.4 0.7
O A:HOH618 4.0 25.1 0.9
CB A:ASP257 4.1 13.5 0.6
O A:HOH522 4.2 13.7 1.0
CB A:ASP257 4.2 11.6 0.4
CB A:ASP255 4.2 12.8 0.4
HA A:ASP257 4.2 12.6 0.4
HA A:ASP257 4.3 13.2 0.6
HG2 A:GLU217 4.3 10.5 0.1
O A:HOH614 4.3 83.9 1.0
HB3 A:ASP255 4.4 15.3 0.4
OD2 A:ASP287 4.4 15.1 1.0
CG A:GLU217 4.4 10.2 0.9
O A:HOH523 4.4 35.8 1.0
CG A:GLU217 4.4 8.7 0.1
CB A:ASP255 4.5 12.0 0.6
HG2 A:GLU217 4.5 12.2 0.9
HE3 A:LYS183 4.5 13.1 0.3
H A:ASP257 4.5 12.3 0.6
H A:ASP257 4.5 12.3 0.4
HZ2 A:LYS183 4.5 14.0 0.3
CE1 A:HIS220 4.6 9.4 0.3
HB3 A:ASP257 4.6 13.9 0.4
HB2 A:ASP257 4.6 16.2 0.6
HB3 A:ASP257 4.6 16.2 0.6
O A:ASP287 4.6 12.0 1.0
HB2 A:ASP255 4.6 15.3 0.4
CA A:ASP257 4.6 11.0 0.6
CA A:ASP257 4.7 10.5 0.4
HZ1 A:LYS183 4.7 14.0 0.3
MG A:MG416 4.7 13.4 0.5
CG A:ASP287 4.7 12.3 1.0
HE3 A:LYS183 4.7 16.5 0.7
HB3 A:ASP255 4.8 14.4 0.6
HZ2 A:LYS289 4.8 22.4 0.7
CG A:HIS220 4.8 10.0 0.7
HG3 A:GLU217 4.8 12.2 0.9
HZ3 A:LYS289 4.8 22.4 0.7
N A:ASP257 4.8 10.3 1.0
HB2 A:ASP257 4.8 13.9 0.4
ND1 A:HIS220 4.8 10.8 0.7
OD1 A:ASP287 4.9 12.4 1.0
HB2 A:ASP255 4.9 14.4 0.6
MN A:MN415 4.9 16.3 0.6
HZ2 A:LYS183 4.9 19.3 0.7
NZ A:LYS183 4.9 11.6 0.3
HB3 A:ASP287 4.9 13.9 1.0
HE1 A:HIS220 4.9 11.3 0.3

