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Manganese in PDB 6qrt: X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy

Enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy:
5.3.1.5;

Protein crystallography data

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy, PDB code: 6qrt 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) 35.33 / 1.17
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.523, 97.518, 102.522, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 11.8

Other elements in 6qrt:

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy (pdb code 6qrt). 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 - 1.38 Mgy, PDB code: 6qrt:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6qrt

Go back to Manganese Binding Sites List in 6qrt
Manganese binding site 1 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:9.0
occ:0.41
MN A:MN414 0.0 9.0 0.4
MN A:MN414 0.8 9.4 0.6
OD1 A:ASP257 1.7 12.2 0.7
MN A:MN414 1.8 6.5 0.0
OD1 A:ASP257 1.8 9.9 0.3
OD2 A:ASP255 1.9 12.1 0.4
O A:HOH583 2.0 14.2 1.0
OE2 A:GLU217 2.0 9.2 0.9
OE2 A:GLU217 2.1 6.8 0.1
CG A:ASP257 2.6 12.2 0.7
OD2 A:ASP255 2.6 11.3 0.6
OD1 A:ASP255 2.6 9.2 0.6
CG A:ASP257 2.7 9.8 0.3
CG A:ASP255 2.8 11.6 0.4
OD2 A:ASP257 2.9 14.0 0.7
OD1 A:ASP255 2.9 12.6 0.4
OD2 A:ASP257 3.0 10.0 0.3
CG A:ASP255 3.0 9.7 0.6
CD A:GLU217 3.0 8.7 0.9
NE2 A:HIS220 3.0 9.5 0.7
HD21 A:ASN247 3.2 10.6 1.0
CD A:GLU217 3.3 7.1 0.1
OE1 A:GLU217 3.3 10.1 0.9
HD22 A:ASN247 3.4 10.6 1.0
NE2 A:HIS220 3.6 7.5 0.3
ND2 A:ASN247 3.6 8.9 1.0
HD2 A:HIS220 3.6 8.8 0.3
O A:HOH534 3.7 59.5 0.6
O A:HOH529 3.7 29.3 0.9
CD2 A:HIS220 3.8 9.2 0.7
HD2 A:HIS220 3.8 11.1 0.7
OE1 A:GLU217 3.8 7.2 0.1
CD2 A:HIS220 3.9 7.3 0.3
CE1 A:HIS220 4.0 9.1 0.7
O A:HOH661 4.0 15.5 0.7
CB A:ASP257 4.0 11.2 0.7
CB A:ASP257 4.1 9.6 0.3
O A:HOH528 4.1 11.6 1.0
HE1 A:HIS220 4.1 10.9 0.7
HA A:ASP257 4.1 10.7 0.3
HA A:ASP257 4.1 11.2 0.7
CB A:ASP255 4.3 10.2 0.4
HG2 A:GLU217 4.3 8.6 0.1
O A:HOH566 4.3 73.8 1.0
OD2 A:ASP287 4.3 11.2 1.0
O A:HOH520 4.3 26.0 0.9
CG A:GLU217 4.4 8.5 0.9
H A:ASP257 4.4 10.6 0.3
H A:ASP257 4.4 10.6 0.7
HB3 A:ASP255 4.4 12.3 0.4
HG2 A:GLU217 4.4 10.2 0.9
CG A:GLU217 4.4 7.1 0.1
CB A:ASP255 4.5 9.5 0.6
HB2 A:ASP257 4.5 13.5 0.7
HB3 A:ASP257 4.5 11.6 0.3
O A:ASP287 4.5 9.5 1.0
CA A:ASP257 4.5 9.3 0.7
CA A:ASP257 4.5 8.9 0.3
HB3 A:ASP257 4.6 13.5 0.7
CG A:ASP287 4.6 9.5 1.0
HE3 A:LYS183 4.6 12.6 0.3
HZ2 A:LYS289 4.7 16.2 0.7
HB2 A:ASP255 4.7 12.3 0.4
HB2 A:ASP257 4.7 11.6 0.3
N A:ASP257 4.7 8.8 1.0
HB3 A:ASP255 4.8 11.4 0.6
HG3 A:GLU217 4.8 10.2 0.9
CE1 A:HIS220 4.8 7.6 0.3
HZ2 A:LYS183 4.8 13.6 0.3
MG A:MG416 4.8 6.8 0.6
HZ3 A:LYS289 4.8 16.2 0.7
OD1 A:ASP287 4.8 9.7 1.0
HE3 A:LYS183 4.8 13.2 0.7
HB3 A:ASP287 4.9 10.9 1.0
CG A:HIS220 4.9 8.5 0.7
MN A:MN415 4.9 16.2 0.5
HB2 A:ASP255 4.9 11.4 0.6
CG A:ASN247 4.9 8.0 1.0
HZ1 A:LYS183 5.0 13.6 0.3
ND1 A:HIS220 5.0 9.2 0.7

Manganese binding site 2 out of 4 in 6qrt

Go back to Manganese Binding Sites List in 6qrt
Manganese binding site 2 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:9.4
occ:0.55
MN A:MN414 0.0 9.4 0.6
MN A:MN414 0.8 9.0 0.4
MN A:MN414 1.3 6.5 0.0
OD2 A:ASP255 1.6 12.1 0.4
OE2 A:GLU217 2.0 9.2 0.9
OE2 A:GLU217 2.2 6.8 0.1
OD2 A:ASP255 2.2 11.3 0.6
OD1 A:ASP255 2.3 9.2 0.6
NE2 A:HIS220 2.3 9.5 0.7
O A:HOH583 2.3 14.2 1.0
OD1 A:ASP257 2.4 12.2 0.7
CG A:ASP255 2.4 11.6 0.4
OD1 A:ASP257 2.5 9.9 0.3
CG A:ASP255 2.6 9.7 0.6
OD1 A:ASP255 2.7 12.6 0.4
NE2 A:HIS220 2.9 7.5 0.3
HD2 A:HIS220 2.9 8.8 0.3
CD A:GLU217 3.0 8.7 0.9
CD2 A:HIS220 3.0 9.2 0.7
HD2 A:HIS220 3.1 11.1 0.7
CD2 A:HIS220 3.2 7.3 0.3
O A:HOH529 3.2 29.3 0.9
OE1 A:GLU217 3.3 10.1 0.9
CE1 A:HIS220 3.3 9.1 0.7
CD A:GLU217 3.3 7.1 0.1
CG A:ASP257 3.3 12.2 0.7
CG A:ASP257 3.4 9.8 0.3
HD21 A:ASN247 3.5 10.6 1.0
OD2 A:ASP257 3.5 10.0 0.3
HE1 A:HIS220 3.6 10.9 0.7
OD2 A:ASP257 3.6 14.0 0.7
O A:HOH534 3.8 59.5 0.6
O A:HOH661 3.8 15.5 0.7
HE3 A:LYS183 3.9 12.6 0.3
CB A:ASP255 3.9 10.2 0.4
OE1 A:GLU217 3.9 7.2 0.1
HD22 A:ASN247 4.1 10.6 1.0
HE3 A:LYS183 4.1 13.2 0.7
O A:HOH566 4.1 73.8 1.0
CB A:ASP255 4.1 9.5 0.6
ND2 A:ASN247 4.1 8.9 1.0
HB3 A:ASP255 4.1 12.3 0.4
CE1 A:HIS220 4.1 7.6 0.3
HB2 A:ASP255 4.2 12.3 0.4
HZ2 A:LYS183 4.2 13.6 0.3
CG A:HIS220 4.2 8.5 0.7
O A:HOH528 4.2 11.6 1.0
HG2 A:GLU217 4.3 8.6 0.1
ND1 A:HIS220 4.3 9.2 0.7
CG A:GLU217 4.3 8.5 0.9
HG2 A:GLU217 4.3 10.2 0.9
HZ1 A:LYS183 4.4 13.6 0.3
HB2 A:ASP255 4.4 11.4 0.6
CG A:GLU217 4.4 7.1 0.1
HB3 A:ASP255 4.5 11.4 0.6
CG A:HIS220 4.5 7.0 0.3
HZ2 A:LYS183 4.5 15.2 0.7
HE1 A:HIS220 4.6 9.1 0.3
O A:HOH520 4.6 26.0 0.9
NZ A:LYS183 4.6 11.3 0.3
CE A:LYS183 4.6 10.5 0.3
OD2 A:ASP287 4.6 11.2 1.0
CB A:ASP257 4.7 11.2 0.7
HD2 A:LYS183 4.7 11.8 0.3
H A:ASP257 4.8 10.6 0.3
H A:ASP257 4.8 10.6 0.7
HA A:ASP257 4.8 10.7 0.3
HA A:ASP257 4.8 11.2 0.7
CB A:ASP257 4.8 9.6 0.3
MG A:MG416 4.8 6.8 0.6
HD2 A:LYS183 4.8 11.4 0.7
HG3 A:GLU217 4.9 10.2 0.9
CE A:LYS183 4.9 10.9 0.7
ND1 A:HIS220 4.9 7.0 0.3
HA A:ASP255 4.9 10.8 1.0
MN A:MN415 4.9 16.2 0.5
HB3 A:GLU217 4.9 8.8 0.1
CA A:ASP255 5.0 9.0 1.0