Manganese binding site 2 out of 4 in 6qrx

Go back to Manganese Binding Sites List in 6qrx
Manganese binding site 2 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:12.1
occ:0.50
MN A:MN414 0.0 12.1 0.5
MN A:MN414 0.7 14.6 0.5
MN A:MN414 1.3 7.7 0.0
OD2 A:ASP255 1.5 14.6 0.4
OE2 A:GLU217 2.0 11.4 0.9
OD1 A:ASP255 2.2 11.9 0.6
NE2 A:HIS220 2.2 11.4 0.7
OE2 A:GLU217 2.3 9.0 0.1
OD2 A:ASP255 2.3 13.3 0.6
O A:HOH566 2.3 18.8 1.0
OD1 A:ASP257 2.3 15.0 0.6
CG A:ASP255 2.4 14.3 0.4
OD1 A:ASP257 2.5 11.7 0.4
CG A:ASP255 2.6 12.1 0.6
OD1 A:ASP255 2.7 15.4 0.4
NE2 A:HIS220 2.9 9.5 0.3
HD2 A:HIS220 2.9 10.6 0.3
CD A:GLU217 3.0 10.9 0.9
CD2 A:HIS220 3.0 10.8 0.7
HD2 A:HIS220 3.1 12.9 0.7
CD2 A:HIS220 3.2 8.8 0.3
CE1 A:HIS220 3.3 11.2 0.7
CG A:ASP257 3.3 14.9 0.6
OE1 A:GLU217 3.3 13.2 0.9
O A:HOH548 3.4 39.4 1.0
CD A:GLU217 3.4 8.8 0.1
CG A:ASP257 3.4 11.8 0.4
HD21 A:ASN247 3.5 12.7 1.0
OD2 A:ASP257 3.5 16.6 0.6
HE1 A:HIS220 3.5 13.4 0.7
OD2 A:ASP257 3.6 12.5 0.4
O A:HOH572 3.7 64.1 0.6
HE3 A:LYS183 3.8 13.1 0.3
CB A:ASP255 3.9 12.8 0.4
O A:HOH618 4.0 25.1 0.9
HZ2 A:LYS183 4.0 14.0 0.3
HE3 A:LYS183 4.0 16.5 0.7
CE1 A:HIS220 4.1 9.4 0.3
HD22 A:ASN247 4.1 12.7 1.0
OE1 A:GLU217 4.1 8.5 0.1
CB A:ASP255 4.1 12.0 0.6
HB3 A:ASP255 4.1 15.3 0.4
ND2 A:ASN247 4.1 10.6 1.0
HB2 A:ASP255 4.1 15.3 0.4
CG A:HIS220 4.2 10.0 0.7
HZ1 A:LYS183 4.2 14.0 0.3
O A:HOH522 4.2 13.7 1.0
HG2 A:GLU217 4.2 10.5 0.1
O A:HOH614 4.2 83.9 1.0
ND1 A:HIS220 4.3 10.8 0.7
CG A:GLU217 4.3 10.2 0.9
HG2 A:GLU217 4.3 12.2 0.9
NZ A:LYS183 4.4 11.6 0.3
HB2 A:ASP255 4.4 14.4 0.6
CG A:GLU217 4.4 8.7 0.1
HZ2 A:LYS183 4.5 19.3 0.7
HB3 A:ASP255 4.5 14.4 0.6
CG A:HIS220 4.5 8.4 0.3
HE1 A:HIS220 4.5 11.3 0.3
CE A:LYS183 4.5 10.9 0.3
O A:HOH523 4.6 35.8 1.0
HD2 A:LYS183 4.7 12.3 0.3
CB A:ASP257 4.7 13.5 0.6
H A:ASP257 4.7 12.3 0.6
H A:ASP257 4.7 12.3 0.4
HA A:ASP257 4.7 12.6 0.4
OD2 A:ASP287 4.8 15.1 1.0
HA A:ASP257 4.8 13.2 0.6
MG A:MG416 4.8 13.4 0.5
HD2 A:LYS183 4.8 14.3 0.7
CB A:ASP257 4.8 11.6 0.4
CE A:LYS183 4.8 13.8 0.7
ND1 A:HIS220 4.9 8.7 0.3
HG3 A:GLU217 4.9 12.2 0.9
HA A:ASP255 4.9 13.5 1.0
HZ1 A:LYS183 4.9 19.3 0.7
NZ A:LYS183 4.9 16.1 0.7
HB3 A:GLU217 4.9 10.4 0.1
CA A:ASP255 5.0 11.2 1.0
H A:HIS220 5.0 10.6 0.3