Manganese binding site 3 out of 4 in 6qrt

Go back to Manganese Binding Sites List in 6qrt
Manganese binding site 3 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn414

b:6.5
occ:0.04
MN A:MN414 0.0 6.5 0.0
MN A:MN414 1.3 9.4 0.6
MN A:MN414 1.8 9.0 0.4
NE2 A:HIS220 1.8 9.5 0.7
O A:HOH583 2.0 14.2 1.0
NE2 A:HIS220 2.1 7.5 0.3
OE2 A:GLU217 2.2 6.8 0.1
OE2 A:GLU217 2.3 9.2 0.9
CE1 A:HIS220 2.4 9.1 0.7
HE1 A:HIS220 2.4 10.9 0.7
O A:HOH661 2.5 15.5 0.7
OE1 A:GLU217 2.6 10.1 0.9
OD2 A:ASP255 2.6 12.1 0.4
CD A:GLU217 2.7 8.7 0.9
O A:HOH529 2.8 29.3 0.9
OD2 A:ASP255 2.9 11.3 0.6
CD A:GLU217 2.9 7.1 0.1
CD2 A:HIS220 3.0 7.3 0.3
CD2 A:HIS220 3.0 9.2 0.7
HD2 A:HIS220 3.1 8.8 0.3
O A:HOH566 3.1 73.8 1.0
CE1 A:HIS220 3.1 7.6 0.3
OE1 A:GLU217 3.2 7.2 0.1
OD1 A:ASP255 3.4 9.2 0.6
HE1 A:HIS220 3.4 9.1 0.3
HD2 A:HIS220 3.5 11.1 0.7
OD1 A:ASP257 3.5 12.2 0.7
O A:HOH534 3.5 59.5 0.6
CG A:ASP255 3.5 11.6 0.4
CG A:ASP255 3.5 9.7 0.6
ND1 A:HIS220 3.5 9.2 0.7
OD1 A:ASP257 3.6 9.9 0.3
MG A:MG416 3.8 6.8 0.6
OD1 A:ASP255 3.9 12.6 0.4
CG A:HIS220 3.9 8.5 0.7
HE3 A:LYS183 3.9 12.6 0.3
MN A:MN415 3.9 16.2 0.5
HZ2 A:LYS183 3.9 13.6 0.3
OD2 A:ASP287 3.9 11.2 1.0
HD2 A:LYS183 4.1 11.8 0.3
CG A:HIS220 4.1 7.0 0.3
HE3 A:LYS183 4.1 13.2 0.7
CG A:GLU217 4.1 8.5 0.9
ND1 A:HIS220 4.1 7.0 0.3
HD2 A:LYS183 4.2 11.4 0.7
OD2 A:ASP257 4.2 14.0 0.7
HD21 A:ASN247 4.2 10.6 1.0
CG A:GLU217 4.2 7.1 0.1
HD1 A:HIS220 4.2 11.0 0.7
OE2 A:GLU181 4.2 11.4 1.0
CG A:ASP257 4.3 12.2 0.7
OD2 A:ASP257 4.3 10.0 0.3
HG2 A:GLU217 4.3 8.6 0.1
CG A:ASP257 4.4 9.8 0.3
HG2 A:GLU217 4.4 10.2 0.9
HZ2 A:LYS183 4.4 15.2 0.7
NZ A:LYS183 4.5 11.3 0.3
HB3 A:GLU217 4.5 8.8 0.1
CE A:LYS183 4.5 10.5 0.3
HZ1 A:LYS183 4.6 13.6 0.3
HB3 A:GLU217 4.6 9.7 0.9
HO2 A:EDO401 4.6 15.3 1.0
CG A:ASP287 4.7 9.5 1.0
HO1 A:EDO409 4.7 65.2 1.0
HG3 A:GLU217 4.7 10.2 0.9
HB2 A:GLU217 4.7 8.8 0.1
HB2 A:GLU217 4.8 9.7 0.9
HD22 A:ASN247 4.8 10.6 1.0
CB A:GLU217 4.8 8.1 0.9
CB A:ASP255 4.8 10.2 0.4
CB A:GLU217 4.8 7.3 0.1
CD A:LYS183 4.8 9.8 0.3
CE A:LYS183 4.8 10.9 0.7
ND2 A:ASN247 4.8 8.9 1.0
HB2 A:ASP255 4.9 12.3 0.4
CD A:LYS183 4.9 9.5 0.7
HD1 A:HIS220 4.9 8.4 0.3
HB3 A:ASP255 5.0 12.3 0.4
HG3 A:GLU217 5.0 8.6 0.1
CB A:ASP255 5.0 9.5 0.6
HG3 A:LYS183 5.0 10.2 0.7