Manganese binding site 3 out of 4 in 6qrx

Go back to Manganese Binding Sites List in 6qrx
Manganese binding site 3 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:7.7
occ:0.04
MN A:MN414 0.0 7.7 0.0
MN A:MN414 1.3 12.1 0.5
MN A:MN414 1.6 14.6 0.5
NE2 A:HIS220 1.8 11.4 0.7
O A:HOH566 2.0 18.8 1.0
NE2 A:HIS220 2.2 9.5 0.3
OE2 A:GLU217 2.2 9.0 0.1
OE2 A:GLU217 2.3 11.4 0.9
CE1 A:HIS220 2.4 11.2 0.7
HE1 A:HIS220 2.4 13.4 0.7
OD2 A:ASP255 2.5 14.6 0.4
OE1 A:GLU217 2.6 13.2 0.9
O A:HOH618 2.7 25.1 0.9
CD A:GLU217 2.7 10.9 0.9
O A:HOH548 2.8 39.4 1.0
OD2 A:ASP255 2.9 13.3 0.6
CD2 A:HIS220 3.0 8.8 0.3
CD A:GLU217 3.0 8.8 0.1
CD2 A:HIS220 3.0 10.8 0.7
CE1 A:HIS220 3.1 9.4 0.3
HD2 A:HIS220 3.2 10.6 0.3
O A:HOH614 3.2 83.9 1.0
OE1 A:GLU217 3.3 8.5 0.1
HE1 A:HIS220 3.4 11.3 0.3
OD1 A:ASP255 3.4 11.9 0.6
OD1 A:ASP257 3.4 15.0 0.6
O A:HOH572 3.5 64.1 0.6
HD2 A:HIS220 3.5 12.9 0.7
OD1 A:ASP257 3.5 11.7 0.4
CG A:ASP255 3.5 14.3 0.4
CG A:ASP255 3.5 12.1 0.6
ND1 A:HIS220 3.6 10.8 0.7
HZ2 A:LYS183 3.7 14.0 0.3
MG A:MG416 3.7 13.4 0.5
HE3 A:LYS183 3.8 13.1 0.3
CG A:HIS220 3.9 10.0 0.7
OD1 A:ASP255 3.9 15.4 0.4
OD2 A:ASP287 4.0 15.1 1.0
MN A:MN415 4.0 16.3 0.6
HD2 A:LYS183 4.1 12.3 0.3
OD2 A:ASP257 4.1 16.6 0.6
HE3 A:LYS183 4.1 16.5 0.7
CG A:HIS220 4.1 8.4 0.3
ND1 A:HIS220 4.1 8.7 0.3
CG A:GLU217 4.2 10.2 0.9
HD21 A:ASN247 4.2 12.7 1.0
CG A:ASP257 4.2 14.9 0.6
HD2 A:LYS183 4.2 14.3 0.7
CG A:GLU217 4.2 8.7 0.1
HD1 A:HIS220 4.3 13.0 0.7
HG2 A:GLU217 4.3 10.5 0.1
OE2 A:GLU181 4.3 15.1 1.0
HZ2 A:LYS183 4.3 19.3 0.7
NZ A:LYS183 4.3 11.6 0.3
OD2 A:ASP257 4.3 12.5 0.4
CG A:ASP257 4.3 11.8 0.4
HZ1 A:LYS183 4.4 14.0 0.3
HG2 A:GLU217 4.4 12.2 0.9
CE A:LYS183 4.4 10.9 0.3
HB3 A:GLU217 4.6 10.4 0.1
HB3 A:GLU217 4.6 11.4 0.9
HO2 A:EDO401 4.7 22.2 1.0
HD22 A:ASN247 4.7 12.7 1.0
CG A:ASP287 4.7 12.3 1.0
HG3 A:GLU217 4.8 12.2 0.9
CD A:LYS183 4.8 10.2 0.3
HO1 A:EDO409 4.8 82.0 1.0
CE A:LYS183 4.8 13.8 0.7
CB A:ASP255 4.8 12.8 0.4
ND2 A:ASN247 4.8 10.6 1.0
HB2 A:GLU217 4.8 10.4 0.1
HB2 A:GLU217 4.8 11.4 0.9
CB A:GLU217 4.8 9.5 0.9
CB A:GLU217 4.8 8.7 0.1
HB2 A:ASP255 4.9 15.3 0.4
HD1 A:HIS220 4.9 10.4 0.3
CD A:LYS183 4.9 11.9 0.7
NZ A:LYS183 4.9 16.1 0.7
HB3 A:ASP255 4.9 15.3 0.4
HG3 A:LYS183 5.0 12.7 0.7
HG3 A:GLU217 5.0 10.5 0.1
CB A:ASP255 5.0 12.0 0.6