Manganese binding site 4 out of 4 in 6qrt

Go back to Manganese Binding Sites List in 6qrt
Manganese binding site 4 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn415

b:16.2
occ:0.47
MG A:MG416 0.2 6.8 0.6
HO2 A:EDO401 1.3 15.3 1.0
OE1 A:GLU217 1.8 7.2 0.1
OD2 A:ASP245 2.0 11.7 1.0
OD2 A:ASP287 2.0 11.2 1.0
O2 A:EDO401 2.1 12.7 1.0
OE2 A:GLU181 2.1 11.4 1.0
OE1 A:GLU217 2.2 10.1 0.9
O A:HOH661 2.4 15.5 0.7
CD A:GLU181 3.0 10.9 1.0
CD A:GLU217 3.0 7.1 0.1
CG A:ASP287 3.1 9.5 1.0
C2 A:EDO401 3.1 13.3 1.0
CG A:ASP245 3.2 10.3 1.0
OE1 A:GLU181 3.3 12.0 1.0
H22 A:EDO401 3.3 16.0 1.0
HB3 A:ASP287 3.3 10.9 1.0
HB2 A:ASP287 3.4 10.9 1.0
H21 A:EDO401 3.4 16.0 1.0
CD A:GLU217 3.5 8.7 0.9
CB A:ASP287 3.5 9.1 1.0
HB2 A:GLU217 3.6 9.7 0.9
HB2 A:GLU217 3.6 8.8 0.1
HB3 A:ASP245 3.7 11.3 1.0
OE2 A:GLU217 3.7 6.8 0.1
HE1 A:HIS220 3.8 10.9 0.7
O A:HOH719 3.8 15.6 0.9
CB A:ASP245 3.9 9.4 1.0
HB2 A:ASP245 3.9 11.3 1.0
MN A:MN414 3.9 6.5 0.0
O A:HOH583 4.1 14.2 1.0
OD1 A:ASP245 4.1 11.4 1.0
CG A:GLU217 4.1 7.1 0.1
OD1 A:ASP287 4.2 9.7 1.0
HE1 A:HIS220 4.2 9.1 0.3
HG3 A:GLU217 4.2 8.6 0.1
CG A:GLU217 4.3 8.5 0.9
CE1 A:HIS220 4.3 9.1 0.7
CB A:GLU217 4.3 8.1 0.9
HD21 A:ASN215 4.3 13.3 1.0
HG3 A:GLU217 4.3 10.2 0.9
CB A:GLU217 4.3 7.3 0.1
HZ2 A:TRP16 4.4 12.6 1.0
OE2 A:GLU217 4.4 9.2 0.9
CG A:GLU181 4.4 10.4 1.0
O A:HOH566 4.5 73.8 1.0
C1 A:EDO401 4.5 13.7 1.0
CE1 A:HIS220 4.5 7.6 0.3
HD22 A:ASN215 4.6 13.3 1.0
HG3 A:GLU181 4.6 12.4 1.0
H12 A:EDO401 4.6 16.5 1.0
HB3 A:GLU217 4.6 9.7 0.9
NE2 A:HIS220 4.7 7.5 0.3
HG2 A:GLU181 4.7 12.4 1.0
HO1 A:EDO409 4.7 65.2 1.0
ND2 A:ASN215 4.7 11.1 1.0
HB3 A:GLU217 4.8 8.8 0.1
H11 A:EDO401 4.8 16.5 1.0
NE2 A:HIS220 4.9 9.5 0.7
MN A:MN414 4.9 9.0 0.4
HG2 A:GLU217 4.9 8.6 0.1
MN A:MN414 4.9 9.4 0.6
CA A:ASP287 5.0 8.8 1.0

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 06:02:09 2024

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