Manganese binding site 4 out of 4 in 6qrx

Go back to Manganese Binding Sites List in 6qrx
Manganese binding site 4 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn415

b:16.3
occ:0.56
MG A:MG416 0.3 13.4 0.5
HO2 A:EDO401 1.3 22.2 1.0
OE1 A:GLU217 1.8 8.5 0.1
OD2 A:ASP245 1.9 15.2 1.0
OD2 A:ASP287 2.0 15.1 1.0
OE2 A:GLU181 2.1 15.1 1.0
O2 A:EDO401 2.1 18.5 1.0
OE1 A:GLU217 2.2 13.2 0.9
O A:HOH618 2.4 25.1 0.9
CD A:GLU181 3.0 14.7 1.0
CD A:GLU217 3.0 8.8 0.1
CG A:ASP287 3.1 12.3 1.0
CG A:ASP245 3.1 13.0 1.0
C2 A:EDO401 3.2 20.2 1.0
OE1 A:GLU181 3.2 16.2 1.0
H22 A:EDO401 3.3 24.3 1.0
HB3 A:ASP287 3.4 13.9 1.0
HB2 A:ASP287 3.4 13.9 1.0
H21 A:EDO401 3.5 24.3 1.0
CD A:GLU217 3.5 10.9 0.9
HB2 A:GLU217 3.5 11.4 0.9
CB A:ASP287 3.5 11.6 1.0
HB2 A:GLU217 3.6 10.4 0.1
OE2 A:GLU217 3.7 9.0 0.1
HB3 A:ASP245 3.7 13.9 1.0
HE1 A:HIS220 3.8 13.4 0.7
O A:HOH706 3.8 22.1 0.9
CB A:ASP245 3.9 11.6 1.0
HB2 A:ASP245 3.9 13.9 1.0
MN A:MN414 4.0 7.7 0.0
CG A:GLU217 4.1 8.7 0.1
OD1 A:ASP245 4.1 14.6 1.0
O A:HOH566 4.1 18.8 1.0
HE1 A:HIS220 4.2 11.3 0.3
OD1 A:ASP287 4.2 12.4 1.0
HG3 A:GLU217 4.2 10.5 0.1
CG A:GLU217 4.2 10.2 0.9
CB A:GLU217 4.3 9.5 0.9
HD21 A:ASN215 4.3 16.7 1.0
HG3 A:GLU217 4.3 12.2 0.9
CB A:GLU217 4.3 8.7 0.1
CE1 A:HIS220 4.3 11.2 0.7
CG A:GLU181 4.3 13.3 1.0
OE2 A:GLU217 4.4 11.4 0.9
HZ2 A:TRP16 4.4 14.6 1.0
O A:HOH614 4.4 83.9 1.0
C1 A:EDO401 4.5 20.7 1.0
CE1 A:HIS220 4.5 9.4 0.3
HG3 A:GLU181 4.5 16.0 1.0
HD22 A:ASN215 4.6 16.7 1.0
HG2 A:GLU181 4.6 16.0 1.0
HB3 A:GLU217 4.6 11.4 0.9
H12 A:EDO401 4.6 24.9 1.0
ND2 A:ASN215 4.7 13.9 1.0
HB3 A:GLU217 4.7 10.4 0.1
NE2 A:HIS220 4.7 9.5 0.3
H11 A:EDO401 4.8 24.9 1.0
HO1 A:EDO409 4.8 82.0 1.0
HG2 A:GLU217 4.9 10.5 0.1
MN A:MN414 4.9 14.6 0.5
NE2 A:HIS220 5.0 11.4 0.7

Reference:

H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman. Structural Knowledge or X-Ray Damage? A Case Study on Xylose Isomerase Illustrating Both. J.Synchrotron Radiat. V. 26 931 2019.
ISSN: ESSN 1600-5775
PubMed: 31274415
DOI: 10.1107/S1600577519005599
Page generated: Sun Oct 6 06:04:52 2024

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